Citrus Sinensis ID: 039883

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--
Protein Sequence
MTTTNGVLLSRLMSDGSDGFDLSPTDTEEVHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENILARIDR
Secondary Structure (PSIPRED)
ccccHHHHHHHHHcccccccccccccHHHHHcccccEEEEEcccccccHHHHHHHHHHcccccccccEEEEEcccccccccc
Secondary Structure Prediction (SSPRO)
cccHHHHHHHHHHcccccccccccccHHHcccccEEEEEEccccccccHHHHHHHHHHcccccccccEEEEEccccccHccc
Coil and Loop (DISEMBL)
MTTTNGVLLSRLmsdgsdgfdlsptdteEVHVLAVDLIItdycmpgmtgCELIKKIklqsftfreiptviissenILARIDR
Flexible Loop (DISEMBL)
MTTTNGVLLSRLMSDGSDGFDLSPTDTEEVHVLAVDLIITDYCMPGMTGCELIKKIKLQsftfreiptviissenilaridr
Low Complexity Region (SEG)
MTTTNGVLLSRLMSDGSDGFDLSPTDTEEVHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENILARIDR
Disordered region (IsUnstruct)
***************************EEVHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENILA****
Disordered Region (DISOPRED)
****NG*LLSRLMS******************LAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSEN*******
Disordered Region (DISEMBL)
MTTTNGVLLSRLMSDGSDGFDLSPTDTEEVHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENILARIDR
Disordered Region (DISPRO)
*****G*******************DTEEVHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISS*********
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MTTTNGVLLSRLMSDGSDGFDLSPTDTEEVHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENILARIDR
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	82	2.2.26 [Sep-21-2011]
O82798	259	Two-component response re	yes	no	0.670	0.212	0.696	4e-15
Q9ZWS9	231	Two-component response re	no	no	0.646	0.229	0.685	1e-14
O80366	234	Two-component response re	no	no	0.792	0.277	0.536	1e-13
Q9SB04	184	Two-component response re	no	no	0.768	0.342	0.611	2e-13
Q9ZWS6	186	Two-component response re	no	no	0.682	0.301	0.655	2e-13
O80365	225	Two-component response re	no	no	0.829	0.302	0.513	1e-12
Q9FPR6	153	Two-component response re	no	no	0.707	0.379	0.566	4e-12
Q9SHC2	164	Two-component response re	no	no	0.682	0.341	0.596	6e-12
Q7G8V2	206	Two-component response re	no	no	0.597	0.237	0.64	1e-10
Q9ZWS7	206	Two-component response re	no	no	0.585	0.233	0.632	1e-10

>sp|O82798|ARR4_ARATH Two-component response regulator ARR4 OS=Arabidopsis thaliana GN=ARR4 PE=1 SV=1

 Score = 79.7 bits (195), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 39/56 (69%), Positives = 45/56 (80%), Gaps = 1/56 (1%)

Query: 27  TEEVHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENILARIDR 82
           + E   L VDLIITDYCMPGMTG EL+KKIK +S  FRE+P VI+SSEN+L RIDR
Sbjct: 81  SAEFDRLKVDLIITDYCMPGMTGYELLKKIK-ESSNFREVPVVIMSSENVLTRIDR 135

Functions as response regulator involved in His-to-Asp phosphorelay signal transduction system. Phosphorylation of the Asp residue in the receiver domain activates the ability of the protein to promote the transcription of target genes. Type-A response regulators seem to act as negative regulators of the cytokinin signaling. Modulates red light signaling through its interaction with the phytochrome B photoreceptor.
Arabidopsis thaliana (taxid: 3702)

>sp|Q9ZWS9|ARR3_ARATH Two-component response regulator ARR3 OS=Arabidopsis thaliana GN=ARR3 PE=2 SV=1

 Score = 78.6 bits (192), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 37/54 (68%), Positives = 45/54 (83%), Gaps = 1/54 (1%)

Query: 29  EVHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENILARIDR 82
           E   L VDLIITDYCMPGMTG EL+KKIK +S +F+E+P VI+SSEN++ RIDR
Sbjct: 82  EFDRLKVDLIITDYCMPGMTGYELLKKIK-ESTSFKEVPVVIMSSENVMTRIDR 134

Functions as response regulator involved in His-to-Asp phosphorelay signal transduction system. Phosphorylation of the Asp residue in the receiver domain activates the ability of the protein to promote the transcription of target genes. Type-A response regulators seem to act as negative regulators of the cytokinin signaling.

Arabidopsis thaliana (taxid: 3702)

>sp|O80366|ARR9_ARATH Two-component response regulator ARR9 OS=Arabidopsis thaliana GN=ARR9 PE=1 SV=1

 Score = 74.7 bits (182), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 37/69 (53%), Positives = 51/69 (73%), Gaps = 4/69 (5%)

Query: 14  SDGSDGFDLSPTDTEEVHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISS 73
           S+  + F  +P + +   V+ V+LIITDYCMPGMTG +L+KK+K +S  FR+IP VI+SS
Sbjct: 56  SNDPNAFSKAPVNHQ---VVEVNLIITDYCMPGMTGYDLLKKVK-ESSAFRDIPVVIMSS 111

Query: 74  ENILARIDR 82
           EN+ ARI R
Sbjct: 112 ENVPARISR 120

Functions as response regulator involved in His-to-Asp phosphorelay signal transduction system. Phosphorylation of the Asp residue in the receiver domain activates the ability of the protein to promote the transcription of target genes. Type-A response regulators seem to act as negative regulators of the cytokinin signaling.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9SB04|ARR5_ARATH Two-component response regulator ARR5 OS=Arabidopsis thaliana GN=ARR5 PE=1 SV=2

 Score = 74.7 bits (182), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 41/67 (61%), Positives = 49/67 (73%), Gaps = 4/67 (5%)

Query: 16  GSDGFDLSPTDTEEVHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSEN 75
           G DG + S    E+   L ++LI+TDY MPGMTG EL+KKIK +S  FREIP VI+SSEN
Sbjct: 65  GLDGENNSSVGFED---LKINLIMTDYSMPGMTGYELLKKIK-ESSAFREIPVVIMSSEN 120

Query: 76  ILARIDR 82
           IL RIDR
Sbjct: 121 ILPRIDR 127

Functions as response regulator involved in His-to-Asp phosphorelay signal transduction system. Phosphorylation of the Asp residue in the receiver domain activates the ability of the protein to promote the transcription of target genes. Type-A response regulators seem to act as negative regulators of the cytokinin signaling.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9ZWS6|ARR6_ARATH Two-component response regulator ARR6 OS=Arabidopsis thaliana GN=ARR6 PE=1 SV=2

 Score = 74.3 bits (181), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 40/61 (65%), Positives = 46/61 (75%), Gaps = 5/61 (8%)

Query: 26  DTEEVHV----LAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENILARID 81
           D EE  V    L V+LI+TDY MPGMTG EL+KKIK +S  FRE+P VI+SSENIL RID
Sbjct: 67  DVEEKSVGFEDLKVNLIMTDYSMPGMTGYELLKKIK-ESSAFREVPVVIMSSENILPRID 125

Query: 82  R 82
           R
Sbjct: 126 R 126

Functions as response regulator involved in His-to-Asp phosphorelay signal transduction system. Phosphorylation of the Asp residue in the receiver domain activates the ability of the protein to promote the transcription of target genes. Type-A response regulators seem to act as negative regulators of the cytokinin signaling.

Arabidopsis thaliana (taxid: 3702)

>sp|O80365|ARR8_ARATH Two-component response regulator ARR8 OS=Arabidopsis thaliana GN=ARR8 PE=1 SV=1

 Score = 71.6 bits (174), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 37/72 (51%), Positives = 49/72 (68%), Gaps = 4/72 (5%)

Query: 11  RLMSDGSDGFDLSPTDTEEVHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVI 70
           R+  +  +    SP   +EV +   +LIITDYCMPGMTG +L+KK+K +S  FR IP VI
Sbjct: 51  RVDDNDPNALSTSPQIHQEVEI---NLIITDYCMPGMTGYDLLKKVK-ESAAFRSIPVVI 106

Query: 71  ISSENILARIDR 82
           +SSEN+ ARI R
Sbjct: 107 MSSENVPARISR 118

Functions as response regulator involved in His-to-Asp phosphorelay signal transduction system. Phosphorylation of the Asp residue in the receiver domain activates the ability of the protein to promote the transcription of target genes. Type-A response regulators seem to act as negative regulators of the cytokinin signaling.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9FPR6|ARR17_ARATH Two-component response regulator ARR17 OS=Arabidopsis thaliana GN=ARR17 PE=2 SV=1

 Score = 69.7 bits (169), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 34/60 (56%), Positives = 47/60 (78%), Gaps = 2/60 (3%)

Query: 24  PTDTEEV-HVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENILARIDR 82
           P  T+ + +V+ V+LIITDYCMPGMTG EL+KK+K +S   +E+P VI+SSENI  RI++
Sbjct: 64  PQQTDSLTNVMKVNLIITDYCMPGMTGFELLKKVK-ESSNLKEVPVVILSSENIPTRINK 122

Functions as response regulator involved in His-to-Asp phosphorelay signal transduction system. Phosphorylation of the Asp residue in the receiver domain activates the ability of the protein to promote the transcription of target genes. Type-A response regulators seem to act as negative regulators of the cytokinin signaling.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9SHC2|ARR16_ARATH Two-component response regulator ARR16 OS=Arabidopsis thaliana GN=ARR16 PE=1 SV=1

 Score = 69.3 bits (168), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 34/57 (59%), Positives = 43/57 (75%), Gaps = 1/57 (1%)

Query: 26  DTEEVHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENILARIDR 82
           D    +V+ V LIITDYCMPGMTG EL+KK+K +S   RE+P VI+SSENI  RI++
Sbjct: 78  DALTCNVMKVSLIITDYCMPGMTGFELLKKVK-ESSNLREVPVVIMSSENIPTRINK 133

Functions as response regulator involved in His-to-Asp phosphorelay signal transduction system. Phosphorylation of the Asp residue in the receiver domain activates the ability of the protein to promote the transcription of target genes. Type-A response regulators seem to act as negative regulators of the cytokinin signaling.

Arabidopsis thaliana (taxid: 3702)

>sp|Q7G8V2|ARR15_ARATH Two-component response regulator ARR15 OS=Arabidopsis thaliana GN=ARR15 PE=1 SV=1

 Score = 65.5 bits (158), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 32/50 (64%), Positives = 40/50 (80%), Gaps = 1/50 (2%)

Query: 33  LAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENILARIDR 82
           L V+LI+TDY MPG+TG EL+KKIK +S   REIP VI+SSENI  RI++
Sbjct: 71  LKVNLIVTDYSMPGLTGYELLKKIK-ESSALREIPVVIMSSENIQPRIEQ 119

Functions as response regulator involved in His-to-Asp phosphorelay signal transduction system. Phosphorylation of the Asp residue in the receiver domain activates the ability of the protein to promote the transcription of target genes. Type-A response regulators seem to act as negative regulators of the cytokinin signaling.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9ZWS7|ARR7_ARATH Two-component response regulator ARR7 OS=Arabidopsis thaliana GN=ARR7 PE=1 SV=1

 Score = 65.5 bits (158), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 31/49 (63%), Positives = 40/49 (81%), Gaps = 1/49 (2%)

Query: 33  LAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENILARID 81
           L V+LI+TDY MPG++G +L+KKIK +S  FRE+P VI+SSENIL RI 
Sbjct: 77  LKVNLIVTDYSMPGLSGYDLLKKIK-ESSAFREVPVVIMSSENILPRIQ 124

Functions as response regulator involved in His-to-Asp phosphorelay signal transduction system. Phosphorylation of the Asp residue in the receiver domain activates the ability of the protein to promote the transcription of target genes. Type-A response regulators seem to act as negative regulators of the cytokinin signaling.

Arabidopsis thaliana (taxid: 3702)

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	82
255558348	258	two-component sensor protein histidine p	0.939	0.298	0.417	1e-15
309951226	257	putative A-type response regulator 1b [P	0.609	0.194	0.803	9e-15
309951224	255	putative A-type response regulator 1a [P	0.609	0.196	0.803	9e-15
224102663	258	type-a response regulator [Populus trich	0.609	0.193	0.803	1e-14
118489969	248	unknown [Populus trichocarpa x Populus d	0.597	0.197	0.78	4e-14
309951228	251	putative A-type response regulator 2 [Po	0.597	0.195	0.78	4e-14
224102495	247	type-a response regulator [Populus trich	0.597	0.198	0.78	4e-14
296086487	221	unnamed protein product [Vitis vinifera]	0.939	0.348	0.441	5e-14
297849384	258	hypothetical protein ARALYDRAFT_888316 [	0.670	0.213	0.696	1e-13
15218550	259	two-component response regulator ARR4 [A	0.670	0.212	0.696	2e-13

>gi|255558348|ref|XP_002520201.1| two-component sensor protein histidine protein kinase, putative [Ricinus communis] gi|223540693|gb|EEF42256.1| two-component sensor protein histidine protein kinase, putative [Ricinus communis]

 Score = 87.0 bits (214), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 53/127 (41%), Positives = 63/127 (49%), Gaps = 50/127 (39%)

Query: 5   NGVLLSRLMSDGSDGFDLSPTDTEEVHVLAVD---------------------------- 36
           NG+   R  S+  +GF+ S  D +EVHVLAVD                            
Sbjct: 4   NGIASRRWRSEKIEGFEFSSCDNDEVHVLAVDDSLVDRKVIERLLKITSCKVTAVDSGRR 63

Query: 37  ---------------------LIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSEN 75
                                LIITDYCMPGMTG EL+KKIK +S TFREIP VI+SSEN
Sbjct: 64  ALQFLGLDEEKSTSIQGLKVDLIITDYCMPGMTGYELLKKIK-ESSTFREIPVVIMSSEN 122

Query: 76  ILARIDR 82
           ++ARIDR
Sbjct: 123 VMARIDR 129

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|309951226|emb|CBX43983.1| putative A-type response regulator 1b [Populus x canadensis]

 Score = 84.3 bits (207), Expect = 9e-15,   Method: Compositional matrix adjust.
 Identities = 41/51 (80%), Positives = 46/51 (90%), Gaps = 1/51 (1%)

Query: 32  VLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENILARIDR 82
           VL VDLIITDYCMPGMTG EL+KKIK +S TFREIP VI+SSEN++ARIDR
Sbjct: 93  VLKVDLIITDYCMPGMTGYELLKKIK-ESTTFREIPVVIMSSENVVARIDR 142

Source: Populus x canadensis

Species: Populus x canadensis

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|309951224|emb|CBX43982.1| putative A-type response regulator 1a [Populus x canadensis]

 Score = 84.3 bits (207), Expect = 9e-15,   Method: Compositional matrix adjust.
 Identities = 41/51 (80%), Positives = 46/51 (90%), Gaps = 1/51 (1%)

Query: 32  VLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENILARIDR 82
           VL VDLIITDYCMPGMTG EL+KKIK +S TFREIP VI+SSEN++ARIDR
Sbjct: 95  VLKVDLIITDYCMPGMTGYELLKKIK-ESTTFREIPVVIMSSENVVARIDR 144

Source: Populus x canadensis

Species: Populus x canadensis

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224102663|ref|XP_002312769.1| type-a response regulator [Populus trichocarpa] gi|222852589|gb|EEE90136.1| type-a response regulator [Populus trichocarpa]

 Score = 84.0 bits (206), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 41/51 (80%), Positives = 46/51 (90%), Gaps = 1/51 (1%)

Query: 32  VLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENILARIDR 82
           VL VDLIITDYCMPGMTG EL+KKIK +S TFREIP VI+SSEN++ARIDR
Sbjct: 95  VLKVDLIITDYCMPGMTGYELLKKIK-ESTTFREIPVVIMSSENVVARIDR 144

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|118489969|gb|ABK96781.1| unknown [Populus trichocarpa x Populus deltoides]

 Score = 82.0 bits (201), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 39/50 (78%), Positives = 45/50 (90%), Gaps = 1/50 (2%)

Query: 33  LAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENILARIDR 82
           L VDLIITDYCMPGMTG EL+KKIK +S +FREIP VI+SSEN++ARIDR
Sbjct: 100 LKVDLIITDYCMPGMTGYELLKKIK-ESSSFREIPVVIMSSENVMARIDR 148

Source: Populus trichocarpa x Populus deltoides

Species: Populus trichocarpa x Populus deltoides

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|309951228|emb|CBX43984.1| putative A-type response regulator 2 [Populus x canadensis]

 Score = 82.0 bits (201), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 39/50 (78%), Positives = 45/50 (90%), Gaps = 1/50 (2%)

Query: 33  LAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENILARIDR 82
           L VDLIITDYCMPGMTG EL+KKIK +S +FREIP VI+SSEN++ARIDR
Sbjct: 103 LKVDLIITDYCMPGMTGYELLKKIK-ESSSFREIPVVIMSSENVMARIDR 151

Source: Populus x canadensis

Species: Populus x canadensis

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224102495|ref|XP_002312699.1| type-a response regulator [Populus trichocarpa] gi|222852519|gb|EEE90066.1| type-a response regulator [Populus trichocarpa]

 Score = 82.0 bits (201), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 39/50 (78%), Positives = 45/50 (90%), Gaps = 1/50 (2%)

Query: 33  LAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENILARIDR 82
           L VDLIITDYCMPGMTG EL+KKIK +S +FREIP VI+SSEN++ARIDR
Sbjct: 99  LKVDLIITDYCMPGMTGYELLKKIK-ESSSFREIPVVIMSSENVMARIDR 147

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|296086487|emb|CBI32076.3| unnamed protein product [Vitis vinifera]

 Score = 81.6 bits (200), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 57/129 (44%), Positives = 62/129 (48%), Gaps = 52/129 (40%)

Query: 5   NGVLLSRLMSDGSDGFDLSPTDTEE-VHVLAVD--------------------------- 36
           +GVL  R M D   GFDLSP  +EE  HVLAVD                           
Sbjct: 4   SGVLSRRNMPDEIGGFDLSPGHSEEEAHVLAVDDSLVDRKVIERLLKISSCKVTAVDSGR 63

Query: 37  -----------------------LIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISS 73
                                  LIITDYCMPGMTG EL+KKIK +S TFRE P VI+SS
Sbjct: 64  RALQFLGLDEEKNSAGLDGLKVDLIITDYCMPGMTGYELLKKIK-ESSTFRETPVVIMSS 122

Query: 74  ENILARIDR 82
           ENIL RIDR
Sbjct: 123 ENILTRIDR 131

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297849384|ref|XP_002892573.1| hypothetical protein ARALYDRAFT_888316 [Arabidopsis lyrata subsp. lyrata] gi|297338415|gb|EFH68832.1| hypothetical protein ARALYDRAFT_888316 [Arabidopsis lyrata subsp. lyrata]

 Score = 80.5 bits (197), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 39/56 (69%), Positives = 45/56 (80%), Gaps = 1/56 (1%)

Query: 27  TEEVHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENILARIDR 82
           + E   L VDLIITDYCMPGMTG EL+KKIK +S  FRE+P VI+SSEN+L RIDR
Sbjct: 78  SAEFDRLKVDLIITDYCMPGMTGYELLKKIK-ESSNFREVPVVIMSSENVLTRIDR 132

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15218550|ref|NP_172517.1| two-component response regulator ARR4 [Arabidopsis thaliana] gi|51315817|sp|O82798.1|ARR4_ARATH RecName: Full=Two-component response regulator ARR4; AltName: Full=Response regulator 1 gi|5091539|gb|AAD39568.1|AC007067_8 T10O24.8 [Arabidopsis thaliana] gi|3273196|dbj|BAA31143.1| responce regulator1 [Arabidopsis thaliana] gi|3323583|gb|AAC26636.1| two-component response regulator homolog [Arabidopsis thaliana] gi|3953597|dbj|BAA34726.1| response regulator 4 [Arabidopsis thaliana] gi|87116590|gb|ABD19659.1| At1g10470 [Arabidopsis thaliana] gi|110740750|dbj|BAE98474.1| putative response regulator 3 [Arabidopsis thaliana] gi|332190462|gb|AEE28583.1| two-component response regulator ARR4 [Arabidopsis thaliana]

 Score = 79.7 bits (195), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 39/56 (69%), Positives = 45/56 (80%), Gaps = 1/56 (1%)

Query: 27  TEEVHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENILARIDR 82
           + E   L VDLIITDYCMPGMTG EL+KKIK +S  FRE+P VI+SSEN+L RIDR
Sbjct: 81  SAEFDRLKVDLIITDYCMPGMTGYELLKKIK-ESSNFREVPVVIMSSENVLTRIDR 135

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

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Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	82
TAIR|locus:2194584	259	ARR4 "response regulator 4" [A	0.597	0.189	0.76	5.4e-15
TAIR|locus:2025911	231	ARR3 "response regulator 3" [A	0.597	0.212	0.72	1.4e-14
TAIR|locus:2027237	206	ARR15 "response regulator 15"	0.597	0.237	0.64	3e-14
TAIR|locus:2097870	184	RR5 "response regulator 5" [Ar	0.768	0.342	0.611	1.3e-13
TAIR|locus:2080590	234	ARR9 "response regulator 9" [A	0.829	0.290	0.527	1.6e-13
TAIR|locus:2170723	186	ARR6 "response regulator 6" [A	0.682	0.301	0.655	2.7e-13
TAIR|locus:2102509	153	RR17 "response regulator 17" [	0.707	0.379	0.566	7.1e-13
UNIPROTKB|Q4GZK2	201	rr9 "Type A response regulator	0.719	0.293	0.590	9.1e-13
TAIR|locus:2040282	225	RR3 "response regulator 3" [Ar	0.829	0.302	0.513	9.1e-13
UNIPROTKB|Q4GZK7	232	rr4 "Type A response regulator	0.841	0.297	0.492	2.4e-12

TAIR|locus:2194584 ARR4 "response regulator 4" [Arabidopsis thaliana (taxid:3702)]

 Score = 190 (71.9 bits), Expect = 5.4e-15, P = 5.4e-15
 Identities = 38/50 (76%), Positives = 43/50 (86%)

Query:    33 LAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENILARIDR 82
             L VDLIITDYCMPGMTG EL+KKIK +S  FRE+P VI+SSEN+L RIDR
Sbjct:    87 LKVDLIITDYCMPGMTGYELLKKIK-ESSNFREVPVVIMSSENVLTRIDR 135

GO:0000156 "phosphorelay response regulator activity" evidence=IEA;ISS;TAS

GO:0000160 "phosphorelay signal transduction system" evidence=IEA

GO:0005634 "nucleus" evidence=ISM;IDA

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

GO:0005515 "protein binding" evidence=IPI

GO:0005737 "cytoplasm" evidence=IDA

GO:0010017 "red or far-red light signaling pathway" evidence=IMP

GO:0009736 "cytokinin mediated signaling pathway" evidence=RCA;IMP;TAS

GO:0010114 "response to red light" evidence=IMP

GO:0009793 "embryo development ending in seed dormancy" evidence=IMP

GO:0007623 "circadian rhythm" evidence=RCA;IMP

GO:0042752 "regulation of circadian rhythm" evidence=IGI

GO:0009735 "response to cytokinin stimulus" evidence=IEP

GO:0004674 "protein serine/threonine kinase activity" evidence=IDA

GO:0046777 "protein autophosphorylation" evidence=IDA

GO:0006612 "protein targeting to membrane" evidence=RCA

GO:0009963 "positive regulation of flavonoid biosynthetic process" evidence=RCA

GO:0010363 "regulation of plant-type hypersensitive response" evidence=RCA

TAIR|locus:2025911 ARR3 "response regulator 3" [Arabidopsis thaliana (taxid:3702)]

 Score = 186 (70.5 bits), Expect = 1.4e-14, P = 1.4e-14
 Identities = 36/50 (72%), Positives = 44/50 (88%)

Query:    33 LAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENILARIDR 82
             L VDLIITDYCMPGMTG EL+KKIK +S +F+E+P VI+SSEN++ RIDR
Sbjct:    86 LKVDLIITDYCMPGMTGYELLKKIK-ESTSFKEVPVVIMSSENVMTRIDR 134

GO:0000156 "phosphorelay response regulator activity" evidence=IEA;ISS;IDA

GO:0000160 "phosphorelay signal transduction system" evidence=IEA;IDA;TAS

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

GO:0009736 "cytokinin mediated signaling pathway" evidence=TAS

GO:0010114 "response to red light" evidence=IMP

GO:0010161 "red light signaling pathway" evidence=IMP

GO:0007623 "circadian rhythm" evidence=IMP

GO:0042752 "regulation of circadian rhythm" evidence=IGI

GO:0005634 "nucleus" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

GO:0009735 "response to cytokinin stimulus" evidence=IEP

TAIR|locus:2027237 ARR15 "response regulator 15" [Arabidopsis thaliana (taxid:3702)]

 Score = 152 (58.6 bits), Expect = 3.0e-14, Sum P(2) = 3.0e-14
 Identities = 32/50 (64%), Positives = 40/50 (80%)

Query:    33 LAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENILARIDR 82
             L V+LI+TDY MPG+TG EL+KKIK +S   REIP VI+SSENI  RI++
Sbjct:    71 LKVNLIVTDYSMPGLTGYELLKKIK-ESSALREIPVVIMSSENIQPRIEQ 119

GO:0000156 "phosphorelay response regulator activity" evidence=IEA;ISS

GO:0000160 "phosphorelay signal transduction system" evidence=IEA

GO:0005634 "nucleus" evidence=ISM;IDA

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

GO:0009735 "response to cytokinin stimulus" evidence=IEP

GO:0009736 "cytokinin mediated signaling pathway" evidence=IGI;RCA;TAS

GO:0005515 "protein binding" evidence=IPI

GO:0005737 "cytoplasm" evidence=IDA

GO:0007623 "circadian rhythm" evidence=RCA

TAIR|locus:2097870 RR5 "response regulator 5" [Arabidopsis thaliana (taxid:3702)]

 Score = 177 (67.4 bits), Expect = 1.3e-13, P = 1.3e-13
 Identities = 41/67 (61%), Positives = 49/67 (73%)

Query:    16 GSDGFDLSPTDTEEVHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSEN 75
             G DG + S    E+   L ++LI+TDY MPGMTG EL+KKIK +S  FREIP VI+SSEN
Sbjct:    65 GLDGENNSSVGFED---LKINLIMTDYSMPGMTGYELLKKIK-ESSAFREIPVVIMSSEN 120

Query:    76 ILARIDR 82
             IL RIDR
Sbjct:   121 ILPRIDR 127

GO:0000156 "phosphorelay response regulator activity" evidence=IEA;ISS;IMP

GO:0000160 "phosphorelay signal transduction system" evidence=IEA

GO:0005634 "nucleus" evidence=ISM;IDA

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

GO:0009735 "response to cytokinin stimulus" evidence=IEP

GO:0009736 "cytokinin mediated signaling pathway" evidence=RCA;IMP;TAS

GO:0010114 "response to red light" evidence=IMP

GO:0007623 "circadian rhythm" evidence=RCA;IMP

GO:0005515 "protein binding" evidence=IPI

GO:0005737 "cytoplasm" evidence=IDA

GO:0006612 "protein targeting to membrane" evidence=RCA

GO:0009963 "positive regulation of flavonoid biosynthetic process" evidence=RCA

GO:0010363 "regulation of plant-type hypersensitive response" evidence=RCA

TAIR|locus:2080590 ARR9 "response regulator 9" [Arabidopsis thaliana (taxid:3702)]

 Score = 176 (67.0 bits), Expect = 1.6e-13, P = 1.6e-13
 Identities = 39/74 (52%), Positives = 53/74 (71%)

Query:    11 RLMSDGSD--GFDLSPTDTEEVHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPT 68
             R  +D +D   F  +P + +   V+ V+LIITDYCMPGMTG +L+KK+K +S  FR+IP 
Sbjct:    51 RQSTDSNDPNAFSKAPVNHQ---VVEVNLIITDYCMPGMTGYDLLKKVK-ESSAFRDIPV 106

Query:    69 VIISSENILARIDR 82
             VI+SSEN+ ARI R
Sbjct:   107 VIMSSENVPARISR 120

GO:0000156 "phosphorelay response regulator activity" evidence=IEA;ISS

GO:0000160 "phosphorelay signal transduction system" evidence=IEA;IPI

GO:0005634 "nucleus" evidence=ISM;IDA

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

GO:0005515 "protein binding" evidence=IPI

GO:0009736 "cytokinin mediated signaling pathway" evidence=RCA;IMP;TAS

GO:0007623 "circadian rhythm" evidence=RCA;IMP

GO:0009735 "response to cytokinin stimulus" evidence=IEP

GO:0009740 "gibberellic acid mediated signaling pathway" evidence=RCA

GO:0010162 "seed dormancy process" evidence=RCA

TAIR|locus:2170723 ARR6 "response regulator 6" [Arabidopsis thaliana (taxid:3702)]

 Score = 174 (66.3 bits), Expect = 2.7e-13, P = 2.7e-13
 Identities = 40/61 (65%), Positives = 46/61 (75%)

Query:    26 DTEEVHV----LAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENILARID 81
             D EE  V    L V+LI+TDY MPGMTG EL+KKIK +S  FRE+P VI+SSENIL RID
Sbjct:    67 DVEEKSVGFEDLKVNLIMTDYSMPGMTGYELLKKIK-ESSAFREVPVVIMSSENILPRID 125

Query:    82 R 82
             R
Sbjct:   126 R 126

GO:0000156 "phosphorelay response regulator activity" evidence=IEA;ISS;TAS

GO:0000160 "phosphorelay signal transduction system" evidence=IEA;TAS

GO:0005634 "nucleus" evidence=ISM;IDA

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

GO:0009735 "response to cytokinin stimulus" evidence=IEP

GO:0009736 "cytokinin mediated signaling pathway" evidence=RCA;IMP;TAS

GO:0005515 "protein binding" evidence=IPI

GO:0007623 "circadian rhythm" evidence=RCA

TAIR|locus:2102509 RR17 "response regulator 17" [Arabidopsis thaliana (taxid:3702)]

 Score = 170 (64.9 bits), Expect = 7.1e-13, P = 7.1e-13
 Identities = 34/60 (56%), Positives = 47/60 (78%)

Query:    24 PTDTEEV-HVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENILARIDR 82
             P  T+ + +V+ V+LIITDYCMPGMTG EL+KK+K +S   +E+P VI+SSENI  RI++
Sbjct:    64 PQQTDSLTNVMKVNLIITDYCMPGMTGFELLKKVK-ESSNLKEVPVVILSSENIPTRINK 122

GO:0000156 "phosphorelay response regulator activity" evidence=IEA;ISS

GO:0000160 "phosphorelay signal transduction system" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

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

GO:0009736 "cytokinin mediated signaling pathway" evidence=TAS

UNIPROTKB|Q4GZK2 rr9 "Type A response regulator 9" [Oryza sativa Indica Group (taxid:39946)]

 Score = 169 (64.5 bits), Expect = 9.1e-13, P = 9.1e-13
 Identities = 36/61 (59%), Positives = 48/61 (78%)

Query:    23 SPTDTE-EVHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENILARID 81
             SP  T+ +   +AV+LIITDYCMPGMTG +L+KKIK  S+  R+IP VI+SS+NI +RI+
Sbjct:    56 SPISTQSDQQEVAVNLIITDYCMPGMTGYDLLKKIKESSY-LRDIPVVIMSSDNIPSRIN 114

Query:    82 R 82
             R
Sbjct:   115 R 115

GO:0009735 "response to cytokinin stimulus" evidence=IC

TAIR|locus:2040282 RR3 "response regulator 3" [Arabidopsis thaliana (taxid:3702)]

 Score = 169 (64.5 bits), Expect = 9.1e-13, P = 9.1e-13
 Identities = 37/72 (51%), Positives = 49/72 (68%)

Query:    11 RLMSDGSDGFDLSPTDTEEVHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVI 70
             R+  +  +    SP   +EV +   +LIITDYCMPGMTG +L+KK+K +S  FR IP VI
Sbjct:    51 RVDDNDPNALSTSPQIHQEVEI---NLIITDYCMPGMTGYDLLKKVK-ESAAFRSIPVVI 106

Query:    71 ISSENILARIDR 82
             +SSEN+ ARI R
Sbjct:   107 MSSENVPARISR 118

GO:0000156 "phosphorelay response regulator activity" evidence=IEA;ISS

GO:0000160 "phosphorelay signal transduction system" evidence=IEA;ISS

GO:0005634 "nucleus" evidence=ISM;IDA

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

GO:0009736 "cytokinin mediated signaling pathway" evidence=RCA;IMP;TAS

GO:0007623 "circadian rhythm" evidence=RCA;IMP

GO:0005515 "protein binding" evidence=IPI

GO:0010029 "regulation of seed germination" evidence=RCA

GO:0031537 "regulation of anthocyanin metabolic process" evidence=RCA

GO:0048831 "regulation of shoot system development" evidence=RCA

UNIPROTKB|Q4GZK7 rr4 "Type A response regulator 4" [Oryza sativa Indica Group (taxid:39946)]

 Score = 165 (63.1 bits), Expect = 2.4e-12, P = 2.4e-12
 Identities = 35/71 (49%), Positives = 50/71 (70%)

Query:    13 MSDGSDGFDLSPTDTEEVHV-LAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVII 71
             + D  D    SP+ +   H  + V+LIITDYCMPGMTG +L+K++K  S + ++IP VI+
Sbjct:    51 LRDEGDDSSSSPSSSSPDHQEIDVNLIITDYCMPGMTGYDLLKRVKGSS-SLKDIPVVIM 109

Query:    72 SSENILARIDR 82
             SSEN+ ARI+R
Sbjct:   110 SSENVPARINR 120

GO:0009735 "response to cytokinin stimulus" evidence=IC

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input:
	gw1.VIII.35.1	type-a response regulator (147 aa)
		(Populus trichocarpa)
Predicted Functional Partners:
	eugene3.151650001	Predicted protein (347 aa)	•						•		0.556
	GA2ox7	gibberellin 2-oxidase (322 aa)							•		0.510
	eugene3.00140701	response regulator (144 aa)							•		0.508
	GA2ox5	gibberellin 2-oxidase (306 aa)							•		0.508
	GA2ox2	gibberellin 2-oxidase (322 aa)							•		0.507
	GA2ox4	gibberellin 2-oxidase (322 aa)							•		0.506
	GA2ox3	gibberellin 2-oxidase (332 aa)							•		0.506
	GA2ox1	hypothetical protein (332 aa)							•		0.504
	GA2ox6	gibberellin 2-oxidase (332 aa)							•		0.504
	gw1.XIII.1446.1	serine/threonine protein kinase (574 aa)							•		0.502

---

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	82
PLN03029	222	PLN03029, PLN03029, type-a response regulator prot	1e-18
COG4753	475	COG4753, COG4753, Response regulator containing Ch	1e-07
cd00156	113	cd00156, REC, Signal receiver domain; originally t	1e-05
PRK10693	303	PRK10693, PRK10693, response regulator of RpoS; Pr	2e-05
COG2204	464	COG2204, AtoC, Response regulator containing CheY-	2e-04
pfam00072	111	pfam00072, Response_reg, Response regulator receiv	2e-04
COG0784	130	COG0784, CheY, FOG: CheY-like receiver [Signal tra	4e-04
COG3706	435	COG3706, PleD, Response regulator containing a Che	4e-04
COG2197	211	COG2197, CitB, Response regulator containing a Che	6e-04
PRK10161	229	PRK10161, PRK10161, transcriptional regulator PhoB	0.001
TIGR01818	463	TIGR01818, ntrC, nitrogen regulation protein NR(I)	0.001
TIGR02154	226	TIGR02154, PhoB, phosphate regulon transcriptional	0.002
COG3947	361	COG3947, COG3947, Response regulator containing Ch	0.003

>gnl|CDD|215544 PLN03029, PLN03029, type-a response regulator protein; Provisional

 Score = 75.8 bits (186), Expect = 1e-18
 Identities = 36/61 (59%), Positives = 46/61 (75%), Gaps = 4/61 (6%)

Query: 22  LSPTDTEEVHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENILARID 81
           +SP   +EV V   +LIITDYCMPGMTG +L+KKIK +S + R IP VI+SSEN+ +RI 
Sbjct: 63  VSPNSHQEVEV---NLIITDYCMPGMTGYDLLKKIK-ESSSLRNIPVVIMSSENVPSRIT 118

Query: 82  R 82
           R
Sbjct: 119 R 119

Length = 222

>gnl|CDD|227095 COG4753, COG4753, Response regulator containing CheY-like receiver domain and AraC-type DNA-binding domain [Signal transduction mechanisms]

 Score = 46.6 bits (111), Expect = 1e-07
 Identities = 18/39 (46%), Positives = 23/39 (58%), Gaps = 3/39 (7%)

Query: 35 VDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISS 73
           D++ITD  MPGM G +LIK IK QS        +I+S 
Sbjct: 49 PDIVITDINMPGMDGLDLIKAIKEQSPD---TEFIILSG 84

Length = 475

>gnl|CDD|238088 cd00156, REC, Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; contains a phosphoacceptor site that is phosphorylated by histidine kinase homologs; usually found N-terminal to a DNA binding effector domain; forms homodimers

 Score = 39.5 bits (93), Expect = 1e-05
 Identities = 14/48 (29%), Positives = 25/48 (52%), Gaps = 3/48 (6%)

Query: 35 VDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENILARIDR 82
           DLI+ D  MPGM G EL+++I+ +     +IP + +++         
Sbjct: 42 PDLILLDIMMPGMDGLELLRRIRKR---GPDIPIIFLTAHGDDEDAVE 86

Length = 113

>gnl|CDD|182652 PRK10693, PRK10693, response regulator of RpoS; Provisional

 Score = 40.0 bits (94), Expect = 2e-05
 Identities = 19/72 (26%), Positives = 33/72 (45%), Gaps = 10/72 (13%)

Query: 11 RLMSDGSDGFDLSPTDTEEVHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVI 70
           L ++G D  +L       +     DLII D  MP M G E ++ ++ +       P ++
Sbjct: 1  VLAANGVDALEL-------LGGFTPDLIICDLAMPRMNGIEFVEHLRNRGDQ---TPVLV 50

Query: 71 ISSENILARIDR 82
          IS+   +A I +
Sbjct: 51 ISATENMADIAK 62

Length = 303

>gnl|CDD|225114 COG2204, AtoC, Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]

 Score = 37.3 bits (87), Expect = 2e-04
 Identities = 14/37 (37%), Positives = 25/37 (67%), Gaps = 3/37 (8%)

Query: 36 DLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIIS 72
          DL++ D  MPGM G EL+K+IK +     ++P ++++
Sbjct: 50 DLVLLDIRMPGMDGLELLKEIKSRD---PDLPVIVMT 83

Length = 464

>gnl|CDD|200976 pfam00072, Response_reg, Response regulator receiver domain

 Score = 36.4 bits (85), Expect = 2e-04
 Identities = 14/48 (29%), Positives = 26/48 (54%), Gaps = 3/48 (6%)

Query: 28 EEVHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSEN 75
          E +     DLI+ D  MPGM G EL+++I+ +       P +++++  
Sbjct: 36 ELLKEKRPDLILLDIRMPGMDGLELLRRIRRRP---PTTPVIVLTAHG 80

This domain receives the signal from the sensor partner in bacterial two-component systems. It is usually found N-terminal to a DNA binding effector domain. Length = 111

>gnl|CDD|223855 COG0784, CheY, FOG: CheY-like receiver [Signal transduction mechanisms]

 Score = 36.0 bits (83), Expect = 4e-04
 Identities = 15/47 (31%), Positives = 28/47 (59%), Gaps = 3/47 (6%)

Query: 36 DLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENILARIDR 82
          DLI+ D  MPGM G EL+++++ +      IP +++++    A  +R
Sbjct: 53 DLILLDINMPGMDGIELLRRLRAR---GPNIPVILLTAYADEADRER 96

Length = 130

>gnl|CDD|226229 COG3706, PleD, Response regulator containing a CheY-like receiver domain and a GGDEF domain [Signal transduction mechanisms]

 Score = 36.5 bits (85), Expect = 4e-04
 Identities = 19/72 (26%), Positives = 35/72 (48%), Gaps = 8/72 (11%)

Query: 11  RLMSDGSDGFDLSPTDTEEVHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVI 70
              +DG +          ++  L  DL++ D  MP M G EL  +++    T R+IP ++
Sbjct: 160 VEATDGEEALL-------QLAELPPDLVLLDANMPDMDGLELCTRLRQLERT-RDIPIIL 211

Query: 71  ISSENILARIDR 82
           +SS++    + R
Sbjct: 212 LSSKDDDELVVR 223

Length = 435

>gnl|CDD|225107 COG2197, CitB, Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]

 Score = 35.7 bits (83), Expect = 6e-04
 Identities = 14/50 (28%), Positives = 29/50 (58%), Gaps = 3/50 (6%)

Query: 33 LAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENILARIDR 82
          L  D+++ D  MPGM G E +K+++ +     +I  V++++ +  A + R
Sbjct: 45 LKPDVVLLDLSMPGMDGLEALKQLRAR---GPDIKVVVLTAHDDPAYVIR 91

Length = 211

>gnl|CDD|182277 PRK10161, PRK10161, transcriptional regulator PhoB; Provisional

 Score = 35.5 bits (81), Expect = 0.001
 Identities = 16/38 (42%), Positives = 28/38 (73%), Gaps = 1/38 (2%)

Query: 36 DLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISS 73
          DLI+ D+ +PG +G + IK +K +S T R+IP V++++
Sbjct: 48 DLILLDWMLPGGSGIQFIKHLKRESMT-RDIPVVMLTA 84

Length = 229

>gnl|CDD|233585 TIGR01818, ntrC, nitrogen regulation protein NR(I)

 Score = 35.1 bits (81), Expect = 0.001
 Identities = 14/43 (32%), Positives = 27/43 (62%), Gaps = 3/43 (6%)

Query: 36 DLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENILA 78
          DL+ITD  MPG  G +L+ +IK +     ++P +++++ + L 
Sbjct: 44 DLLITDVRMPGEDGLDLLPQIKKRH---PQLPVIVMTAHSDLD 83

This model represents NtrC, a DNA-binding response regulator that is phosphorylated by NtrB and interacts with sigma-54. NtrC usually controls the expression of glutamine synthase, GlnA, and may be called GlnL, GlnG, etc [Central intermediary metabolism, Nitrogen metabolism, Regulatory functions, DNA interactions, Signal transduction, Two-component systems]. Length = 463

>gnl|CDD|131209 TIGR02154, PhoB, phosphate regulon transcriptional regulatory protein PhoB

 Score = 34.2 bits (79), Expect = 0.002
 Identities = 18/61 (29%), Positives = 34/61 (55%), Gaps = 6/61 (9%)

Query: 17 SDGFD-LSPTDTEEVHVLAV----DLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVII 71
            G+D +   D +E   L      DLI+ D+ +PG +G EL ++++ +  T R IP +++
Sbjct: 24 KAGYDVVEAGDGDEALTLINERGPDLILLDWMLPGTSGIELCRRLRRRPET-RAIPIIML 82

Query: 72 S 72
          +
Sbjct: 83 T 83

PhoB is a DNA-binding response regulator protein acting with PhoR in a 2-component system responding to phosphate ion. PhoB acts as a positive regulator of gene expression for phosphate-related genes such as phoA, phoS, phoE and ugpAB as well as itself. It is often found proximal to genes for the high-affinity phosphate ABC transporter (pstSCAB; GenProp0190) and presumably regulates these as well [Regulatory functions, DNA interactions, Signal transduction, Two-component systems]. Length = 226

>gnl|CDD|226456 COG3947, COG3947, Response regulator containing CheY-like receiver and SARP domains [Signal transduction mechanisms]

 Score = 34.1 bits (78), Expect = 0.003
 Identities = 18/69 (26%), Positives = 28/69 (40%), Gaps = 6/69 (8%)

Query: 8  LLSRLMSDGSD---GFDLSPTDTEEVHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFR 64
          LLS ++S                + + V   DLI  D  MP M G E  ++++       
Sbjct: 15 LLSVILSRAGHEVRSCSHPVEALDLLEVFKPDLIFLDIVMPYMNGIEFAEQVRDIE---S 71

Query: 65 EIPTVIISS 73
           +P + ISS
Sbjct: 72 AVPIIFISS 80

Length = 361

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	82
COG0745	229	OmpR Response regulators consisting of a CheY-like	99.43
COG2204	464	AtoC Response regulator containing CheY-like recei	99.38
COG4566	202	TtrR Response regulator [Signal transduction mecha	99.36
COG4565	224	CitB Response regulator of citrate/malate metaboli	99.35
COG4753	475	Response regulator containing CheY-like receiver d	99.3
COG2197	211	CitB Response regulator containing a CheY-like rec	99.24
COG3437	360	Response regulator containing a CheY-like receiver	99.19
PF00072	112	Response_reg: Response regulator receiver domain;	99.18
COG3947	361	Response regulator containing CheY-like receiver a	99.07
COG3706	435	PleD Response regulator containing a CheY-like rec	99.02
KOG0519	786	consensus Sensory transduction histidine kinase [S	98.94
PRK10046	225	dpiA two-component response regulator DpiA; Provis	98.94
COG0784	130	CheY FOG: CheY-like receiver [Signal transduction	98.91
PRK11107	919	hybrid sensory histidine kinase BarA; Provisional	98.87
PRK10841	924	hybrid sensory kinase in two-component regulatory	98.87
PLN03029	222	type-a response regulator protein; Provisional	98.83
PRK10816	223	DNA-binding transcriptional regulator PhoP; Provis	98.81
PRK10643	222	DNA-binding transcriptional regulator BasR; Provis	98.79
PRK11475	207	DNA-binding transcriptional activator BglJ; Provis	98.78
PRK11466	914	hybrid sensory histidine kinase TorS; Provisional	98.78
COG2201	350	CheB Chemotaxis response regulator containing a Ch	98.77
PRK10336	219	DNA-binding transcriptional regulator QseB; Provis	98.77
TIGR02956	968	TMAO_torS TMAO reductase sytem sensor TorS. This p	98.76
PRK15029	755	arginine decarboxylase; Provisional	98.76
PRK09468	239	ompR osmolarity response regulator; Provisional	98.76
PRK15115	444	response regulator GlrR; Provisional	98.76
PRK09836	227	DNA-binding transcriptional activator CusR; Provis	98.76
PRK10529	225	DNA-binding transcriptional activator KdpE; Provis	98.75
COG4567	182	Response regulator consisting of a CheY-like recei	98.74
PRK13558	665	bacterio-opsin activator; Provisional	98.74
PRK15347	921	two component system sensor kinase SsrA; Provision	98.73
TIGR02154	226	PhoB phosphate regulon transcriptional regulatory	98.72
PRK11173	237	two-component response regulator; Provisional	98.72
TIGR01387	218	cztR_silR_copR heavy metal response regulator. Mem	98.72
PRK09959	1197	hybrid sensory histidine kinase in two-component r	98.72
PRK10430	239	DNA-binding transcriptional activator DcuR; Provis	98.71
PRK10161	229	transcriptional regulator PhoB; Provisional	98.71
TIGR03787	227	marine_sort_RR proteobacterial dedicated sortase s	98.71
PRK11083	228	DNA-binding response regulator CreB; Provisional	98.7
TIGR01818	463	ntrC nitrogen regulation protein NR(I). This model	98.69
PRK10923	469	glnG nitrogen regulation protein NR(I); Provisiona	98.68
PRK15411	207	rcsA colanic acid capsular biosynthesis activation	98.68
PRK10365	441	transcriptional regulatory protein ZraR; Provision	98.68
PRK11361	457	acetoacetate metabolism regulatory protein AtoC; P	98.67
PRK10766	221	DNA-binding transcriptional regulator TorR; Provis	98.65
PRK10840	216	transcriptional regulator RcsB; Provisional	98.65
PRK09483	217	response regulator; Provisional	98.64
PRK10693	303	response regulator of RpoS; Provisional	98.64
PRK10100	216	DNA-binding transcriptional regulator CsgD; Provis	98.64
PRK09958	204	DNA-binding transcriptional activator EvgA; Provis	98.63
PRK09581	457	pleD response regulator PleD; Reviewed	98.62
PRK13856	241	two-component response regulator VirG; Provisional	98.62
PRK10701	240	DNA-binding transcriptional regulator RstA; Provis	98.62
PRK10955	232	DNA-binding transcriptional regulator CpxR; Provis	98.59
PRK11091	779	aerobic respiration control sensor protein ArcB; P	98.59
PRK11517	223	transcriptional regulatory protein YedW; Provision	98.58
TIGR02875	262	spore_0_A sporulation transcription factor Spo0A.	98.58
TIGR02915	445	PEP_resp_reg putative PEP-CTERM system response re	98.58
PRK09390	202	fixJ response regulator FixJ; Provisional	98.56
CHL00148	240	orf27 Ycf27; Reviewed	98.55
PRK14084	246	two-component response regulator; Provisional	98.54
PRK09935	210	transcriptional regulator FimZ; Provisional	98.53
PRK09581	457	pleD response regulator PleD; Reviewed	98.43
PRK15479	221	transcriptional regulatory protein TctD; Provision	98.43
PRK12555	337	chemotaxis-specific methylesterase; Provisional	98.41
PRK11697	238	putative two-component response-regulatory protein	98.33
PRK10710	240	DNA-binding transcriptional regulator BaeR; Provis	98.33
PRK00742	354	chemotaxis-specific methylesterase; Provisional	98.32
PRK09191	261	two-component response regulator; Provisional	98.28
COG3707	194	AmiR Response regulator with putative antiterminat	98.22
PRK15369	211	two component system sensor kinase SsrB; Provision	98.22
PRK10360	196	DNA-binding transcriptional activator UhpA; Provis	98.19
PRK10651	216	transcriptional regulator NarL; Provisional	98.18
PRK10403	215	transcriptional regulator NarP; Provisional	98.13
cd00156	113	REC Signal receiver domain; originally thought to	98.03
PRK10610	129	chemotaxis regulatory protein CheY; Provisional	98.0
PRK13435	145	response regulator; Provisional	97.97
COG3279	244	LytT Response regulator of the LytR/AlgR family [T	97.9
PRK13837	828	two-component VirA-like sensor kinase; Provisional	97.87
PRK13557	540	histidine kinase; Provisional	97.71
COG3706	435	PleD Response regulator containing a CheY-like rec	96.99
PRK11107	919	hybrid sensory histidine kinase BarA; Provisional	94.59
PF14606	178	Lipase_GDSL_3: GDSL-like Lipase/Acylhydrolase fami	92.28
cd01844	177	SGNH_hydrolase_like_6 SGNH_hydrolase subfamily. SG	91.86
cd02067	119	B12-binding B12 binding domain (B12-BD). This doma	90.56
PF03709	115	OKR_DC_1_N: Orn/Lys/Arg decarboxylase, N-terminal	90.52
PF08415	58	NRPS: Nonribosomal peptide synthase; InterPro: IPR	90.3
smart00448	55	REC cheY-homologous receiver domain. CheY regulate	88.58
PF02310	121	B12-binding: B12 binding domain; InterPro: IPR0061	88.3
PF06490	109	FleQ: Flagellar regulatory protein FleQ; InterPro:	86.75
COG0647	269	NagD Predicted sugar phosphatases of the HAD super	86.55
PRK14089	347	ipid-A-disaccharide synthase; Provisional	86.48
PRK01021	608	lpxB lipid-A-disaccharide synthase; Reviewed	86.39
cd02071	122	MM_CoA_mut_B12_BD methylmalonyl CoA mutase B12 bin	85.56
TIGR02370	197	pyl_corrinoid methyltransferase cognate corrinoid	85.17
PF13528	318	Glyco_trans_1_3: Glycosyl transferase family 1	85.11
PLN02775	286	Probable dihydrodipicolinate reductase	84.56
PRK06843	404	inosine 5-monophosphate dehydrogenase; Validated	84.25
cd02069	213	methionine_synthase_B12_BD B12 binding domain of m	84.13
cd02068	127	radical_SAM_B12_BD B12 binding domain_like associa	83.78
cd02070	201	corrinoid_protein_B12-BD B12 binding domain of cor	83.66
cd05014	128	SIS_Kpsf KpsF-like protein. KpsF is an arabinose-5	80.99
COG4594	310	FecB ABC-type Fe3+-citrate transport system, perip	80.81
PRK05458	326	guanosine 5'-monophosphate oxidoreductase; Provisi	80.21
PRK10558	256	alpha-dehydro-beta-deoxy-D-glucarate aldolase; Pro	80.12

>COG0745 OmpR Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]

Probab=99.43  E-value=1e-12  Score=73.60  Aligned_cols=74  Identities=14%  Similarity=0.257  Sum_probs=55.7

Q ss_pred             CchhHHHHHHHHhcCCCceeeecCh--hH---HhhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCc
Q 039883            2 TTTNGVLLSRLMSDGSDGFDLSPTD--TE---EVHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENI   76 (82)
Q Consensus         2 d~~~~~~~~~~~~~~~~~~~~~~~~--~~---~~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~   76 (82)
                      ++++.........+...||++..+.  .+   .+... ||+||+|+.||+++|+++|+++| .. ....+|||++|+..+
T Consensus         7 eDd~~i~~~l~~~L~~~g~~v~~~~~~~~a~~~~~~~-~dlviLD~~lP~~dG~~~~~~iR-~~-~~~~~PIi~Lta~~~   83 (229)
T COG0745           7 EDDPELAELLKEYLEEEGYEVDVAADGEEALEAAREQ-PDLVLLDLMLPDLDGLELCRRLR-AK-KGSGPPIIVLTARDD   83 (229)
T ss_pred             cCCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHhcC-CCEEEEECCCCCCCHHHHHHHHH-hh-cCCCCcEEEEECCCc
Confidence            4556666666666666777665543  33   34445 99999999999999999999999 43 678889999999865


Q ss_pred             hh
Q 039883           77 LA   78 (82)
Q Consensus        77 ~~   78 (82)
                      ..
T Consensus        84 ~~   85 (229)
T COG0745          84 EE   85 (229)
T ss_pred             HH
Confidence            44

>COG2204 AtoC Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]

Probab=99.38  E-value=2.7e-12  Score=77.58  Aligned_cols=76  Identities=21%  Similarity=0.348  Sum_probs=59.6

Q ss_pred             CchhHHHHHHHHhcCCCceeeecC--hh---HHhhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCc
Q 039883            2 TTTNGVLLSRLMSDGSDGFDLSPT--DT---EEVHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENI   76 (82)
Q Consensus         2 d~~~~~~~~~~~~~~~~~~~~~~~--~~---~~~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~   76 (82)
                      ||+..++......+...||.+..+  +.   +++....||+|++|++||+++|+++++.++   ...+..|||++|++++
T Consensus        11 DDd~~ir~~l~~~L~~~G~~v~~a~~~~~al~~i~~~~~~lvl~Di~mp~~~Gl~ll~~i~---~~~~~~pVI~~Tg~g~   87 (464)
T COG2204          11 DDDPDIRELLEQALELAGYEVVTAESAEEALEALSESPFDLVLLDIRMPGMDGLELLKEIK---SRDPDLPVIVMTGHGD   87 (464)
T ss_pred             eCCHHHHHHHHHHHHHcCCeEEEeCCHHHHHHHHhcCCCCEEEEecCCCCCchHHHHHHHH---hhCCCCCEEEEeCCCC
Confidence            667777766666666666666554  34   344455799999999999999999999999   6679999999999988


Q ss_pred             hhhh
Q 039883           77 LARI   80 (82)
Q Consensus        77 ~~~~   80 (82)
                      .+.+
T Consensus        88 i~~A   91 (464)
T COG2204          88 IDTA   91 (464)
T ss_pred             HHHH
Confidence            6654

>COG4566 TtrR Response regulator [Signal transduction mechanisms]

Probab=99.36  E-value=1.2e-11  Score=66.95  Aligned_cols=75  Identities=15%  Similarity=0.180  Sum_probs=56.8

Q ss_pred             CchhHHHHHHHH--hcCCCceeeecChhHHhhcc---CccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCc
Q 039883            2 TTTNGVLLSRLM--SDGSDGFDLSPTDTEEVHVL---AVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENI   76 (82)
Q Consensus         2 d~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~---~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~   76 (82)
                      |++..++.....  ...+....++.++.+.+...   .|.|+|+|++||+++|.++..+|.   ......|||++|++++
T Consensus        11 DDD~~vr~al~~Ll~s~G~~v~~~~s~~~fL~~~~~~~pGclllDvrMPg~sGlelq~~L~---~~~~~~PVIfiTGhgD   87 (202)
T COG4566          11 DDDESVRDALAFLLESAGFQVKCFASAEEFLAAAPLDRPGCLLLDVRMPGMSGLELQDRLA---ERGIRLPVIFLTGHGD   87 (202)
T ss_pred             cCcHHHHHHHHHHHHhCCceeeeecCHHHHHhhccCCCCCeEEEecCCCCCchHHHHHHHH---hcCCCCCEEEEeCCCC
Confidence            455555544444  44444455566677666654   688999999999999999999999   7889999999999988


Q ss_pred             hhh
Q 039883           77 LAR   79 (82)
Q Consensus        77 ~~~   79 (82)
                      ...
T Consensus        88 Ipm   90 (202)
T COG4566          88 IPM   90 (202)
T ss_pred             hHH
Confidence            654

>COG4565 CitB Response regulator of citrate/malate metabolism [Transcription / Signal transduction mechanisms]

Probab=99.35  E-value=9.3e-12  Score=68.38  Aligned_cols=70  Identities=21%  Similarity=0.358  Sum_probs=56.4

Q ss_pred             HHHHHhcCCCceeeecChh------HHhhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCchhhhh
Q 039883            9 LSRLMSDGSDGFDLSPTDT------EEVHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENILARID   81 (82)
Q Consensus         9 ~~~~~~~~~~~~~~~~~~~------~~~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~~~~~~   81 (82)
                      ........-.+|+++..+.      ..+...+||+|++|..||+.+|++++..++   ..+..+-||++|+..+.+.++
T Consensus        15 ih~~yv~~~~gF~~vg~A~~~~ea~~~i~~~~pDLILLDiYmPd~~Gi~lL~~ir---~~~~~~DVI~iTAA~d~~tI~   90 (224)
T COG4565          15 IHRRYVKQIPGFSVVGTAGTLEEAKMIIEEFKPDLILLDIYMPDGNGIELLPELR---SQHYPVDVIVITAASDMETIK   90 (224)
T ss_pred             HHHHHHHhCCCceEEEeeccHHHHHHHHHhhCCCEEEEeeccCCCccHHHHHHHH---hcCCCCCEEEEeccchHHHHH
Confidence            4444445567787766533      456677999999999999999999999999   788899999999999887664

>COG4753 Response regulator containing CheY-like receiver domain and AraC-type DNA-binding domain [Signal transduction mechanisms]

Probab=99.30  E-value=1.3e-11  Score=74.76  Aligned_cols=77  Identities=25%  Similarity=0.268  Sum_probs=57.3

Q ss_pred             CchhHHHHHHHH--hcCCCceeeecC---hhHHh---hccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEee
Q 039883            2 TTTNGVLLSRLM--SDGSDGFDLSPT---DTEEV---HVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISS   73 (82)
Q Consensus         2 d~~~~~~~~~~~--~~~~~~~~~~~~---~~~~~---~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~   73 (82)
                      ||.+.++.-...  .-...+++++..   |.+++   ...+||+||+|++||+++|+++++.++   ...+.+.+|++|+
T Consensus         8 DDE~lIr~GLk~lI~w~~~g~eiVgtA~NG~eAleli~e~~pDiviTDI~MP~mdGLdLI~~ik---e~~p~~~~IILSG   84 (475)
T COG4753           8 DDEPLIREGLKSLIDWEALGIEVVGTAANGKEALELIQETQPDIVITDINMPGMDGLDLIKAIK---EQSPDTEFIILSG   84 (475)
T ss_pred             cChHHHHHHHHHhCChhhcCCeEEEecccHHHHHHHHHhcCCCEEEEecCCCCCcHHHHHHHHH---HhCCCceEEEEec
Confidence            445444432222  234457777554   44554   466899999999999999999999999   6789999999999


Q ss_pred             CCchhhhh
Q 039883           74 ENILARID   81 (82)
Q Consensus        74 ~~~~~~~~   81 (82)
                      ..+.+.++
T Consensus        85 y~eFeYak   92 (475)
T COG4753          85 YDEFEYAK   92 (475)
T ss_pred             cchhHHHH
Confidence            99887654

>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]

Probab=99.24  E-value=5.5e-11  Score=66.00  Aligned_cols=77  Identities=19%  Similarity=0.228  Sum_probs=55.4

Q ss_pred             CchhHHHHHHHHhc-CCCceeeec---ChhHHh---hccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeC
Q 039883            2 TTTNGVLLSRLMSD-GSDGFDLSP---TDTEEV---HVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSE   74 (82)
Q Consensus         2 d~~~~~~~~~~~~~-~~~~~~~~~---~~~~~~---~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~   74 (82)
                      |+.+.++.-..... ....+++..   ++.+++   ...+||++|+|+.||+++|++.++.++   ...+..+++++|..
T Consensus         7 DDh~l~r~gl~~~L~~~~~~~vv~~a~~~~~~l~~~~~~~pdvvl~Dl~mP~~~G~e~~~~l~---~~~p~~~vvvlt~~   83 (211)
T COG2197           7 DDHPLVREGLRQLLELEPDLEVVGEASNGEEALDLARELKPDVVLLDLSMPGMDGLEALKQLR---ARGPDIKVVVLTAH   83 (211)
T ss_pred             CCcHHHHHHHHHHHhhCCCCEEEEEeCCHHHHHHHhhhcCCCEEEEcCCCCCCChHHHHHHHH---HHCCCCcEEEEecc
Confidence            45555554433332 233366533   244444   466899999999999999999999999   67888899999999


Q ss_pred             Cchhhhh
Q 039883           75 NILARID   81 (82)
Q Consensus        75 ~~~~~~~   81 (82)
                      .+...+.
T Consensus        84 ~~~~~v~   90 (211)
T COG2197          84 DDPAYVI   90 (211)
T ss_pred             CCHHHHH
Confidence            8876653

>COG3437 Response regulator containing a CheY-like receiver domain and an HD-GYP domain [Transcription / Signal transduction mechanisms]

Probab=99.19  E-value=1.2e-10  Score=68.11  Aligned_cols=79  Identities=22%  Similarity=0.246  Sum_probs=57.6

Q ss_pred             CchhHHHHHHHHhcCCCceeeecC--hhH---HhhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCc
Q 039883            2 TTTNGVLLSRLMSDGSDGFDLSPT--DTE---EVHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENI   76 (82)
Q Consensus         2 d~~~~~~~~~~~~~~~~~~~~~~~--~~~---~~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~   76 (82)
                      |+.+.........+...+|.+..+  +..   .....+||++++|++||+++|+++|.+++...+....+|++++|+..+
T Consensus        21 DD~~~~~~~~~~lL~~~~y~v~~ae~g~~a~kl~~~~~~dlvllD~~mp~mdg~ev~~~lk~~~p~t~~ip~i~lT~~~d  100 (360)
T COG3437          21 DDEPDNLEALRQLLRMIGYRVIEAENGEEALKLLQEEPPDLVLLDVRMPEMDGAEVLNKLKAMSPSTRRIPVILLTAYAD  100 (360)
T ss_pred             cCchhHHHHHHHHHHhcccceeeecCchHHHHHhcccCCceEEeeccCCCccHHHHHHHHHhcCCcccccceEEEeecCC
Confidence            555555555444555566666544  443   334457999999999999999999999993256788899999999988


Q ss_pred             hhhh
Q 039883           77 LARI   80 (82)
Q Consensus        77 ~~~~   80 (82)
                      .+..
T Consensus       101 ~~~~  104 (360)
T COG3437         101 SEDR  104 (360)
T ss_pred             hHHH
Confidence            7654

>PF00072 Response_reg: Response regulator receiver domain; InterPro: IPR001789 Two-component signal transduction systems enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions []

Probab=99.18  E-value=6.1e-11  Score=59.22  Aligned_cols=60  Identities=25%  Similarity=0.455  Sum_probs=46.8

Q ss_pred             CCce-ee--ecChh---HHhhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCchhh
Q 039883           17 SDGF-DL--SPTDT---EEVHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENILAR   79 (82)
Q Consensus        17 ~~~~-~~--~~~~~---~~~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~~~~   79 (82)
                      ..++ .+  +.+..   ..+....||++++|+.+++.+|.++++.++   ...+.+|+|++|...+...
T Consensus        20 ~~~~~~v~~~~~~~~~~~~~~~~~~d~iiid~~~~~~~~~~~~~~i~---~~~~~~~ii~~t~~~~~~~   85 (112)
T PF00072_consen   20 RAGYEEVTTASSGEEALELLKKHPPDLIIIDLELPDGDGLELLEQIR---QINPSIPIIVVTDEDDSDE   85 (112)
T ss_dssp             HTTEEEEEEESSHHHHHHHHHHSTESEEEEESSSSSSBHHHHHHHHH---HHTTTSEEEEEESSTSHHH
T ss_pred             hCCCCEEEEECCHHHHHHHhcccCceEEEEEeeeccccccccccccc---cccccccEEEecCCCCHHH
Confidence            5555 44  44444   445677899999999999999999999999   4458999999998776543

Some bacteria can contain up to as many as 200 two-component systems that need tight regulation to prevent unwanted cross-talk []. These pathways have been adapted to response to a wide variety of stimuli, including nutrients, cellular redox state, changes in osmolarity, quorum signals, antibiotics, and more []. Two-component systems are comprised of a sensor histidine kinase (HK) and its cognate response regulator (RR) []. The HK catalyses its own auto-phosphorylation followed by the transfer of the phosphoryl group to the receiver domain on RR; phosphorylation of the RR usually activates an attached output domain, which can then effect changes in cellular physiology, often by regulating gene expression. Some HK are bifunctional, catalysing both the phosphorylation and dephosphorylation of their cognate RR. The input stimuli can regulate either the kinase or phosphatase activity of the bifunctional HK. A variant of the two-component system is the phospho-relay system. Here a hybrid HK auto-phosphorylates and then transfers the phosphoryl group to an internal receiver domain, rather than to a separate RR protein. The phosphoryl group is then shuttled to histidine phosphotransferase (HPT) and subsequently to a terminal RR, which can evoke the desired response [, ]. Bipartite response regulator proteins are involved in a two-component signal transduction system in bacteria, and certain eukaryotes like protozoa, that functions to detect and respond to environmental changes []. These systems have been detected during host invasion, drug resistance, motility, phosphate uptake, osmoregulation, and nitrogen fixation, amongst others []. The two-component system consists of a histidine protein kinase environmental sensor that phosphorylates the receiver domain of a response regulator protein; phosphorylation induces a conformational change in the response regulator, which activates the effector domain, triggering the cellular response []. The domains of the two-component proteins are highly modular, but the core structures and activities are maintained. The response regulators act as phosphorylation-activated switches to affect a cellular response, usually by transcriptional regulation. Most of these proteins consist of two domains, an N-terminal response regulator receiver domain, and a variable C-terminal effector domain with DNA-binding activity. This entry represents the response regulator receiver domain, which belongs to the CheY family, and receives the signal from the sensor partner in the two-component system.; GO: 0000156 two-component response regulator activity, 0000160 two-component signal transduction system (phosphorelay), 0006355 regulation of transcription, DNA-dependent; PDB: 2QR3_A 2QXY_A 1I3C_A 1JLK_A 2PKX_A 2PL1_A 3H1F_A 3H1E_A 3GWG_A 3H1G_A ....

>COG3947 Response regulator containing CheY-like receiver and SARP domains [Signal transduction mechanisms]

Probab=99.07  E-value=4.5e-10  Score=64.62  Aligned_cols=73  Identities=21%  Similarity=0.276  Sum_probs=52.2

Q ss_pred             CchhHHHHHHHHhcCCCc--eeeecChh---HHhhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCc
Q 039883            2 TTTNGVLLSRLMSDGSDG--FDLSPTDT---EEVHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENI   76 (82)
Q Consensus         2 d~~~~~~~~~~~~~~~~~--~~~~~~~~---~~~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~   76 (82)
                      |++..+.......+...+  ...+....   +.+...+||++++|+.||+++|++|+..++   ...+.+|+|++|++..
T Consensus         7 Ddd~a~~~~l~~iLs~~~~~~~~~~~~~eal~~Le~~kpDLifldI~mp~~ngiefaeQvr---~i~~~v~iifIssh~e   83 (361)
T COG3947           7 DDDAAIVKLLSVILSRAGHEVRSCSHPVEALDLLEVFKPDLIFLDIVMPYMNGIEFAEQVR---DIESAVPIIFISSHAE   83 (361)
T ss_pred             cchHHHHHHHHHHHHhccchhhccCCHHHHHHHHHhcCCCEEEEEeecCCccHHHHHHHHH---HhhccCcEEEEecchh
Confidence            445555554444444434  22222222   445677999999999999999999999999   6779999999998855


Q ss_pred             h
Q 039883           77 L   77 (82)
Q Consensus        77 ~   77 (82)
                      .
T Consensus        84 y   84 (361)
T COG3947          84 Y   84 (361)
T ss_pred             h
Confidence            3

>COG3706 PleD Response regulator containing a CheY-like receiver domain and a GGDEF domain [Signal transduction mechanisms]

Probab=99.02  E-value=2.1e-09  Score=64.94  Aligned_cols=75  Identities=25%  Similarity=0.310  Sum_probs=53.2

Q ss_pred             hhHHHHHHHHhcCCCceeeecC--hhHH---hhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCchh
Q 039883            4 TNGVLLSRLMSDGSDGFDLSPT--DTEE---VHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENILA   78 (82)
Q Consensus         4 ~~~~~~~~~~~~~~~~~~~~~~--~~~~---~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~~~   78 (82)
                      ...........+...|+.+..+  +.++   +...+||+||+|+.||+++|+++++++| .......+|+|++++..+..
T Consensus       141 ~~~~~~~l~~~L~~~g~~v~~a~~~~~Al~~~~e~~~dlil~d~~mp~~dg~el~~~lr-~~~~t~~ipii~~~~~~d~~  219 (435)
T COG3706         141 DATQRERLRRILQVEGFRVVEATDGEEALLQLAELPPDLVLLDANMPDMDGLELCTRLR-QLERTRDIPIILLSSKDDDE  219 (435)
T ss_pred             cHHHHHHHHHHHHhccceeeeecCHHHHHHHHhcCCCcEEEEecCCCccCHHHHHHHHh-cccccccccEEEEecccchH
Confidence            3333333333444444555444  4443   3455899999999999999999999999 55667889999999987765


Q ss_pred             h
Q 039883           79 R   79 (82)
Q Consensus        79 ~   79 (82)
                      .
T Consensus       220 ~  220 (435)
T COG3706         220 L  220 (435)
T ss_pred             H
Confidence            4

>KOG0519 consensus Sensory transduction histidine kinase [Signal transduction mechanisms]

Probab=98.94  E-value=7.6e-09  Score=66.59  Aligned_cols=69  Identities=19%  Similarity=0.303  Sum_probs=51.8

Q ss_pred             HHHHhcCCCceeeecChhHHhhcc----CccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCchhhh
Q 039883           10 SRLMSDGSDGFDLSPTDTEEVHVL----AVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENILARI   80 (82)
Q Consensus        10 ~~~~~~~~~~~~~~~~~~~~~~~~----~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~~~~~   80 (82)
                      ...+...+..+....++.+++...    .||++++|+.||.+||++..+++| .... +++|||++|+..+....
T Consensus       683 ~~~l~~~g~~~~~~~sg~e~l~~~~~~~~y~~ifmD~qMP~mDG~e~~~~ir-k~~~-~~~pIvAlTa~~~~~~~  755 (786)
T KOG0519|consen  683 TGMLKKLGAEVTEVNSGQEALDKLKPPHSYDVIFMDLQMPEMDGYEATREIR-KKER-WHLPIVALTADADPSTE  755 (786)
T ss_pred             HHHHHHhCCeeEeecCcHHHHHhcCCCCcccEEEEEcCCcccchHHHHHHHH-Hhhc-CCCCEEEEecCCcHHHH
Confidence            334444455555555666777654    599999999999999999999999 4333 89999999998766543

>PRK10046 dpiA two-component response regulator DpiA; Provisional

Probab=98.94  E-value=8e-09  Score=57.62  Aligned_cols=48  Identities=15%  Similarity=0.218  Sum_probs=39.7

Q ss_pred             HhhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCchhh
Q 039883           29 EVHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENILAR   79 (82)
Q Consensus        29 ~~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~~~~   79 (82)
                      .+...+||++++|+.||+++|+++++.++   ...+..++|++|+..+...
T Consensus        45 ~~~~~~pdlvllD~~mp~~~gle~~~~l~---~~~~~~~iivls~~~~~~~   92 (225)
T PRK10046         45 MIERFKPGLILLDNYLPDGRGINLLHELV---QAHYPGDVVFTTAASDMET   92 (225)
T ss_pred             HHHhcCCCEEEEeCCCCCCcHHHHHHHHH---hcCCCCCEEEEEcCCCHHH
Confidence            34556799999999999999999999999   4456678999998776543

>COG0784 CheY FOG: CheY-like receiver [Signal transduction mechanisms]

Probab=98.91  E-value=1.8e-08  Score=51.43  Aligned_cols=58  Identities=28%  Similarity=0.417  Sum_probs=42.8

Q ss_pred             CceeeecChh-HHh---hcc-CccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCchh
Q 039883           18 DGFDLSPTDT-EEV---HVL-AVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENILA   78 (82)
Q Consensus        18 ~~~~~~~~~~-~~~---~~~-~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~~~   78 (82)
                      ..+....++. +++   ... .||++++|..||+++|+++++.++   ...+..|++++|+.....
T Consensus        30 ~~v~~a~~g~~~al~~~~~~~~~dlii~D~~mp~~~G~~~~~~l~---~~~~~~pvv~~t~~~~~~   92 (130)
T COG0784          30 YEVVEAADGEEEALELLRELPQPDLILLDINMPGMDGIELLRRLR---ARGPNIPVILLTAYADEA   92 (130)
T ss_pred             CeEEEeCChHHHHHHHHHhCCCCCEEEEeCCCCCCCHHHHHHHHH---hCCCCCCEEEEEcCcCHH
Confidence            4444455553 444   444 399999999999999999999999   335677788888776654

>PRK11107 hybrid sensory histidine kinase BarA; Provisional

Probab=98.87  E-value=1.1e-08  Score=66.21  Aligned_cols=61  Identities=21%  Similarity=0.348  Sum_probs=45.7

Q ss_pred             CceeeecChhHH---hhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCchhh
Q 039883           18 DGFDLSPTDTEE---VHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENILAR   79 (82)
Q Consensus        18 ~~~~~~~~~~~~---~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~~~~   79 (82)
                      ..+..+.++.++   +...+||+||+|+.||+++|+++++.++ .....+.+|+|++|+..+.+.
T Consensus       692 ~~v~~~~~~~~al~~~~~~~~dlil~D~~mp~~~g~~~~~~lr-~~~~~~~~pii~lt~~~~~~~  755 (919)
T PRK11107        692 EHVVLCDSGHQAVEQAKQRPFDLILMDIQMPGMDGIRACELIR-QLPHNQNTPIIAVTAHAMAGE  755 (919)
T ss_pred             CEEEEECCHHHHHHHHHhCCCCEEEEeCCCCCCcHHHHHHHHH-hcccCCCCCEEEEeCCCCHHH
Confidence            333444455544   4456899999999999999999999999 433466789999998766543

>PRK10841 hybrid sensory kinase in two-component regulatory system with RcsB and YojN; Provisional

Probab=98.87  E-value=1e-08  Score=66.91  Aligned_cols=59  Identities=19%  Similarity=0.402  Sum_probs=45.5

Q ss_pred             CCceee--ecChhHH---hhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCchh
Q 039883           17 SDGFDL--SPTDTEE---VHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENILA   78 (82)
Q Consensus        17 ~~~~~~--~~~~~~~---~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~~~   78 (82)
                      ..+|++  +.++.++   +...+||+||+|+.||+++|+++++.+|   ...+.+|+|++|+....+
T Consensus       823 ~~G~~v~~a~~g~eal~~l~~~~~DlVl~D~~mP~mdG~el~~~ir---~~~~~~pII~lTa~~~~~  886 (924)
T PRK10841        823 SLGYQCKTANDGVDALNVLSKNHIDIVLTDVNMPNMDGYRLTQRLR---QLGLTLPVIGVTANALAE  886 (924)
T ss_pred             HcCCEEEEECCHHHHHHHHHhCCCCEEEEcCCCCCCCHHHHHHHHH---hcCCCCCEEEEECCCCHH
Confidence            344444  4455544   4455799999999999999999999999   456778999999876544

>PLN03029 type-a response regulator protein; Provisional

Probab=98.83  E-value=7.8e-08  Score=53.82  Aligned_cols=44  Identities=68%  Similarity=1.125  Sum_probs=35.9

Q ss_pred             ccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCchhh
Q 039883           35 VDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENILAR   79 (82)
Q Consensus        35 ~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~~~~   79 (82)
                      +|+||+|+.||+++|+++++.++ .......+|+|++++......
T Consensus        73 ~dlVllD~~mp~~~G~e~l~~ir-~~~~~~~ipvIils~~~~~~~  116 (222)
T PLN03029         73 VNLIITDYCMPGMTGYDLLKKIK-ESSSLRNIPVVIMSSENVPSR  116 (222)
T ss_pred             CCEEEEcCCCCCCCHHHHHHHHH-hccccCCCcEEEEeCCCCHHH
Confidence            67999999999999999999999 322346789999998765543

>PRK10816 DNA-binding transcriptional regulator PhoP; Provisional

Probab=98.81  E-value=4e-08  Score=54.25  Aligned_cols=59  Identities=17%  Similarity=0.347  Sum_probs=44.4

Q ss_pred             CCceee--ecChhHH---hhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCchh
Q 039883           17 SDGFDL--SPTDTEE---VHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENILA   78 (82)
Q Consensus        17 ~~~~~~--~~~~~~~---~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~~~   78 (82)
                      ..++.+  ..+..++   +....||++++|..+|+.+|+++++.++   ...+.+|+|++++..+.+
T Consensus        22 ~~g~~v~~~~~~~~~l~~~~~~~~dlvild~~l~~~~g~~l~~~lr---~~~~~~pii~ls~~~~~~   85 (223)
T PRK10816         22 DAGHQVDAAEDAKEADYYLNEHLPDIAIVDLGLPDEDGLSLIRRWR---SNDVSLPILVLTARESWQ   85 (223)
T ss_pred             HCCCEEEEECCHHHHHHHHhhCCCCEEEEECCCCCCCHHHHHHHHH---hcCCCCCEEEEEcCCCHH
Confidence            344444  3444433   4455799999999999999999999999   456788999999876654

>PRK10643 DNA-binding transcriptional regulator BasR; Provisional

Probab=98.79  E-value=5.1e-08  Score=53.54  Aligned_cols=46  Identities=17%  Similarity=0.392  Sum_probs=38.6

Q ss_pred             hhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCchh
Q 039883           30 VHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENILA   78 (82)
Q Consensus        30 ~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~~~   78 (82)
                      +....||++++|+.+|+.+|.++++.++   ...+..|+|++++..+..
T Consensus        40 ~~~~~~d~illd~~~~~~~g~~~~~~l~---~~~~~~pii~ls~~~~~~   85 (222)
T PRK10643         40 LESGHYSLVVLDLGLPDEDGLHLLRRWR---QKKYTLPVLILTARDTLE   85 (222)
T ss_pred             HHhCCCCEEEEECCCCCCCHHHHHHHHH---hcCCCCcEEEEECCCCHH
Confidence            4455799999999999999999999998   456778999999876544

>PRK11475 DNA-binding transcriptional activator BglJ; Provisional

Probab=98.78  E-value=2.9e-08  Score=55.12  Aligned_cols=59  Identities=10%  Similarity=0.240  Sum_probs=43.8

Q ss_pred             CCcee--eecChhHHh---hccCccEEE---EeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCchh
Q 039883           17 SDGFD--LSPTDTEEV---HVLAVDLII---TDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENILA   78 (82)
Q Consensus        17 ~~~~~--~~~~~~~~~---~~~~~d~vi---~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~~~   78 (82)
                      ..+|.  ...++.+++   ...+||++|   +|..||+++|++++++++   ...+..|||++|+..+..
T Consensus        15 ~~~~~v~~~~~~~~~l~~~~~~~pd~vl~dl~d~~mp~~~Gl~~~~~l~---~~~p~~~iIvlt~~~~~~   81 (207)
T PRK11475         15 GNPYKLHTFSSQSSFQDAMSRISFSAVIFSLSAMRSERREGLSCLTELA---IKFPRMRRLVIADDDIEA   81 (207)
T ss_pred             CCeeEEEEeCCHHHHHHHhccCCCCEEEeeccccCCCCCCHHHHHHHHH---HHCCCCCEEEEeCCCCHH
Confidence            34554  333444444   344789998   688899999999999998   568889999999876543

>PRK11466 hybrid sensory histidine kinase TorS; Provisional

Probab=98.78  E-value=3.2e-08  Score=64.21  Aligned_cols=59  Identities=12%  Similarity=0.237  Sum_probs=44.8

Q ss_pred             CCceee--ecChhHHhh---c-cCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCchh
Q 039883           17 SDGFDL--SPTDTEEVH---V-LAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENILA   78 (82)
Q Consensus        17 ~~~~~~--~~~~~~~~~---~-~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~~~   78 (82)
                      ..++++  +.++.+++.   . .+||+|++|+.||+++|+++++.++   ...+.+|+|++|+.....
T Consensus       703 ~~g~~v~~a~~~~~al~~~~~~~~~Dlvl~D~~mp~~~G~~~~~~lr---~~~~~~~ii~~t~~~~~~  767 (914)
T PRK11466        703 TSGAQVVAVGNAAQALETLQNSEPFAAALVDFDLPDYDGITLARQLA---QQYPSLVLIGFSAHVIDE  767 (914)
T ss_pred             hcCCceEEeCCHHHHHHHHHcCCCCCEEEEeCCCCCCCHHHHHHHHH---hhCCCCCEEEEeCCCchh
Confidence            344444  445555443   2 3689999999999999999999999   456789999999886554

>COG2201 CheB Chemotaxis response regulator containing a CheY-like receiver domain and a methylesterase domain [Cell motility and secretion / Signal transduction mechanisms]

Probab=98.77  E-value=7.3e-08  Score=56.95  Aligned_cols=71  Identities=27%  Similarity=0.289  Sum_probs=52.2

Q ss_pred             CchhHHHHHHHHhcCCCc-eeeecC---hh---HHhhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeC
Q 039883            2 TTTNGVLLSRLMSDGSDG-FDLSPT---DT---EEVHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSE   74 (82)
Q Consensus         2 d~~~~~~~~~~~~~~~~~-~~~~~~---~~---~~~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~   74 (82)
                      |++..++........+.+ .+++..   +.   +.+....||+|.+|..||.++|+++++.+-   . ...+|||++++.
T Consensus         8 ddsal~R~~i~~~l~~~~~i~vv~~a~ng~~a~~~~~~~~PDVi~ld~emp~mdgl~~l~~im---~-~~p~pVimvssl   83 (350)
T COG2201           8 DDSALMRKVISDILNSDPDIEVVGTARNGREAIDKVKKLKPDVITLDVEMPVMDGLEALRKIM---R-LRPLPVIMVSSL   83 (350)
T ss_pred             cCcHHHHHHHHHHHhcCCCeEEEEecCCHHHHHHHHHhcCCCEEEEecccccccHHHHHHHHh---c-CCCCcEEEEecc
Confidence            566666655555544444 565443   33   455677899999999999999999999987   3 478899999975


Q ss_pred             Cc
Q 039883           75 NI   76 (82)
Q Consensus        75 ~~   76 (82)
                      ..
T Consensus        84 t~   85 (350)
T COG2201          84 TE   85 (350)
T ss_pred             cc
Confidence            44

>PRK10336 DNA-binding transcriptional regulator QseB; Provisional

Probab=98.77  E-value=6.9e-08  Score=52.96  Aligned_cols=46  Identities=24%  Similarity=0.480  Sum_probs=38.9

Q ss_pred             hhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCchh
Q 039883           30 VHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENILA   78 (82)
Q Consensus        30 ~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~~~   78 (82)
                      +....||++++|..+++.+|.++++.++   ...+..|+|++|+..+..
T Consensus        40 ~~~~~~dlvild~~l~~~~g~~~~~~i~---~~~~~~~ii~lt~~~~~~   85 (219)
T PRK10336         40 LYSAPYDAVILDLTLPGMDGRDILREWR---EKGQREPVLILTARDALA   85 (219)
T ss_pred             HhhCCCCEEEEECCCCCCCHHHHHHHHH---hcCCCCcEEEEECCCCHH
Confidence            4455799999999999999999999999   456778999999876654

>TIGR02956 TMAO_torS TMAO reductase sytem sensor TorS

Probab=98.76  E-value=4e-08  Score=64.00  Aligned_cols=62  Identities=18%  Similarity=0.298  Sum_probs=44.0

Q ss_pred             CCceeeecChhH---HhhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCC-CCccEEEEeeCCchhh
Q 039883           17 SDGFDLSPTDTE---EVHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTF-REIPTVIISSENILAR   79 (82)
Q Consensus        17 ~~~~~~~~~~~~---~~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~-~~~~vi~ls~~~~~~~   79 (82)
                      ++.+..+.++.+   .+...+||+||+|+.||+++|+++++.++ ..... ..+|+|++|+....+.
T Consensus       726 g~~v~~~~~~~~a~~~l~~~~~dlvl~D~~mp~~~g~~~~~~ir-~~~~~~~~~pii~lta~~~~~~  791 (968)
T TIGR02956       726 GHKVTLAESGQSALECFHQHAFDLALLDINLPDGDGVTLLQQLR-AIYGAKNEVKFIAFSAHVFNED  791 (968)
T ss_pred             CCEEEEECCHHHHHHHHHCCCCCEEEECCCCCCCCHHHHHHHHH-hCccccCCCeEEEEECCCCHHH
Confidence            333444445554   34556799999999999999999999999 22222 2289999998766543

This protein, TorS, is part of a regulatory system for the torCAD operon that encodes the pterin molybdenum cofactor-containing enzyme trimethylamine-N-oxide (TMAO) reductase (TorA), a cognate chaperone (TorD), and a penta-haem cytochrome (TorC). TorS works together with the inducer-binding protein TorT and the response regulator TorR. TorS contains histidine kinase ATPase (pfam02518), HAMP (pfam00672), phosphoacceptor (pfam00512), and phosphotransfer (pfam01627) domains and a response regulator receiver domain (pfam00072).

>PRK15029 arginine decarboxylase; Provisional

Probab=98.76  E-value=6.8e-08  Score=61.98  Aligned_cols=60  Identities=13%  Similarity=0.189  Sum_probs=45.4

Q ss_pred             hcCCCceeeec--Chh---HHhhc-cCccEEEEeCCCCCCCHH----HHHHHHHhhcCCCCCccEEEEeeCCc
Q 039883           14 SDGSDGFDLSP--TDT---EEVHV-LAVDLIITDYCMPGMTGC----ELIKKIKLQSFTFREIPTVIISSENI   76 (82)
Q Consensus        14 ~~~~~~~~~~~--~~~---~~~~~-~~~d~vi~d~~~~~~~~~----~~~~~l~~~~~~~~~~~vi~ls~~~~   76 (82)
                      .+...+|++..  ++.   +.+.. ..||+||+|+.||+++|+    ++++++|   .....+|||++|+..+
T Consensus        27 ~Le~~G~eV~~a~s~~dAl~~l~~~~~~DlVLLD~~LPd~dG~~~~~ell~~IR---~~~~~iPIIlLTar~~   96 (755)
T PRK15029         27 ALSQQNVTVIKSTSFDDGFAILSSNEAIDCLMFSYQMEHPDEHQNVRQLIGKLH---ERQQNVPVFLLGDREK   96 (755)
T ss_pred             HHHHCCCEEEEECCHHHHHHHHHhcCCCcEEEEECCCCCCccchhHHHHHHHHH---hhCCCCCEEEEEcCCc
Confidence            33445565544  444   34444 479999999999999997    8999999   5567899999998875

>PRK09468 ompR osmolarity response regulator; Provisional

Probab=98.76  E-value=7.3e-08  Score=53.76  Aligned_cols=59  Identities=14%  Similarity=0.381  Sum_probs=44.2

Q ss_pred             CCceeee--cChhH---HhhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCchh
Q 039883           17 SDGFDLS--PTDTE---EVHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENILA   78 (82)
Q Consensus        17 ~~~~~~~--~~~~~---~~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~~~   78 (82)
                      ..++++.  .++.+   .+....||++|+|..+|+.+|+++++.++   ...+.+|+|++++..+..
T Consensus        27 ~~g~~v~~~~~~~~~~~~~~~~~~dlvild~~l~~~~g~~~~~~lr---~~~~~~pii~ls~~~~~~   90 (239)
T PRK09468         27 EQGFQVRSAANAEQMDRLLTRESFHLMVLDLMLPGEDGLSICRRLR---SQNNPTPIIMLTAKGEEV   90 (239)
T ss_pred             HCCCEEEEECCHHHHHHHHhcCCCCEEEEeCCCCCCCHHHHHHHHH---hcCCCCCEEEEECCCcHH
Confidence            3445443  34443   34456799999999999999999999999   455788999999876544

>PRK15115 response regulator GlrR; Provisional

Probab=98.76  E-value=4.6e-08  Score=59.30  Aligned_cols=59  Identities=25%  Similarity=0.493  Sum_probs=44.7

Q ss_pred             CCceeeec--ChhHH---hhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCchh
Q 039883           17 SDGFDLSP--TDTEE---VHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENILA   78 (82)
Q Consensus        17 ~~~~~~~~--~~~~~---~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~~~   78 (82)
                      ..++.+..  +..++   +....||+||+|..||+++|+++++.++   ...+.+|+|++|+..+..
T Consensus        27 ~~g~~v~~~~~~~eal~~l~~~~~dlvilD~~lp~~~g~~ll~~l~---~~~~~~pvIvlt~~~~~~   90 (444)
T PRK15115         27 SEGYSVVTAESGQEALRVLNREKVDLVISDLRMDEMDGMQLFAEIQ---KVQPGMPVIILTAHGSIP   90 (444)
T ss_pred             HCCCEEEEeCCHHHHHHHHhcCCCCEEEEcCCCCCCCHHHHHHHHH---hcCCCCcEEEEECCCCHH
Confidence            34455443  44443   4455799999999999999999999998   557788999999876543

>PRK09836 DNA-binding transcriptional activator CusR; Provisional

Probab=98.76  E-value=6.9e-08  Score=53.44  Aligned_cols=46  Identities=17%  Similarity=0.443  Sum_probs=38.7

Q ss_pred             hhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCchh
Q 039883           30 VHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENILA   78 (82)
Q Consensus        30 ~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~~~   78 (82)
                      +....||++++|+.+|+.+|+++++.++   ...+.+|+|++++..+.+
T Consensus        40 ~~~~~~dlvild~~~~~~~g~~~~~~lr---~~~~~~pii~ls~~~~~~   85 (227)
T PRK09836         40 AMTGDYDLIILDIMLPDVNGWDIVRMLR---SANKGMPILLLTALGTIE   85 (227)
T ss_pred             HhhCCCCEEEEECCCCCCCHHHHHHHHH---hcCCCCCEEEEEcCCCHH
Confidence            3455799999999999999999999999   455788999999876544

>PRK10529 DNA-binding transcriptional activator KdpE; Provisional

Probab=98.75  E-value=9e-08  Score=52.86  Aligned_cols=58  Identities=26%  Similarity=0.432  Sum_probs=42.5

Q ss_pred             CCceeeec--ChhHH---hhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCchh
Q 039883           17 SDGFDLSP--TDTEE---VHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENILA   78 (82)
Q Consensus        17 ~~~~~~~~--~~~~~---~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~~~   78 (82)
                      ..++.+..  ++.++   +....||++++|+.+|+.+|.++++.++   . .+..|+|++++..+.+
T Consensus        23 ~~g~~v~~~~~~~~~~~~~~~~~~dlvild~~l~~~~g~~~~~~lr---~-~~~~pvi~lt~~~~~~   85 (225)
T PRK10529         23 GDGMRVFEAETLQRGLLEAATRKPDLIILDLGLPDGDGIEFIRDLR---Q-WSAIPVIVLSARSEES   85 (225)
T ss_pred             HCCCEEEEeCCHHHHHHHHhcCCCCEEEEeCCCCCCCHHHHHHHHH---c-CCCCCEEEEECCCCHH
Confidence            34555433  33333   3445799999999999999999999999   3 3568999999766543

>COG4567 Response regulator consisting of a CheY-like receiver domain and a Fis-type HTH domain [Signal transduction mechanisms / Transcription]

Probab=98.74  E-value=8.4e-08  Score=50.73  Aligned_cols=75  Identities=12%  Similarity=0.189  Sum_probs=57.1

Q ss_pred             CchhHHHHHHHHhcCCCceeeecChh--HH---hhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCc
Q 039883            2 TTTNGVLLSRLMSDGSDGFDLSPTDT--EE---VHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENI   76 (82)
Q Consensus         2 d~~~~~~~~~~~~~~~~~~~~~~~~~--~~---~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~   76 (82)
                      |++..+.....-.....||++..+.+  ++   .+...|.-.++|+.+.+.+|+.+++.|+   .......+|++|++.+
T Consensus        16 dDD~~f~~~LaRa~e~RGf~v~~a~~~~eal~~art~~PayAvvDlkL~~gsGL~~i~~lr---~~~~d~rivvLTGy~s   92 (182)
T COG4567          16 DDDTPFLRTLARAMERRGFAVVTAESVEEALAAARTAPPAYAVVDLKLGDGSGLAVIEALR---ERRADMRIVVLTGYAS   92 (182)
T ss_pred             cCChHHHHHHHHHHhccCceeEeeccHHHHHHHHhcCCCceEEEEeeecCCCchHHHHHHH---hcCCcceEEEEecchH
Confidence            45555554445555667777765544  44   4556899999999999999999999999   7788999999999877


Q ss_pred             hhh
Q 039883           77 LAR   79 (82)
Q Consensus        77 ~~~   79 (82)
                      ...
T Consensus        93 IAT   95 (182)
T COG4567          93 IAT   95 (182)
T ss_pred             HHH
Confidence            543

>PRK13558 bacterio-opsin activator; Provisional

Probab=98.74  E-value=5.9e-08  Score=61.32  Aligned_cols=59  Identities=19%  Similarity=0.258  Sum_probs=45.0

Q ss_pred             Cceeee--cChhHH---hhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCchhh
Q 039883           18 DGFDLS--PTDTEE---VHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENILAR   79 (82)
Q Consensus        18 ~~~~~~--~~~~~~---~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~~~~   79 (82)
                      .+|.+.  .++.++   +....||+||+|+.||+++|.++++.++   ...+.+|+|++|+..+...
T Consensus        30 ~~~~v~~~~~~~~al~~~~~~~~Dlvl~d~~lp~~~g~~~l~~l~---~~~~~~piI~lt~~~~~~~   93 (665)
T PRK13558         30 GRLDVTQIRDFVAARDRVEAGEIDCVVADHEPDGFDGLALLEAVR---QTTAVPPVVVVPTAGDEAV   93 (665)
T ss_pred             cCcceEeeCCHHHHHHHhhccCCCEEEEeccCCCCcHHHHHHHHH---hcCCCCCEEEEECCCCHHH
Confidence            345443  444444   4455799999999999999999999999   5677899999998766543

>PRK15347 two component system sensor kinase SsrA; Provisional

Probab=98.73  E-value=5.2e-08  Score=63.19  Aligned_cols=63  Identities=17%  Similarity=0.202  Sum_probs=45.3

Q ss_pred             CCceeeecChhHH---hhccCccEEEEeCCCCCCCHHHHHHHHHhhc-CCCCCccEEEEeeCCchhh
Q 039883           17 SDGFDLSPTDTEE---VHVLAVDLIITDYCMPGMTGCELIKKIKLQS-FTFREIPTVIISSENILAR   79 (82)
Q Consensus        17 ~~~~~~~~~~~~~---~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~-~~~~~~~vi~ls~~~~~~~   79 (82)
                      +..+..+.++.++   +...+||+|++|+.||+++|+++++.+|... ...+.+|+|++|+..+...
T Consensus       714 g~~v~~a~~~~~al~~~~~~~~dlil~D~~mp~~~G~~~~~~ir~~~~~~~~~~pii~lt~~~~~~~  780 (921)
T PRK15347        714 GQQVTTAASGTEALELGRQHRFDLVLMDIRMPGLDGLETTQLWRDDPNNLDPDCMIVALTANAAPEE  780 (921)
T ss_pred             CCEEEEECCHHHHHHHHhcCCCCEEEEeCCCCCCCHHHHHHHHHhchhhcCCCCcEEEEeCCCCHHH
Confidence            3444444555554   4455799999999999999999999998211 1246789999998766543

>TIGR02154 PhoB phosphate regulon transcriptional regulatory protein PhoB

Probab=98.72  E-value=1.2e-07  Score=52.17  Aligned_cols=48  Identities=25%  Similarity=0.549  Sum_probs=38.5

Q ss_pred             hhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCchh
Q 039883           30 VHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENILA   78 (82)
Q Consensus        30 ~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~~~   78 (82)
                      +....||++++|..+|+.+|.++++.++ .....+.+|+|++++..+..
T Consensus        42 ~~~~~~d~vi~d~~~~~~~g~~~~~~l~-~~~~~~~~~ii~ls~~~~~~   89 (226)
T TIGR02154        42 INERGPDLILLDWMLPGTSGIELCRRLR-RRPETRAIPIIMLTARGEEE   89 (226)
T ss_pred             HHhcCCCEEEEECCCCCCcHHHHHHHHH-ccccCCCCCEEEEecCCCHH
Confidence            4455799999999999999999999998 32234678999999876544

PhoB is a DNA-binding response regulator protein acting with PhoR in a 2-component system responding to phosphate ion. PhoB acts as a positive regulator of gene expression for phosphate-related genes such as phoA, phoS, phoE and ugpAB as well as itself. It is often found proximal to genes for the high-affinity phosphate ABC transporter (pstSCAB; GenProp0190) and presumably regulates these as well.

>PRK11173 two-component response regulator; Provisional

Probab=98.72  E-value=9.5e-08  Score=53.32  Aligned_cols=58  Identities=17%  Similarity=0.421  Sum_probs=42.9

Q ss_pred             CCceee--ecChhH---HhhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCchh
Q 039883           17 SDGFDL--SPTDTE---EVHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENILA   78 (82)
Q Consensus        17 ~~~~~~--~~~~~~---~~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~~~   78 (82)
                      ..++.+  ..++.+   .+....||++++|+.+|+.+|+++++.++   .. +..|+|++++..+..
T Consensus        25 ~~g~~v~~~~~~~~~~~~~~~~~~dlvild~~l~~~~g~~~~~~lr---~~-~~~pii~lt~~~~~~   87 (237)
T PRK11173         25 AEGYDVFEATDGAEMHQILSENDINLVIMDINLPGKNGLLLARELR---EQ-ANVALMFLTGRDNEV   87 (237)
T ss_pred             HcCCEEEEECCHHHHHHHHhhCCCCEEEEcCCCCCCCHHHHHHHHh---cC-CCCCEEEEECCCCHH
Confidence            344544  344443   34455799999999999999999999999   33 468999999876543

>TIGR01387 cztR_silR_copR heavy metal response regulator

Probab=98.72  E-value=1.1e-07  Score=52.05  Aligned_cols=47  Identities=23%  Similarity=0.465  Sum_probs=39.3

Q ss_pred             HhhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCchh
Q 039883           29 EVHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENILA   78 (82)
Q Consensus        29 ~~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~~~   78 (82)
                      .+....||++++|+.+|+.+|.++++.++   ...+..|+|++++..+..
T Consensus        37 ~~~~~~~dlvl~d~~~~~~~g~~~~~~l~---~~~~~~~iivls~~~~~~   83 (218)
T TIGR01387        37 LALKDDYDLIILDVMLPGMDGWQILQTLR---RSGKQTPVLFLTARDSVA   83 (218)
T ss_pred             HHhcCCCCEEEEeCCCCCCCHHHHHHHHH---ccCCCCcEEEEEcCCCHH
Confidence            34455799999999999999999999999   556788999999776654

Members of this family contain a response regulator receiver domain (Pfam:PF00072) and an associated transcriptional regulatory region (Pfam:PF00486). This group is separated phylogenetically from related proteins with similar architecture and contains a number of proteins associated with heavy metal resistance efflux systems for copper, silver, cadmium, and/or zinc. Most members encoded by genes adjacent to genes for encoding a member of the heavy metal sensor histidine kinase family (TIGRFAMs:TIGR01386), its partner in the two-component response regulator system.

>PRK09959 hybrid sensory histidine kinase in two-component regulatory system with EvgA; Provisional

Probab=98.72  E-value=7.9e-08  Score=63.98  Aligned_cols=75  Identities=23%  Similarity=0.275  Sum_probs=51.1

Q ss_pred             CchhHHHHHHHHhcCCCceee--ecChhHH---hhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCc
Q 039883            2 TTTNGVLLSRLMSDGSDGFDL--SPTDTEE---VHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENI   76 (82)
Q Consensus         2 d~~~~~~~~~~~~~~~~~~~~--~~~~~~~---~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~   76 (82)
                      |+++.............++++  +.++.++   +...+||+||+|+.||+++|+++++.++   ...+..|+|++|+..+
T Consensus       965 dd~~~~~~~l~~~L~~~g~~v~~~~~~~~al~~~~~~~~dlil~D~~mp~~~g~~~~~~i~---~~~~~~pii~lt~~~~ 1041 (1197)
T PRK09959        965 DDHPTNRLLLKRQLNLLGYDVDEATDGVQALHKVSMQHYDLLITDVNMPNMDGFELTRKLR---EQNSSLPIWGLTANAQ 1041 (1197)
T ss_pred             CCCHHHHHHHHHHHHHcCCEEEEECCHHHHHHHhhcCCCCEEEEeCCCCCCCHHHHHHHHH---hcCCCCCEEEEECCCC
Confidence            344444433333233334444  4444444   4455799999999999999999999999   5567889999998866


Q ss_pred             hhh
Q 039883           77 LAR   79 (82)
Q Consensus        77 ~~~   79 (82)
                      ...
T Consensus      1042 ~~~ 1044 (1197)
T PRK09959       1042 ANE 1044 (1197)
T ss_pred             HHH
Confidence            543

>PRK10430 DNA-binding transcriptional activator DcuR; Provisional

Probab=98.71  E-value=1.1e-07  Score=53.42  Aligned_cols=44  Identities=25%  Similarity=0.279  Sum_probs=38.2

Q ss_pred             cCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCchhh
Q 039883           33 LAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENILAR   79 (82)
Q Consensus        33 ~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~~~~   79 (82)
                      .+||++|+|+.||+++|+++++.++   ...+.+|+|++|+..+...
T Consensus        48 ~~~DlvilD~~~p~~~G~eli~~l~---~~~~~~~vI~ls~~~~~~~   91 (239)
T PRK10430         48 TPIDLILLDIYMQQENGLDLLPVLH---EAGCKSDVIVISSAADAAT   91 (239)
T ss_pred             CCCCEEEEecCCCCCCcHHHHHHHH---hhCCCCCEEEEECCCcHHH
Confidence            4699999999999999999999998   5567889999998766543

>PRK10161 transcriptional regulator PhoB; Provisional

Probab=98.71  E-value=1.4e-07  Score=52.32  Aligned_cols=48  Identities=29%  Similarity=0.523  Sum_probs=38.5

Q ss_pred             hhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCchh
Q 039883           30 VHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENILA   78 (82)
Q Consensus        30 ~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~~~   78 (82)
                      +....||++++|..+++.+|.++++.++ .....+.+|+|++++..+..
T Consensus        42 ~~~~~~dlvild~~l~~~~g~~~~~~l~-~~~~~~~~pvi~ls~~~~~~   89 (229)
T PRK10161         42 LNEPWPDLILLDWMLPGGSGIQFIKHLK-RESMTRDIPVVMLTARGEEE   89 (229)
T ss_pred             HhccCCCEEEEeCCCCCCCHHHHHHHHH-hccccCCCCEEEEECCCCHH
Confidence            4455799999999999999999999998 32234678999999876543

>TIGR03787 marine_sort_RR proteobacterial dedicated sortase system response regulator

Probab=98.71  E-value=1.4e-07  Score=52.10  Aligned_cols=58  Identities=14%  Similarity=0.237  Sum_probs=42.8

Q ss_pred             Cceeeec--ChhH---HhhccCccEEEEeCCCCC--CCHHHHHHHHHhhcCCCCCccEEEEeeCCchh
Q 039883           18 DGFDLSP--TDTE---EVHVLAVDLIITDYCMPG--MTGCELIKKIKLQSFTFREIPTVIISSENILA   78 (82)
Q Consensus        18 ~~~~~~~--~~~~---~~~~~~~d~vi~d~~~~~--~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~~~   78 (82)
                      .++++..  ++.+   .+....||++++|+.+|+  .+|.++++.++   ...+..|+|++|+..+..
T Consensus        23 ~~~~v~~~~~~~~~~~~~~~~~~dlvild~~l~~~~~~g~~~~~~i~---~~~~~~pii~ls~~~~~~   87 (227)
T TIGR03787        23 QGYQVTTYADRPSAMQAFRQRLPDLAIIDIGLGEEIDGGFMLCQDLR---SLSATLPIIFLTARDSDF   87 (227)
T ss_pred             CCcEEEEecCHHHHHHHHHhCCCCEEEEECCCCCCCCCHHHHHHHHH---hcCCCCCEEEEECCCCHH
Confidence            4555533  3333   344557999999999997  58999999998   445678999999876654

This model describes a family of DNA-binding response regulator proteins, associated with an adjacent histidine kinase (TIGR03785) to form a two-component system. This system co-occurs with, and often is adjacent to, a proteobacterial variant form of the protein sorting transpeptidase called sortase (TIGR03784), and a single target protein for the sortase. We give this protein the gene symbol pdsR, for Proteobacterial Dedicated Sortase system Response regulator.

>PRK11083 DNA-binding response regulator CreB; Provisional

Probab=98.70  E-value=1.5e-07  Score=51.90  Aligned_cols=47  Identities=19%  Similarity=0.398  Sum_probs=39.1

Q ss_pred             HhhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCchh
Q 039883           29 EVHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENILA   78 (82)
Q Consensus        29 ~~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~~~   78 (82)
                      .+....||++++|..+|+.+|.++++.++   ...+.+|+|++++..+..
T Consensus        42 ~~~~~~~dlvl~d~~~~~~~g~~~~~~l~---~~~~~~~ii~ls~~~~~~   88 (228)
T PRK11083         42 KLRQQPPDLVILDVGLPDISGFELCRQLL---AFHPALPVIFLTARSDEV   88 (228)
T ss_pred             HHhcCCCCEEEEeCCCCCCCHHHHHHHHH---hhCCCCCEEEEEcCCcHH
Confidence            34455799999999999999999999999   455788999999876543

>TIGR01818 ntrC nitrogen regulation protein NR(I)

Probab=98.69  E-value=8.9e-08  Score=58.34  Aligned_cols=59  Identities=25%  Similarity=0.487  Sum_probs=44.1

Q ss_pred             CCceeeec--ChhHH---hhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCchh
Q 039883           17 SDGFDLSP--TDTEE---VHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENILA   78 (82)
Q Consensus        17 ~~~~~~~~--~~~~~---~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~~~   78 (82)
                      ..++++..  +..++   +....||+|++|+.||+++|+++++.++   ...+.+|+|++|+..+..
T Consensus        20 ~~g~~v~~~~~~~~al~~~~~~~~DlVllD~~~p~~~g~~ll~~l~---~~~~~~~vIvlt~~~~~~   83 (463)
T TIGR01818        20 RAGYEVRTFGNAASVLRALARGQPDLLITDVRMPGEDGLDLLPQIK---KRHPQLPVIVMTAHSDLD   83 (463)
T ss_pred             HcCCEEEEECCHHHHHHHHhcCCCCEEEEcCCCCCCCHHHHHHHHH---HhCCCCeEEEEeCCCCHH
Confidence            34455443  33433   4455799999999999999999999998   456778999999776543

This model represents NtrC, a DNA-binding response regulator that is phosphorylated by NtrB and interacts with sigma-54. NtrC usually controls the expression of glutamine synthase, GlnA, and may be called GlnL, GlnG, etc.

>PRK10923 glnG nitrogen regulation protein NR(I); Provisional

Probab=98.68  E-value=1e-07  Score=58.26  Aligned_cols=59  Identities=27%  Similarity=0.483  Sum_probs=44.7

Q ss_pred             CCceee--ecChhH---HhhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCchh
Q 039883           17 SDGFDL--SPTDTE---EVHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENILA   78 (82)
Q Consensus        17 ~~~~~~--~~~~~~---~~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~~~   78 (82)
                      ..++.+  ..++.+   .+....||++|+|+.||+++|+++++.++   ...+.+|+|++|+..+.+
T Consensus        25 ~~g~~v~~~~s~~~al~~l~~~~~DlvllD~~lp~~dgl~~l~~ir---~~~~~~pvIvlt~~~~~~   88 (469)
T PRK10923         25 GAGLTCTTFENGNEVLEALASKTPDVLLSDIRMPGMDGLALLKQIK---QRHPMLPVIIMTAHSDLD   88 (469)
T ss_pred             HcCCEEEEECCHHHHHHHHhcCCCCEEEECCCCCCCCHHHHHHHHH---hhCCCCeEEEEECCCCHH
Confidence            344544  334443   34456799999999999999999999998   456788999999876654

>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional

Probab=98.68  E-value=2.2e-07  Score=51.56  Aligned_cols=46  Identities=9%  Similarity=0.086  Sum_probs=37.6

Q ss_pred             HhhccCccEEEEeCC--CCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCch
Q 039883           29 EVHVLAVDLIITDYC--MPGMTGCELIKKIKLQSFTFREIPTVIISSENIL   77 (82)
Q Consensus        29 ~~~~~~~d~vi~d~~--~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~~   77 (82)
                      .+...+||++|+|+.  ++..+|.++++.++   ...+..++|++|+..+.
T Consensus        42 ~~~~~~pDlvLlDl~~~l~~~~g~~~i~~i~---~~~p~~~iivlt~~~~~   89 (207)
T PRK15411         42 ACDSLRPSVVFINEDCFIHDASNSQRIKQII---NQHPNTLFIVFMAIANI   89 (207)
T ss_pred             HHhccCCCEEEEeCcccCCCCChHHHHHHHH---HHCCCCeEEEEECCCch
Confidence            344567999999965  88788999999998   56778999999987654

>PRK10365 transcriptional regulatory protein ZraR; Provisional

Probab=98.68  E-value=1.2e-07  Score=57.43  Aligned_cols=58  Identities=24%  Similarity=0.402  Sum_probs=43.7

Q ss_pred             Cceee--ecChhHH---hhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCchh
Q 039883           18 DGFDL--SPTDTEE---VHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENILA   78 (82)
Q Consensus        18 ~~~~~--~~~~~~~---~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~~~   78 (82)
                      .++.+  +.++.++   +....||+|++|+.||+++|+++++.++   ...+.+|+|++|+..+.+
T Consensus        28 ~g~~v~~~~~~~~al~~l~~~~~DlvilD~~m~~~~G~~~~~~ir---~~~~~~~vi~lt~~~~~~   90 (441)
T PRK10365         28 WGYNVALANSGRQALEQVREQVFDLVLCDVRMAEMDGIATLKEIK---ALNPAIPVLIMTAYSSVE   90 (441)
T ss_pred             CCCeEEEeCCHHHHHHHHhcCCCCEEEEeCCCCCCCHHHHHHHHH---hhCCCCeEEEEECCCCHH
Confidence            34444  4444444   3445799999999999999999999998   456788999999875543

>PRK11361 acetoacetate metabolism regulatory protein AtoC; Provisional

Probab=98.67  E-value=1.3e-07  Score=57.44  Aligned_cols=58  Identities=17%  Similarity=0.380  Sum_probs=44.1

Q ss_pred             Cceeee--cChhHH---hhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCchh
Q 039883           18 DGFDLS--PTDTEE---VHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENILA   78 (82)
Q Consensus        18 ~~~~~~--~~~~~~---~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~~~   78 (82)
                      .++++.  .+..++   +....||++++|+.||+++|+++++.++   ...+.+|+|++|+..+.+
T Consensus        27 ~g~~v~~~~~~~~al~~l~~~~~dlillD~~~p~~~g~~ll~~i~---~~~~~~pvI~lt~~~~~~   89 (457)
T PRK11361         27 QGFETHCANNGRTALHLFADIHPDVVLMDIRMPEMDGIKALKEMR---SHETRTPVILMTAYAEVE   89 (457)
T ss_pred             CCCEEEEECCHHHHHHHHhcCCCCEEEEeCCCCCCCHHHHHHHHH---hcCCCCCEEEEeCCCCHH
Confidence            445544  344443   4455799999999999999999999998   456788999999876544

>PRK10766 DNA-binding transcriptional regulator TorR; Provisional

Probab=98.65  E-value=2.2e-07  Score=51.16  Aligned_cols=57  Identities=18%  Similarity=0.385  Sum_probs=42.3

Q ss_pred             Cceee--ecChhHH---hhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCchh
Q 039883           18 DGFDL--SPTDTEE---VHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENILA   78 (82)
Q Consensus        18 ~~~~~--~~~~~~~---~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~~~   78 (82)
                      .++++  ..++.++   +....||++++|..+|+.+|.++++.++   . .+.+|+|++++..+..
T Consensus        25 ~~~~v~~~~~~~~~~~~~~~~~~dlvild~~l~~~~g~~~~~~lr---~-~~~~~ii~l~~~~~~~   86 (221)
T PRK10766         25 EGYTVSEAASGAGMREIMQNQHVDLILLDINLPGEDGLMLTRELR---S-RSTVGIILVTGRTDSI   86 (221)
T ss_pred             cCCEEEEECCHHHHHHHHhcCCCCEEEEeCCCCCCCHHHHHHHHH---h-CCCCCEEEEECCCcHH
Confidence            44544  3344433   4455799999999999999999999999   3 2478999999776554

>PRK10840 transcriptional regulator RcsB; Provisional

Probab=98.65  E-value=2.5e-07  Score=51.20  Aligned_cols=54  Identities=31%  Similarity=0.413  Sum_probs=42.2

Q ss_pred             ecChhHH---hhccCccEEEEeCCCCC---CCHHHHHHHHHhhcCCCCCccEEEEeeCCchhh
Q 039883           23 SPTDTEE---VHVLAVDLIITDYCMPG---MTGCELIKKIKLQSFTFREIPTVIISSENILAR   79 (82)
Q Consensus        23 ~~~~~~~---~~~~~~d~vi~d~~~~~---~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~~~~   79 (82)
                      +.++.++   +...+||++|+|+.+|+   .+|.++++.++   ...+.+|+|++|...+...
T Consensus        35 ~~~~~~~~~~~~~~~~DlvllD~~l~~~~~~~g~~~~~~l~---~~~~~~~iIvls~~~~~~~   94 (216)
T PRK10840         35 FEDSTALINNLPKLDAHVLITDLSMPGDKYGDGITLIKYIK---RHFPSLSIIVLTMNNNPAI   94 (216)
T ss_pred             ECCHHHHHHHHHhCCCCEEEEeCcCCCCCCCCHHHHHHHHH---HHCCCCcEEEEEecCCHHH
Confidence            3444444   34557999999999999   59999999998   4577889999998876554

>PRK09483 response regulator; Provisional

Probab=98.64  E-value=3.2e-07  Score=50.37  Aligned_cols=47  Identities=23%  Similarity=0.349  Sum_probs=39.4

Q ss_pred             HhhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCchh
Q 039883           29 EVHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENILA   78 (82)
Q Consensus        29 ~~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~~~   78 (82)
                      .+...+||++|+|+.+++.+|.++++.++   ...+.+|+|+++...+..
T Consensus        42 ~~~~~~~dlvi~d~~~~~~~g~~~~~~l~---~~~~~~~ii~ls~~~~~~   88 (217)
T PRK09483         42 WCRTNAVDVVLMDMNMPGIGGLEATRKIL---RYTPDVKIIMLTVHTENP   88 (217)
T ss_pred             HHHhcCCCEEEEeCCCCCCCHHHHHHHHH---HHCCCCeEEEEeCCCCHH
Confidence            34556899999999999999999999998   456788999999776544

>PRK10693 response regulator of RpoS; Provisional

Probab=98.64  E-value=1.3e-07  Score=55.07  Aligned_cols=47  Identities=30%  Similarity=0.508  Sum_probs=39.8

Q ss_pred             hhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCchhh
Q 039883           30 VHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENILAR   79 (82)
Q Consensus        30 ~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~~~~   79 (82)
                      +....||+|++|+.||+++|+++++.++   ...+.+|+|++|+..+.+.
T Consensus        13 l~~~~pDlVL~D~~mp~~~Gle~~~~ir---~~~~~ipiI~lt~~~~~~~   59 (303)
T PRK10693         13 LGGFTPDLIICDLAMPRMNGIEFVEHLR---NRGDQTPVLVISATENMAD   59 (303)
T ss_pred             HhcCCCCEEEEeCCCCCCCHHHHHHHHH---hcCCCCcEEEEECCCCHHH
Confidence            4556799999999999999999999999   4466789999998876543

>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional

Probab=98.64  E-value=3.8e-07  Score=50.97  Aligned_cols=50  Identities=6%  Similarity=0.052  Sum_probs=38.6

Q ss_pred             cChhHHhh-ccCccEEEEeCCCCCCCHHHHH-HHHHhhcCCCCCccEEEEeeCCc
Q 039883           24 PTDTEEVH-VLAVDLIITDYCMPGMTGCELI-KKIKLQSFTFREIPTVIISSENI   76 (82)
Q Consensus        24 ~~~~~~~~-~~~~d~vi~d~~~~~~~~~~~~-~~l~~~~~~~~~~~vi~ls~~~~   76 (82)
                      .++.+++. ..+||++|+|+.||+.+|++++ +.++   ...+.++||++|...+
T Consensus        41 ~~~~~~~~~~~~~DvvllDi~~p~~~G~~~~~~~i~---~~~p~~~vvvlt~~~~   92 (216)
T PRK10100         41 HNIQRSLDDISSGSIILLDMMEADKKLIHYWQDTLS---RKNNNIKILLLNTPED   92 (216)
T ss_pred             cCHHHhhccCCCCCEEEEECCCCCccHHHHHHHHHH---HhCCCCcEEEEECCch
Confidence            34445544 2258999999999999999986 5677   5677899999998765

>PRK09958 DNA-binding transcriptional activator EvgA; Provisional

Probab=98.63  E-value=4.6e-07  Score=49.32  Aligned_cols=59  Identities=19%  Similarity=0.334  Sum_probs=43.7

Q ss_pred             CCceeee---cChhH---HhhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCchh
Q 039883           17 SDGFDLS---PTDTE---EVHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENILA   78 (82)
Q Consensus        17 ~~~~~~~---~~~~~---~~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~~~   78 (82)
                      ..++.+.   .+..+   .+....||++++|..+|+.+|.++++.++   ...+..|+|++++..+..
T Consensus        22 ~~~~~v~~~~~~~~~~~~~~~~~~~dlvi~d~~~~~~~g~~~~~~l~---~~~~~~~ii~ls~~~~~~   86 (204)
T PRK09958         22 KNDIEILAELTEGGSAVQRVETLKPDIVIIDVDIPGVNGIQVLETLR---KRQYSGIIIIVSAKNDHF   86 (204)
T ss_pred             cCCCEEEEEeCCHHHHHHHHHccCCCEEEEeCCCCCCCHHHHHHHHH---hhCCCCeEEEEeCCCCHH
Confidence            4566553   23333   34455799999999999999999999998   455667899998866543

>PRK09581 pleD response regulator PleD; Reviewed

Probab=98.62  E-value=3.1e-07  Score=55.32  Aligned_cols=49  Identities=16%  Similarity=0.217  Sum_probs=40.9

Q ss_pred             hhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCchhh
Q 039883           30 VHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENILAR   79 (82)
Q Consensus        30 ~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~~~~   79 (82)
                      +...+||+|++|+.||+++|+++++.++ .....+.+|+|++|+..+.+.
T Consensus       194 ~~~~~~d~vi~d~~~p~~~g~~l~~~i~-~~~~~~~~~ii~ls~~~~~~~  242 (457)
T PRK09581        194 AAETNYDLVIVSANFENYDPLRLCSQLR-SKERTRYVPILLLVDEDDDPR  242 (457)
T ss_pred             cccCCCCEEEecCCCCCchHhHHHHHHH-hccccCCCcEEEEeCCCChHH
Confidence            4456899999999999999999999999 333457899999999876544

>PRK13856 two-component response regulator VirG; Provisional

Probab=98.62  E-value=3.3e-07  Score=51.35  Aligned_cols=54  Identities=19%  Similarity=0.411  Sum_probs=40.2

Q ss_pred             Cceee--ecChhHH---hhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCC
Q 039883           18 DGFDL--SPTDTEE---VHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSEN   75 (82)
Q Consensus        18 ~~~~~--~~~~~~~---~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~   75 (82)
                      .++.+  +.++.++   +....||++++|+.+|+.+|+++++.++   . ....|+|++++..
T Consensus        24 ~~~~v~~~~~~~~~~~~~~~~~~dlvi~d~~l~~~~g~~l~~~i~---~-~~~~pii~lt~~~   82 (241)
T PRK13856         24 HAFKVTAVADSQQFNRVLASETVDVVVVDLNLGREDGLEIVRSLA---T-KSDVPIIIISGDR   82 (241)
T ss_pred             cCCEEEEECCHHHHHHHHhhCCCCEEEEeCCCCCCCHHHHHHHHH---h-cCCCcEEEEECCC
Confidence            44544  3344433   4456799999999999999999999998   3 3468999998743

>PRK10701 DNA-binding transcriptional regulator RstA; Provisional

Probab=98.62  E-value=3.4e-07  Score=51.17  Aligned_cols=57  Identities=19%  Similarity=0.362  Sum_probs=41.7

Q ss_pred             CCceeee--cChhH---HhhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCch
Q 039883           17 SDGFDLS--PTDTE---EVHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENIL   77 (82)
Q Consensus        17 ~~~~~~~--~~~~~---~~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~~   77 (82)
                      ..++.+.  .++.+   .+....||++++|+.+|+.+|+++++.++   . ....|+|++++..+.
T Consensus        23 ~~g~~v~~~~~~~~~l~~~~~~~~dlvild~~l~~~~g~~~~~~ir---~-~~~~pii~l~~~~~~   84 (240)
T PRK10701         23 KHDIDVTVEPRGDRAEATILREQPDLVLLDIMLPGKDGMTICRDLR---P-KWQGPIVLLTSLDSD   84 (240)
T ss_pred             HcCCEEEEeCCHHHHHHHHhhCCCCEEEEeCCCCCCCHHHHHHHHH---h-cCCCCEEEEECCCCH
Confidence            3455443  34443   34456899999999999999999999999   3 345689999876554

>PRK10955 DNA-binding transcriptional regulator CpxR; Provisional

Probab=98.59  E-value=3.9e-07  Score=50.43  Aligned_cols=42  Identities=21%  Similarity=0.475  Sum_probs=35.2

Q ss_pred             cCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCchh
Q 039883           33 LAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENILA   78 (82)
Q Consensus        33 ~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~~~   78 (82)
                      ..||++++|+.+|+.+|.++++.++   ...+ .|+|++|+..+..
T Consensus        43 ~~~d~vl~d~~~~~~~g~~~~~~l~---~~~~-~~ii~lt~~~~~~   84 (232)
T PRK10955         43 DSIDLLLLDVMMPKKNGIDTLKELR---QTHQ-TPVIMLTARGSEL   84 (232)
T ss_pred             cCCCEEEEeCCCCCCcHHHHHHHHH---hcCC-CcEEEEECCCCHH
Confidence            3799999999999999999999999   3344 8999999776543

>PRK11091 aerobic respiration control sensor protein ArcB; Provisional

Probab=98.59  E-value=3.6e-07  Score=58.72  Aligned_cols=59  Identities=20%  Similarity=0.459  Sum_probs=41.5

Q ss_pred             CCceeeecChhHHh---hccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCC-ccEEEEeeCCc
Q 039883           17 SDGFDLSPTDTEEV---HVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFRE-IPTVIISSENI   76 (82)
Q Consensus        17 ~~~~~~~~~~~~~~---~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~-~~vi~ls~~~~   76 (82)
                      +..+..+.++.+++   ...+||+|++|+.||+++|+++++.++ .....+. +|+|++|+...
T Consensus       549 g~~v~~a~~~~eal~~~~~~~~Dlvl~D~~mp~~~G~e~~~~ir-~~~~~~~~~~ii~~ta~~~  611 (779)
T PRK11091        549 GNSVDVAMTGKEALEMFDPDEYDLVLLDIQLPDMTGLDIARELR-ERYPREDLPPLVALTANVL  611 (779)
T ss_pred             CCEEEEECCHHHHHHHhhcCCCCEEEEcCCCCCCCHHHHHHHHH-hccccCCCCcEEEEECCch
Confidence            34444455555544   455799999999999999999999999 2222244 48888887543

>PRK11517 transcriptional regulatory protein YedW; Provisional

Probab=98.58  E-value=5.9e-07  Score=49.45  Aligned_cols=45  Identities=20%  Similarity=0.485  Sum_probs=37.0

Q ss_pred             hhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCchh
Q 039883           30 VHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENILA   78 (82)
Q Consensus        30 ~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~~~   78 (82)
                      +....||++++|..+|+.+|.++++.++   .. ...|+|++++..+..
T Consensus        40 ~~~~~~dlvi~d~~~~~~~g~~~~~~l~---~~-~~~~ii~ls~~~~~~   84 (223)
T PRK11517         40 ALKDDYALIILDIMLPGMDGWQILQTLR---TA-KQTPVICLTARDSVD   84 (223)
T ss_pred             HhcCCCCEEEEECCCCCCCHHHHHHHHH---cC-CCCCEEEEECCCCHH
Confidence            3455799999999999999999999998   33 468999999766544

>TIGR02875 spore_0_A sporulation transcription factor Spo0A

Probab=98.58  E-value=1e-06  Score=50.12  Aligned_cols=49  Identities=14%  Similarity=0.217  Sum_probs=38.1

Q ss_pred             HhhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCchh
Q 039883           29 EVHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENILA   78 (82)
Q Consensus        29 ~~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~~~   78 (82)
                      .+....||+|++|+.||+++|+++++.++ .......+|+|++|+..+..
T Consensus        43 ~l~~~~~DlvllD~~mp~~dG~~~l~~i~-~~~~~~~~~iI~lt~~~~~~   91 (262)
T TIGR02875        43 LIKEQQPDVVVLDIIMPHLDGIGVLEKLN-EIELSARPRVIMLSAFGQEK   91 (262)
T ss_pred             HHHhcCCCEEEEeCCCCCCCHHHHHHHHH-hhccccCCeEEEEeCCCCHH
Confidence            34456799999999999999999999998 32233348899999776544

Spo0A, the stage 0 sporulation protein A, is a transcription factor critical for the initiation of sporulation. It contains a response regulator receiver domain (pfam00072). In Bacillus subtilis, it works together with response regulator Spo0F and the phosphotransferase Spo0B, both of which are missing from at least some sporulating species and thus not part of the endospore forming bacteria minimal gene set. Spo0A, however, is universal among endospore-forming species.

>TIGR02915 PEP_resp_reg putative PEP-CTERM system response regulator

Probab=98.58  E-value=7.8e-07  Score=54.09  Aligned_cols=59  Identities=12%  Similarity=0.229  Sum_probs=44.2

Q ss_pred             Cceee--ecChhHH---hhccCccEEEEeCCCCC-----CCHHHHHHHHHhhcCCCCCccEEEEeeCCchhh
Q 039883           18 DGFDL--SPTDTEE---VHVLAVDLIITDYCMPG-----MTGCELIKKIKLQSFTFREIPTVIISSENILAR   79 (82)
Q Consensus        18 ~~~~~--~~~~~~~---~~~~~~d~vi~d~~~~~-----~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~~~~   79 (82)
                      .+|++  +.++.++   +....||+|++|+.||+     ++|+++++.++   ...+.+|+|++|+..+.+.
T Consensus        19 ~~~~v~~a~~~~~al~~l~~~~~dlvllD~~mp~~~~~~~~g~~~l~~i~---~~~~~~piI~lt~~~~~~~   87 (445)
T TIGR02915        19 ADYELAVAADRESAIALVRRHEPAVVTLDLGLPPDADGASEGLAALQQIL---AIAPDTKVIVITGNDDREN   87 (445)
T ss_pred             CCCeEEEeCCHHHHHHHHhhCCCCEEEEeCCCCCCcCCCCCHHHHHHHHH---hhCCCCCEEEEecCCCHHH
Confidence            34444  3444443   44557999999999996     89999999998   5677899999998766543

Members of this protein family share full-length homology with (but do not include) the acetoacetate metabolism regulatory protein AtoC. These proteins have a Fis family DNA binding sequence (pfam02954), a response regulator receiver domain (pfam00072), and sigma-54 interaction domain (pfam00158).

>PRK09390 fixJ response regulator FixJ; Provisional

Probab=98.56  E-value=5.6e-07  Score=48.46  Aligned_cols=46  Identities=24%  Similarity=0.505  Sum_probs=38.3

Q ss_pred             hhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCchh
Q 039883           30 VHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENILA   78 (82)
Q Consensus        30 ~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~~~   78 (82)
                      +....||++++|..+++.+|+++++.++   ...+.+|+|+++...+..
T Consensus        43 ~~~~~~d~ii~d~~~~~~~~~~~~~~l~---~~~~~~~ii~l~~~~~~~   88 (202)
T PRK09390         43 LPGLRFGCVVTDVRMPGIDGIELLRRLK---ARGSPLPVIVMTGHGDVP   88 (202)
T ss_pred             hccCCCCEEEEeCCCCCCcHHHHHHHHH---hcCCCCCEEEEECCCCHH
Confidence            4445799999999999999999999998   456788999999765543

>CHL00148 orf27 Ycf27; Reviewed

Probab=98.55  E-value=5.9e-07  Score=49.96  Aligned_cols=45  Identities=20%  Similarity=0.426  Sum_probs=37.4

Q ss_pred             hhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCchh
Q 039883           30 VHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENILA   78 (82)
Q Consensus        30 ~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~~~   78 (82)
                      +....||++++|+.+|+.+|.++++.++   .. +.+|+|++++..+..
T Consensus        46 ~~~~~~d~illd~~~~~~~g~~~~~~l~---~~-~~~~ii~ls~~~~~~   90 (240)
T CHL00148         46 FRKEQPDLVILDVMMPKLDGYGVCQEIR---KE-SDVPIIMLTALGDVS   90 (240)
T ss_pred             HHhcCCCEEEEeCCCCCCCHHHHHHHHH---hc-CCCcEEEEECCCCHH
Confidence            4455799999999999999999999998   33 578999999876544

>PRK14084 two-component response regulator; Provisional

Probab=98.54  E-value=1.4e-06  Score=49.07  Aligned_cols=51  Identities=18%  Similarity=0.204  Sum_probs=39.0

Q ss_pred             ecChhHH---hhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCc
Q 039883           23 SPTDTEE---VHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENI   76 (82)
Q Consensus        23 ~~~~~~~---~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~   76 (82)
                      +.++.++   +....||++++|+.||+++|+++++.++   ...+.+++|++|+..+
T Consensus        32 ~~~~~~~l~~~~~~~~dlv~lDi~m~~~~G~~~~~~i~---~~~~~~~iI~~t~~~~   85 (246)
T PRK14084         32 AENVKETLEALLINQYDIIFLDINLMDESGIELAAKIQ---KMKEPPAIIFATAHDQ   85 (246)
T ss_pred             ECCHHHHHHHHHhcCCCEEEEeCCCCCCCHHHHHHHHH---hcCCCCEEEEEecChH
Confidence            4444444   3445799999999999999999999999   4456677888887543

>PRK09935 transcriptional regulator FimZ; Provisional

Probab=98.53  E-value=1.1e-06  Score=47.93  Aligned_cols=47  Identities=30%  Similarity=0.427  Sum_probs=39.0

Q ss_pred             HhhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCchh
Q 039883           29 EVHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENILA   78 (82)
Q Consensus        29 ~~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~~~   78 (82)
                      .+....||++++|..+|+.+|.++++.++   ...+.+|+|++++..+..
T Consensus        44 ~~~~~~~dlvild~~l~~~~g~~~~~~l~---~~~~~~~ii~ls~~~~~~   90 (210)
T PRK09935         44 YLRTRPVDLIIMDIDLPGTDGFTFLKRIK---QIQSTVKVLFLSSKSECF   90 (210)
T ss_pred             HHHhcCCCEEEEeCCCCCCCHHHHHHHHH---HhCCCCcEEEEECCCcHH
Confidence            34556799999999999999999999998   446678999999876543

>PRK09581 pleD response regulator PleD; Reviewed

Probab=98.43  E-value=1.8e-06  Score=52.02  Aligned_cols=49  Identities=27%  Similarity=0.429  Sum_probs=39.2

Q ss_pred             HhhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCchh
Q 039883           29 EVHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENILA   78 (82)
Q Consensus        29 ~~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~~~   78 (82)
                      .+....||+|++|+.+|+.+|.++++.++ .....+.+|+|++++..+..
T Consensus        41 ~~~~~~~dlvi~d~~~~~~~g~~l~~~i~-~~~~~~~~~ii~~s~~~~~~   89 (457)
T PRK09581         41 ICEREQPDIILLDVMMPGMDGFEVCRRLK-SDPATTHIPVVMVTALDDPE   89 (457)
T ss_pred             HHhhcCCCEEEEeCCCCCCCHHHHHHHHH-cCcccCCCCEEEEECCCCHH
Confidence            34555799999999999999999999998 32234578999999876654

>PRK15479 transcriptional regulatory protein TctD; Provisional

Probab=98.43  E-value=2.1e-06  Score=47.12  Aligned_cols=46  Identities=22%  Similarity=0.493  Sum_probs=38.3

Q ss_pred             hhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCchh
Q 039883           30 VHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENILA   78 (82)
Q Consensus        30 ~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~~~   78 (82)
                      +....||++++|..+|+.+|.++++.++   ...+..|+|++++..+..
T Consensus        40 ~~~~~~d~vild~~~~~~~~~~~~~~i~---~~~~~~~ii~lt~~~~~~   85 (221)
T PRK15479         40 LQSEMYALAVLDINMPGMDGLEVLQRLR---KRGQTLPVLLLTARSAVA   85 (221)
T ss_pred             HhhCCCCEEEEeCCCCCCcHHHHHHHHH---hcCCCCCEEEEECCCCHH
Confidence            4455799999999999999999999998   456678999998776544

>PRK12555 chemotaxis-specific methylesterase; Provisional

Probab=98.41  E-value=1.9e-06  Score=50.89  Aligned_cols=56  Identities=23%  Similarity=0.355  Sum_probs=41.1

Q ss_pred             CCceeee---cChhHH---hhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCc
Q 039883           17 SDGFDLS---PTDTEE---VHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENI   76 (82)
Q Consensus        17 ~~~~~~~---~~~~~~---~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~   76 (82)
                      ..++++.   .++.++   +....||+|++|+.||+++|+++++.++   . ....|++++++...
T Consensus        23 ~~~~~vv~~a~~~~eal~~l~~~~pDlVllD~~mp~~~G~e~l~~l~---~-~~~~pvivvs~~~~   84 (337)
T PRK12555         23 DPDHEVVWVATDGAQAVERCAAQPPDVILMDLEMPRMDGVEATRRIM---A-ERPCPILIVTSLTE   84 (337)
T ss_pred             CCCCEEEEEECCHHHHHHHHhccCCCEEEEcCCCCCCCHHHHHHHHH---H-HCCCcEEEEeCCCC
Confidence            4455543   334443   4455799999999999999999999998   2 23478999987643

>PRK11697 putative two-component response-regulatory protein YehT; Provisional

Probab=98.33  E-value=7.5e-06  Score=45.79  Aligned_cols=43  Identities=23%  Similarity=0.324  Sum_probs=33.4

Q ss_pred             hhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCc
Q 039883           30 VHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENI   76 (82)
Q Consensus        30 ~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~   76 (82)
                      +....||++++|+.||+++|+++++.++   . ...+++|++|+..+
T Consensus        43 ~~~~~~dlv~lDi~~~~~~G~~~~~~l~---~-~~~~~ii~vt~~~~   85 (238)
T PRK11697         43 IHRLKPDVVFLDIQMPRISGLELVGMLD---P-EHMPYIVFVTAFDE   85 (238)
T ss_pred             HHhcCCCEEEEeCCCCCCCHHHHHHHhc---c-cCCCEEEEEeccHH
Confidence            3445799999999999999999999887   2 23456888887643

>PRK10710 DNA-binding transcriptional regulator BaeR; Provisional

Probab=98.33  E-value=5.1e-06  Score=46.19  Aligned_cols=44  Identities=32%  Similarity=0.564  Sum_probs=36.4

Q ss_pred             hhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCch
Q 039883           30 VHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENIL   77 (82)
Q Consensus        30 ~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~~   77 (82)
                      +....||++++|..+++.+|.++++.++   . .+..|++++++..+.
T Consensus        50 ~~~~~~dlvl~d~~~~~~~g~~~~~~l~---~-~~~~pii~l~~~~~~   93 (240)
T PRK10710         50 VRQTPPDLILLDLMLPGTDGLTLCREIR---R-FSDIPIVMVTAKIEE   93 (240)
T ss_pred             HhhCCCCEEEEeCCCCCCCHHHHHHHHH---h-cCCCCEEEEEcCCCH
Confidence            4455799999999999999999999998   3 346899999876544

>PRK00742 chemotaxis-specific methylesterase; Provisional

Probab=98.32  E-value=4.7e-06  Score=49.50  Aligned_cols=41  Identities=34%  Similarity=0.419  Sum_probs=34.6

Q ss_pred             hhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeC
Q 039883           30 VHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSE   74 (82)
Q Consensus        30 ~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~   74 (82)
                      +....||++++|+.||+++|+++++.++   ...+ +|+|+++..
T Consensus        45 ~~~~~~DlVllD~~mp~~dgle~l~~i~---~~~~-~piIvls~~   85 (354)
T PRK00742         45 IKKLNPDVITLDVEMPVMDGLDALEKIM---RLRP-TPVVMVSSL   85 (354)
T ss_pred             HhhhCCCEEEEeCCCCCCChHHHHHHHH---HhCC-CCEEEEecC
Confidence            4455799999999999999999999998   3344 899999864

>PRK09191 two-component response regulator; Provisional

Probab=98.28  E-value=7.9e-06  Score=46.27  Aligned_cols=45  Identities=20%  Similarity=0.318  Sum_probs=36.0

Q ss_pred             HhhccCccEEEEeCCCCC-CCHHHHHHHHHhhcCCCCCccEEEEeeCCch
Q 039883           29 EVHVLAVDLIITDYCMPG-MTGCELIKKIKLQSFTFREIPTVIISSENIL   77 (82)
Q Consensus        29 ~~~~~~~d~vi~d~~~~~-~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~~   77 (82)
                      .+....||++++|+.+|+ .+|.++++.++   ... .+|+|++++..+.
T Consensus       177 ~l~~~~~dlvi~d~~~~~~~~g~e~l~~l~---~~~-~~pii~ls~~~~~  222 (261)
T PRK09191        177 LAKKTRPGLILADIQLADGSSGIDAVNDIL---KTF-DVPVIFITAFPER  222 (261)
T ss_pred             HHhccCCCEEEEecCCCCCCCHHHHHHHHH---HhC-CCCEEEEeCCCcH
Confidence            344557999999999995 78999999998   334 7899999986543

>COG3707 AmiR Response regulator with putative antiterminator output domain [Signal transduction mechanisms]

Probab=98.22  E-value=8e-06  Score=44.77  Aligned_cols=61  Identities=21%  Similarity=0.172  Sum_probs=43.9

Q ss_pred             CCceeeecChh------HHhhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCchhhhh
Q 039883           17 SDGFDLSPTDT------EEVHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENILARID   81 (82)
Q Consensus        17 ~~~~~~~~~~~------~~~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~~~~~~   81 (82)
                      ..||..+.+..      +.....+||+|++|+.+|..+-.+-+.. .   ......|+|++|+.+++..++
T Consensus        27 eag~~~Vg~~~~~~~~~~~~~~~~pDvVildie~p~rd~~e~~~~-~---~~~~~~piv~lt~~s~p~~i~   93 (194)
T COG3707          27 EAGYQRVGEAADGLEAVEVCERLQPDVVILDIEMPRRDIIEALLL-A---SENVARPIVALTAYSDPALIE   93 (194)
T ss_pred             HcCCeEeeeecccccchhHHHhcCCCEEEEecCCCCccHHHHHHH-h---hcCCCCCEEEEEccCChHHHH
Confidence            45666655433      4566779999999999999994333332 3   356778999999999887664

>PRK15369 two component system sensor kinase SsrB; Provisional

Probab=98.22  E-value=3.7e-05  Score=41.53  Aligned_cols=46  Identities=20%  Similarity=0.458  Sum_probs=37.9

Q ss_pred             hhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCchh
Q 039883           30 VHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENILA   78 (82)
Q Consensus        30 ~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~~~   78 (82)
                      +....||++++|..+++.+|.++++.++   ...+..|+|++++..+..
T Consensus        45 ~~~~~~dlvl~d~~~~~~~~~~~~~~l~---~~~~~~~ii~ls~~~~~~   90 (211)
T PRK15369         45 CRQLEPDIVILDLGLPGMNGLDVIPQLH---QRWPAMNILVLTARQEEH   90 (211)
T ss_pred             HHhcCCCEEEEeCCCCCCCHHHHHHHHH---HHCCCCcEEEEeCCCCHH
Confidence            4456799999999999999999999998   445678999999766543

>PRK10360 DNA-binding transcriptional activator UhpA; Provisional

Probab=98.19  E-value=2e-05  Score=42.57  Aligned_cols=43  Identities=26%  Similarity=0.430  Sum_probs=35.0

Q ss_pred             hhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCchh
Q 039883           30 VHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENILA   78 (82)
Q Consensus        30 ~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~~~   78 (82)
                      +...+||++++|+.+++.+|.++++.++   .   ..|+++++...+.+
T Consensus        43 ~~~~~~dlvi~d~~~~~~~g~~~~~~l~---~---~~~vi~~s~~~~~~   85 (196)
T PRK10360         43 LPGRGVQVCICDISMPDISGLELLSQLP---K---GMATIMLSVHDSPA   85 (196)
T ss_pred             HhcCCCCEEEEeCCCCCCCHHHHHHHHc---c---CCCEEEEECCCCHH
Confidence            4445799999999999999999998887   2   46899998876544

>PRK10651 transcriptional regulator NarL; Provisional

Probab=98.18  E-value=2.9e-05  Score=42.30  Aligned_cols=46  Identities=33%  Similarity=0.395  Sum_probs=37.7

Q ss_pred             hhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCchh
Q 039883           30 VHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENILA   78 (82)
Q Consensus        30 ~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~~~   78 (82)
                      +....||++++|..+++.+|.++++.++   ...+..|+++++...+..
T Consensus        48 ~~~~~~dlvl~d~~l~~~~~~~~~~~l~---~~~~~~~vi~l~~~~~~~   93 (216)
T PRK10651         48 AESLDPDLILLDLNMPGMNGLETLDKLR---EKSLSGRIVVFSVSNHEE   93 (216)
T ss_pred             HHhCCCCEEEEeCCCCCCcHHHHHHHHH---HhCCCCcEEEEeCCCCHH
Confidence            4445799999999999999999999998   445678899998765543

>PRK10403 transcriptional regulator NarP; Provisional

Probab=98.13  E-value=4.1e-05  Score=41.64  Aligned_cols=45  Identities=20%  Similarity=0.336  Sum_probs=37.1

Q ss_pred             hhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCch
Q 039883           30 VHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENIL   77 (82)
Q Consensus        30 ~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~~   77 (82)
                      +....||++++|..+++.+|.++++.++   ...+..|+++++...+.
T Consensus        48 ~~~~~~dlvi~d~~~~~~~~~~~~~~l~---~~~~~~~ii~l~~~~~~   92 (215)
T PRK10403         48 ANRLDPDVILLDLNMKGMSGLDTLNALR---RDGVTAQIIILTVSDAS   92 (215)
T ss_pred             HHhcCCCEEEEecCCCCCcHHHHHHHHH---HhCCCCeEEEEeCCCCh
Confidence            4455799999999999999999999998   45667789999866544

>cd00156 REC Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; contains a phosphoacceptor site that is phosphorylated by histidine kinase homologs; usually found N-terminal to a DNA binding effector domain; forms homodimers

Probab=98.03  E-value=8.8e-05  Score=35.22  Aligned_cols=45  Identities=31%  Similarity=0.516  Sum_probs=36.3

Q ss_pred             HhhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCc
Q 039883           29 EVHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENI   76 (82)
Q Consensus        29 ~~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~   76 (82)
                      .+....|+++++|..+++.++.++++.++   ...+..|+++++....
T Consensus        36 ~~~~~~~~~ii~~~~~~~~~~~~~~~~l~---~~~~~~~~i~~~~~~~   80 (113)
T cd00156          36 LLAEEKPDLILLDIMMPGMDGLELLRRIR---KRGPDIPIIFLTAHGD   80 (113)
T ss_pred             HHHhCCCCEEEEecCCCCCchHHHHHHHH---HhCCCCCEEEEEeccc
Confidence            34455799999999999999999999998   3366788898886543

>PRK10610 chemotaxis regulatory protein CheY; Provisional

Probab=98.00  E-value=7.1e-05  Score=37.03  Aligned_cols=47  Identities=26%  Similarity=0.538  Sum_probs=36.5

Q ss_pred             hhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCch
Q 039883           30 VHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENIL   77 (82)
Q Consensus        30 ~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~~   77 (82)
                      +....||++++|..+++.+|+++++.++ .....+..|+++++...+.
T Consensus        46 ~~~~~~di~l~d~~~~~~~~~~~~~~l~-~~~~~~~~~~i~~~~~~~~   92 (129)
T PRK10610         46 LQAGGFGFVISDWNMPNMDGLELLKTIR-ADGAMSALPVLMVTAEAKK   92 (129)
T ss_pred             hhccCCCEEEEcCCCCCCCHHHHHHHHH-hCCCcCCCcEEEEECCCCH
Confidence            4445799999999999999999999998 3223456788988866543

>PRK13435 response regulator; Provisional

Probab=97.97  E-value=7.4e-05  Score=38.82  Aligned_cols=43  Identities=16%  Similarity=0.244  Sum_probs=33.8

Q ss_pred             hhccCccEEEEeCCCC-CCCHHHHHHHHHhhcCCCCCccEEEEeeCCc
Q 039883           30 VHVLAVDLIITDYCMP-GMTGCELIKKIKLQSFTFREIPTVIISSENI   76 (82)
Q Consensus        30 ~~~~~~d~vi~d~~~~-~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~   76 (82)
                      +....||++++|..++ +.+|.++++.++   . ....|+|++++..+
T Consensus        46 ~~~~~~dliivd~~~~~~~~~~~~~~~l~---~-~~~~pii~ls~~~~   89 (145)
T PRK13435         46 GRRRQPDVALVDVHLADGPTGVEVARRLS---A-DGGVEVVFMTGNPE   89 (145)
T ss_pred             hhhcCCCEEEEeeecCCCCcHHHHHHHHH---h-CCCCCEEEEeCCHH
Confidence            3345799999999998 479999999988   2 34789999987543

>COG3279 LytT Response regulator of the LytR/AlgR family [Transcription / Signal transduction mechanisms]

Probab=97.90  E-value=4.1e-05  Score=43.67  Aligned_cols=47  Identities=23%  Similarity=0.357  Sum_probs=40.0

Q ss_pred             HHhhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCch
Q 039883           28 EEVHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENIL   77 (82)
Q Consensus        28 ~~~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~~   77 (82)
                      +.+....||++++|+.||+++|+++.+.++   ...+.++|+++|+..+.
T Consensus        41 ~~~~~~~~~~~fldI~~~~~~G~ela~~i~---~~~~~~~Ivfvt~~~~~   87 (244)
T COG3279          41 QLLQGLRPDLVFLDIAMPDINGIELAARIR---KGDPRPAIVFVTAHDEY   87 (244)
T ss_pred             HHHhccCCCeEEEeeccCccchHHHHHHhc---ccCCCCeEEEEEehHHH
Confidence            556667999999999999999999999999   55777888888887653

>PRK13837 two-component VirA-like sensor kinase; Provisional

Probab=97.87  E-value=8.1e-05  Score=48.72  Aligned_cols=70  Identities=10%  Similarity=0.068  Sum_probs=46.1

Q ss_pred             hhHHHHHHHHhcCCCceeee--cChhHHhhc---c--CccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCc
Q 039883            4 TNGVLLSRLMSDGSDGFDLS--PTDTEEVHV---L--AVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENI   76 (82)
Q Consensus         4 ~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~---~--~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~   76 (82)
                      ++.............+|++.  .+..+++..   .  +||+||+  .+|+++|.++++.++   ...+.+|+|++++...
T Consensus       706 d~~~~~~l~~~L~~~G~~v~~~~s~~~al~~l~~~~~~~DlVll--~~~~~~g~~l~~~l~---~~~~~ipIIvls~~~~  780 (828)
T PRK13837        706 DDATLERYEEKLAALGYEPVGFSTLAAAIAWISKGPERFDLVLV--DDRLLDEEQAAAALH---AAAPTLPIILGGNSKT  780 (828)
T ss_pred             CHHHHHHHHHHHHHCCCEEEEeCCHHHHHHHHHhCCCCceEEEE--CCCCCCHHHHHHHHH---hhCCCCCEEEEeCCCc
Confidence            33333333333334556654  444444332   2  3799999  799999999999999   5677899999998765


Q ss_pred             hh
Q 039883           77 LA   78 (82)
Q Consensus        77 ~~   78 (82)
                      ..
T Consensus       781 ~~  782 (828)
T PRK13837        781 MA  782 (828)
T ss_pred             hh
Confidence            44

>PRK13557 histidine kinase; Provisional

Probab=97.71  E-value=0.00053  Score=42.35  Aligned_cols=41  Identities=29%  Similarity=0.453  Sum_probs=34.8

Q ss_pred             CccEEEEeCCCCC-CCHHHHHHHHHhhcCCCCCccEEEEeeCCch
Q 039883           34 AVDLIITDYCMPG-MTGCELIKKIKLQSFTFREIPTVIISSENIL   77 (82)
Q Consensus        34 ~~d~vi~d~~~~~-~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~~   77 (82)
                      .||++++|..+++ .+|+++++.++   ...+..|+|+++.....
T Consensus       460 ~~d~vi~d~~~~~~~~~~~~~~~l~---~~~~~~~ii~~~~~~~~  501 (540)
T PRK13557        460 EVDLLFTDLIMPGGMNGVMLAREAR---RRQPKIKVLLTTGYAEA  501 (540)
T ss_pred             CceEEEEeccCCCCCCHHHHHHHHH---HhCCCCcEEEEcCCCch
Confidence            5999999999997 89999999999   45667899999876553

>COG3706 PleD Response regulator containing a CheY-like receiver domain and a GGDEF domain [Signal transduction mechanisms]

Probab=96.99  E-value=0.0023  Score=39.51  Aligned_cols=42  Identities=26%  Similarity=0.372  Sum_probs=32.3

Q ss_pred             HHhhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeC
Q 039883           28 EEVHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSE   74 (82)
Q Consensus        28 ~~~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~   74 (82)
                      ..+...+|+.+++|..||+++|+++++.++ .   .+.+ ++++|..
T Consensus        26 ~~~~~~~~~~~lld~~m~~~~~~~~~~~lk-~---~~~~-~v~~t~~   67 (435)
T COG3706          26 AILLDHKPDYKLLDVMMPGMDGFELCRRLK-A---EPAT-VVMVTAL   67 (435)
T ss_pred             HHHhcCCCCeEEeecccCCcCchhHHHHHh-c---CCcc-eEEEEec
Confidence            345577899999999999999999999999 2   2222 5666544

>PRK11107 hybrid sensory histidine kinase BarA; Provisional

Probab=94.59  E-value=0.19  Score=33.64  Aligned_cols=58  Identities=3%  Similarity=-0.033  Sum_probs=34.2

Q ss_pred             CCceeeecChh-HHhhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCC
Q 039883           17 SDGFDLSPTDT-EEVHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSEN   75 (82)
Q Consensus        17 ~~~~~~~~~~~-~~~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~   75 (82)
                      ..++.+..+.. +.+....||++++|..+|+..+...+...... ......++++++...
T Consensus       558 ~~g~~v~~~~~~~~l~~~~~d~il~~~~~~~~~~~~~~~~~~~~-~~~~~~~~i~~~~~~  616 (919)
T PRK11107        558 ETPLEVTYSPTLSQLPEAHYDILLLGLPVTFREPLTMLHERLAK-AKSMTDFLILALPCH  616 (919)
T ss_pred             HCCCEEEEcCCHHHhccCCCCEEEecccCCCCCCHHHHHHHHHh-hhhcCCcEEEEeCCc
Confidence            45555544333 22566789999999999987776654444312 223334566665543

>PF14606 Lipase_GDSL_3: GDSL-like Lipase/Acylhydrolase family; PDB: 3SKV_B

Probab=92.28  E-value=0.45  Score=26.32  Aligned_cols=44  Identities=18%  Similarity=0.241  Sum_probs=27.2

Q ss_pred             HHhhccCccEEEEeCCCC--CC----CHHHHHHHHHhhcCCCCCccEEEEeeC
Q 039883           28 EEVHVLAVDLIITDYCMP--GM----TGCELIKKIKLQSFTFREIPTVIISSE   74 (82)
Q Consensus        28 ~~~~~~~~d~vi~d~~~~--~~----~~~~~~~~l~~~~~~~~~~~vi~ls~~   74 (82)
                      +.+...++|++++|+..-  ..    ....|++.||   ...|.+||++++..
T Consensus        53 ~~ia~~~a~~~~ld~~~N~~~~~~~~~~~~fv~~iR---~~hP~tPIllv~~~  102 (178)
T PF14606_consen   53 DLIAEIDADLIVLDCGPNMSPEEFRERLDGFVKTIR---EAHPDTPILLVSPI  102 (178)
T ss_dssp             HHHHHS--SEEEEEESHHCCTTTHHHHHHHHHHHHH---TT-SSS-EEEEE--
T ss_pred             HHHhcCCCCEEEEEeecCCCHHHHHHHHHHHHHHHH---HhCCCCCEEEEecC
Confidence            456666889999998543  11    1345677778   78999999999954

>cd01844 SGNH_hydrolase_like_6 SGNH_hydrolase subfamily

Probab=91.86  E-value=0.83  Score=24.61  Aligned_cols=42  Identities=21%  Similarity=0.296  Sum_probs=27.4

Q ss_pred             hhccCccEEEEeCCCCCCCHH--------HHHHHHHhhcCCCCCccEEEEeeC
Q 039883           30 VHVLAVDLIITDYCMPGMTGC--------ELIKKIKLQSFTFREIPTVIISSE   74 (82)
Q Consensus        30 ~~~~~~d~vi~d~~~~~~~~~--------~~~~~l~~~~~~~~~~~vi~ls~~   74 (82)
                      +...+||+|++.+..-+....        .+++.++   ...+.+||++++..
T Consensus        53 ~~~~~pd~vii~~G~ND~~~~~~~~~~~~~~i~~i~---~~~p~~~iil~~~~  102 (177)
T cd01844          53 LRDVPADLYIIDCGPNIVGAEAMVRERLGPLVKGLR---ETHPDTPILLVSPR  102 (177)
T ss_pred             HHhcCCCEEEEEeccCCCccHHHHHHHHHHHHHHHH---HHCcCCCEEEEecC
Confidence            445689999997766655333        2344555   45677889988854

SGNH hydrolases are a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely resembles the Ser-His-Asp(Glu) triad found in other serine hydrolases.

>cd02067 B12-binding B12 binding domain (B12-BD)

Probab=90.56  E-value=1.3  Score=22.31  Aligned_cols=54  Identities=19%  Similarity=0.162  Sum_probs=32.8

Q ss_pred             hcCCCceeeecChh--------HHhhccCccEEEEeCCCCCC--CHHHHHHHHHhhcCCCC-CccEEE
Q 039883           14 SDGSDGFDLSPTDT--------EEVHVLAVDLIITDYCMPGM--TGCELIKKIKLQSFTFR-EIPTVI   70 (82)
Q Consensus        14 ~~~~~~~~~~~~~~--------~~~~~~~~d~vi~d~~~~~~--~~~~~~~~l~~~~~~~~-~~~vi~   70 (82)
                      .....||++..-+.        +.+...+||+|.+...+...  ...++++.+|   ...+ .+++++
T Consensus        22 ~l~~~G~~V~~lg~~~~~~~l~~~~~~~~pdvV~iS~~~~~~~~~~~~~i~~l~---~~~~~~~~i~v   86 (119)
T cd02067          22 ALRDAGFEVIDLGVDVPPEEIVEAAKEEDADAIGLSGLLTTHMTLMKEVIEELK---EAGLDDIPVLV   86 (119)
T ss_pred             HHHHCCCEEEECCCCCCHHHHHHHHHHcCCCEEEEeccccccHHHHHHHHHHHH---HcCCCCCeEEE
Confidence            34456777744322        45667799999998875542  3456677777   3344 444444

This domain binds different cobalamid derivates, like B12 (adenosylcobamide) or methylcobalamin or methyl-Co(III) 5-hydroxybenzimidazolylcobamide, it is found in several enzymes, such as glutamate mutase, methionine synthase and methylmalonyl-CoA mutase. Cobalamin undergoes a conformational change on binding the protein; the dimethylbenzimidazole group, which is coordinated to the cobalt in the free cofactor, moves away from the corrin and is replaced by a histidine contributed by the protein. The sequence Asp-X-His-X-X-Gly, which contains this histidine ligand, is conserved in many cobalamin-binding proteins.

>PF03709 OKR_DC_1_N: Orn/Lys/Arg decarboxylase, N-terminal domain; InterPro: IPR005308 This domain has a flavodoxin-like fold, and is termed the "wing" domain because of its position in the overall 3D structure

Probab=90.52  E-value=0.88  Score=23.11  Aligned_cols=38  Identities=16%  Similarity=0.280  Sum_probs=27.5

Q ss_pred             CccEEEEeCCCCC--CCHHHHHHHHHhhcCCCCCccEEEEeeCC
Q 039883           34 AVDLIITDYCMPG--MTGCELIKKIKLQSFTFREIPTVIISSEN   75 (82)
Q Consensus        34 ~~d~vi~d~~~~~--~~~~~~~~~l~~~~~~~~~~~vi~ls~~~   75 (82)
                      ..++|++++. ++  ....++++.++   ..+..+||.+++...
T Consensus        38 ~i~avvi~~d-~~~~~~~~~ll~~i~---~~~~~iPVFl~~~~~   77 (115)
T PF03709_consen   38 DIAAVVISWD-GEEEDEAQELLDKIR---ERNFGIPVFLLAERD   77 (115)
T ss_dssp             TEEEEEEECH-HHHHHHHHHHHHHHH---HHSTT-EEEEEESCC
T ss_pred             CeeEEEEEcc-cccchhHHHHHHHHH---HhCCCCCEEEEecCC
Confidence            5778999998 21  12356778888   678899999999854

Ornithine decarboxylase from Lactobacillus 30a (L30a OrnDC, P43099 from SWISSPROT) is representative of the large, pyridoxal-5'-phosphate-dependent decarboxylases that act on lysine, arginine or ornithine. The crystal structure of the L30a OrnDC has been solved to 3.0 A resolution. Six dimers related by C6 symmetry compose the enzymatically active dodecamer (approximately 106 Da). Each monomer of L30a OrnDC can be described in terms of five sequential folding domains. The amino-terminal domain, residues 1 to 107, consists of a five-stranded beta-sheet termed the "wing" domain. Two wing domains of each dimer project inward towards the centre of the dodecamer and contribute to dodecamer stabilisation [].; GO: 0016831 carboxy-lyase activity; PDB: 3Q16_C 3N75_A 1C4K_A 1ORD_A 2VYC_D.

>PF08415 NRPS: Nonribosomal peptide synthase; InterPro: IPR013624 This domain is found in bacterial non-ribosomal peptide synthetases (NRPS)

Probab=90.30  E-value=0.94  Score=20.10  Aligned_cols=31  Identities=16%  Similarity=0.319  Sum_probs=21.9

Q ss_pred             CCCHHHHHHHHHhh-cCCCCCccEEEEeeCCc
Q 039883           46 GMTGCELIKKIKLQ-SFTFREIPTVIISSENI   76 (82)
Q Consensus        46 ~~~~~~~~~~l~~~-~~~~~~~~vi~ls~~~~   76 (82)
                      ..+|.++++++... .......||++.+.-..
T Consensus         3 ~~sGv~vlRel~r~~~~~~~~~PVVFTS~Lg~   34 (58)
T PF08415_consen    3 SFSGVEVLRELARRGGGRAAVMPVVFTSMLGV   34 (58)
T ss_pred             cccHHHHHHHHHHhcCCCCCcCCEEEeCCCCC
Confidence            56899999999723 34566778888775543

NRPS are megaenzymes organised as iterative modules, one for each amino acid to be built into the peptide product []. NRPS modules are involved in epothilone biosynthesis (EpoB), myxothiazol biosynthesis (MtaC and MtaD), and other functions []. The NRPS domain tends to be found together with the condensation domain (IPR001242 from INTERPRO) and the phosphopantetheine binding domain (IPR006163 from INTERPRO).

>smart00448 REC cheY-homologous receiver domain

Probab=88.58  E-value=0.91  Score=17.62  Aligned_cols=16  Identities=38%  Similarity=0.515  Sum_probs=11.1

Q ss_pred             hhccCccEEEEeCCCC
Q 039883           30 VHVLAVDLIITDYCMP   45 (82)
Q Consensus        30 ~~~~~~d~vi~d~~~~   45 (82)
                      +....|+++++|+.++
T Consensus        40 ~~~~~~~~vi~~~~~~   55 (55)
T smart00448       40 LKEEKPDLILLDIMMP   55 (55)
T ss_pred             HHhcCCCEEEEeccCC
Confidence            3444689999987653

CheY regulates the clockwise rotation of E. coli flagellar motors. This domain contains a phosphoacceptor site that is phosphorylated by histidine kinase homologues.

>PF02310 B12-binding: B12 binding domain; InterPro: IPR006158 The cobalamin (vitamin B12) binding domain can bind two different forms of the cobalamin cofactor, with cobalt bonded either to a methyl group (methylcobalamin) or to 5'-deoxyadenosine (adenosylcobalamin)

Probab=88.30  E-value=2.1  Score=21.45  Aligned_cols=43  Identities=21%  Similarity=0.253  Sum_probs=27.8

Q ss_pred             HHhhccCccEEEEeCC-CCCC-CHHHHHHHHHhhcCCCCCccEEEEee
Q 039883           28 EEVHVLAVDLIITDYC-MPGM-TGCELIKKIKLQSFTFREIPTVIISS   73 (82)
Q Consensus        28 ~~~~~~~~d~vi~d~~-~~~~-~~~~~~~~l~~~~~~~~~~~vi~ls~   73 (82)
                      +.+...+||+|.+... .+.. ...++++.+|   ...+.+++++--.
T Consensus        45 ~~~~~~~pd~V~iS~~~~~~~~~~~~l~~~~k---~~~p~~~iv~GG~   89 (121)
T PF02310_consen   45 EALRAERPDVVGISVSMTPNLPEAKRLARAIK---ERNPNIPIVVGGP   89 (121)
T ss_dssp             HHHHHTTCSEEEEEESSSTHHHHHHHHHHHHH---TTCTTSEEEEEES
T ss_pred             HHHhcCCCcEEEEEccCcCcHHHHHHHHHHHH---hcCCCCEEEEECC
Confidence            4456679999999884 3433 3455666767   5667766666543

Cobalamin-binding domains are mainly found in two families of enzymes present in animals and prokaryotes, which perform distinct kinds of reactions at the cobalt-carbon bond. Enzymes that require methylcobalamin carry out methyl transfer reactions. Enzymes that require adenosylcobalamin catalyse reactions in which the first step is the cleavage of adenosylcobalamin to form cob(II)alamin and the 5'-deoxyadenosyl radical, and thus act as radical generators. In both types of enzymes the B12-binding domain uses a histidine to bind the cobalt atom of cobalamin cofactors. This histidine is embedded in a DXHXXG sequence, the most conserved primary sequence motif of the domain [, , ]. Proteins containing the cobalamin-binding domain include: Animal and prokaryotic methionine synthase (2.1.1.13 from EC), which catalyse the transfer of a methyl group from methyl-cobalamin to homocysteine, yielding enzyme-bound cob(I)alamin and methionine. Animal and prokaryotic methylmalonyl-CoA mutase (5.4.99.2 from EC), which are involved in the degradation of several amino acids, odd-chain fatty acids and cholesterol via propionyl-CoA to the tricarboxylic acid cycle. Prokaryotic lysine 5,6-aminomutase (5.4.3.4 from EC). Prokaryotic glutamate mutase (5.4.99.1 from EC) []. Prokaryotic methyleneglutarate mutase (5.4.99.4 from EC). Prokaryotic isobutyryl-CoA mutase (5.4.99.13 from EC). The core structure of the cobalamin-binding domain is characterised by a five-stranded alpha/beta (Rossmann) fold, which consists of 5 parallel beta-sheets surrounded by 4-5 alpha helices in three layers (alpha/beta/alpha) []. Upon binding cobalamin, important elements of the binding site appear to become structured, including an alpha-helix that forms on one side of the cleft accommodating the nucleotide 'tail' of the cofactor. In cobalamin, the cobalt atom can be either free (dmb-off) or bound to dimethylbenzimidazole (dmb-on) according to the pH. When bound to the cobalamin-binding domain, the dimethylbenzimidazole ligand is replaced by the active histidine (His-on) of the DXHXXG motif. The replacement of dimethylbenzimidazole by histidine allows switching between the catalytic and activation cycles []. In methionine synthase the cobalamin cofactor is sandwiched between the cobalamin-binding domain and an approximately 90 residues N-terminal domain forming a helical bundle comprising two pairs of antiparallel helices []. In methionine synthase, there is a second, adjacent domain involved in cobalamin binding that forms a 4-helical bundle cap (IPR003759 from INTERPRO); in the conversion to the active conformation of this enzyme, the 4-helical cap rotates to allow the cobalamin cofactor to bind the activation domain (IPR004223 from INTERPRO) [].; GO: 0031419 cobalamin binding, 0046872 metal ion binding; PDB: 1Y80_A 3BUL_A 1K7Y_A 1BMT_A 3IV9_A 1K98_A 3IVA_A 3KP1_A 3KOW_A 3KOZ_A ....

>PF06490 FleQ: Flagellar regulatory protein FleQ; InterPro: IPR010518 This domain is found at the N terminus of a subset of sigma54-dependent transcriptional activators that are involved in regulation of flagellar motility e

Probab=86.75  E-value=2.8  Score=21.14  Aligned_cols=61  Identities=8%  Similarity=-0.026  Sum_probs=34.9

Q ss_pred             HhcCCCceeeecChhH--HhhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCch
Q 039883           13 MSDGSDGFDLSPTDTE--EVHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENIL   77 (82)
Q Consensus        13 ~~~~~~~~~~~~~~~~--~~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~~   77 (82)
                      +...++.++...+.+-  .......+.+++-..-.. ...+.++.+.   ...+..|++++......
T Consensus        19 LeFlGe~~~~~~~~~~~~~~~~~~~~~~~v~~g~~~-~~~~~l~~l~---~~~~~~Pvlllg~~~~~   81 (109)
T PF06490_consen   19 LEFLGEQCEAVSSSDWSQADWSSPWEACAVILGSCS-KLAELLKELL---KWAPHIPVLLLGEHDSP   81 (109)
T ss_pred             hhhcCCCeEEecHHHHHHhhhhcCCcEEEEEecCch-hHHHHHHHHH---hhCCCCCEEEECCCCcc
Confidence            3444555555554331  122334444433333333 5566777777   67899999999876654

g. FleQ in Pseudomonas aeruginosa. It is clearly related to IPR001789 from INTERPRO, but lacks the conserved aspartate residue that undergoes phosphorylation in the classic two-component system response regulator (IPR001789 from INTERPRO).

>COG0647 NagD Predicted sugar phosphatases of the HAD superfamily [Carbohydrate transport and metabolism]

Probab=86.55  E-value=2.2  Score=25.22  Aligned_cols=38  Identities=16%  Similarity=0.187  Sum_probs=26.4

Q ss_pred             CccEEEEeCCC-------CCCCHHHHHHHHHhhcCCCCCccEEEEeeCCc
Q 039883           34 AVDLIITDYCM-------PGMTGCELIKKIKLQSFTFREIPTVIISSENI   76 (82)
Q Consensus        34 ~~d~vi~d~~~-------~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~   76 (82)
                      .++.+|+|++=       +---+.++++.|+     ....|++++|....
T Consensus         7 ~y~~~l~DlDGvl~~G~~~ipga~e~l~~L~-----~~g~~~iflTNn~~   51 (269)
T COG0647           7 KYDGFLFDLDGVLYRGNEAIPGAAEALKRLK-----AAGKPVIFLTNNST   51 (269)
T ss_pred             hcCEEEEcCcCceEeCCccCchHHHHHHHHH-----HcCCeEEEEeCCCC
Confidence            57888888732       1122677888888     55679999997754

>PRK14089 ipid-A-disaccharide synthase; Provisional

Probab=86.48  E-value=3  Score=25.53  Aligned_cols=37  Identities=16%  Similarity=0.138  Sum_probs=29.1

Q ss_pred             cCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeC
Q 039883           33 LAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSE   74 (82)
Q Consensus        33 ~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~   74 (82)
                      .+||++|+ +..|+.| +.+.+.+|   ...+.+|++-..++
T Consensus        75 ~~pd~~i~-iD~p~Fn-l~lak~~k---~~~~~i~viyyi~P  111 (347)
T PRK14089         75 KQADKVLL-MDSSSFN-IPLAKKIK---KAYPKKEIIYYILP  111 (347)
T ss_pred             cCCCEEEE-eCCCCCC-HHHHHHHH---hcCCCCCEEEEECc
Confidence            47998777 7778888 67888888   55668899887765

>PRK01021 lpxB lipid-A-disaccharide synthase; Reviewed

Probab=86.39  E-value=3.7  Score=27.20  Aligned_cols=42  Identities=17%  Similarity=0.076  Sum_probs=29.9

Q ss_pred             HHhhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeC
Q 039883           28 EEVHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSE   74 (82)
Q Consensus        28 ~~~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~   74 (82)
                      +.+...+||++|+ ++.||.| +.+.+++|   ....+.|++-..++
T Consensus       304 ~~i~~~kPD~vIl-ID~PgFN-lrLAK~lk---k~Gi~ipviyYVsP  345 (608)
T PRK01021        304 KTILKTNPRTVIC-IDFPDFH-FLLIKKLR---KRGYKGKIVHYVCP  345 (608)
T ss_pred             HHHHhcCCCEEEE-eCCCCCC-HHHHHHHH---hcCCCCCEEEEECc
Confidence            3455668998887 7788988 67888888   34444588877655

>cd02071 MM_CoA_mut_B12_BD methylmalonyl CoA mutase B12 binding domain

Probab=85.56  E-value=3.4  Score=21.10  Aligned_cols=44  Identities=23%  Similarity=0.150  Sum_probs=29.3

Q ss_pred             hcCCCceeeecChh--------HHhhccCccEEEEeCCCCCC--CHHHHHHHHH
Q 039883           14 SDGSDGFDLSPTDT--------EEVHVLAVDLIITDYCMPGM--TGCELIKKIK   57 (82)
Q Consensus        14 ~~~~~~~~~~~~~~--------~~~~~~~~d~vi~d~~~~~~--~~~~~~~~l~   57 (82)
                      .....||++...+.        +++...+||+|.+...+...  ..-++++.++
T Consensus        22 ~l~~~G~~vi~lG~~vp~e~~~~~a~~~~~d~V~iS~~~~~~~~~~~~~~~~L~   75 (122)
T cd02071          22 ALRDAGFEVIYTGLRQTPEEIVEAAIQEDVDVIGLSSLSGGHMTLFPEVIELLR   75 (122)
T ss_pred             HHHHCCCEEEECCCCCCHHHHHHHHHHcCCCEEEEcccchhhHHHHHHHHHHHH
Confidence            45567888766543        45667799999998887643  2244566676

This domain binds to B12 (adenosylcobamide), which initiates the conversion of succinyl CoA and methylmalonyl CoA by forming an adenosyl radical, which then undergoes a rearrangement exchanging a hydrogen atom with a group attached to a neighboring carbon atom. This family is present in both mammals and bacteria. Bacterial members are heterodimers and involved in the fermentation of pyruvate to propionate. Mammalian members are homodimers and responsible for the conversion of odd-chain fatty acids and branched-chain amino acids via propionyl CoA to succinyl CoA for further degradation.

>TIGR02370 pyl_corrinoid methyltransferase cognate corrinoid proteins, Methanosarcina family

Probab=85.17  E-value=4.8  Score=22.48  Aligned_cols=60  Identities=13%  Similarity=0.089  Sum_probs=37.0

Q ss_pred             hcCCCceeeecChh--------HHhhccCccEEEEeCCCCCCC--HHHHHHHHHhhcCCCCCccEEEEeeC
Q 039883           14 SDGSDGFDLSPTDT--------EEVHVLAVDLIITDYCMPGMT--GCELIKKIKLQSFTFREIPTVIISSE   74 (82)
Q Consensus        14 ~~~~~~~~~~~~~~--------~~~~~~~~d~vi~d~~~~~~~--~~~~~~~l~~~~~~~~~~~vi~ls~~   74 (82)
                      .....||++..-+.        +.+...+||+|-+...+....  -.++++.++ .....+.+++++--..
T Consensus       107 ~l~~~G~~vi~LG~~vp~e~~v~~~~~~~pd~v~lS~~~~~~~~~~~~~i~~l~-~~~~~~~v~i~vGG~~  176 (197)
T TIGR02370       107 MLRANGFDVIDLGRDVPIDTVVEKVKKEKPLMLTGSALMTTTMYGQKDINDKLK-EEGYRDSVKFMVGGAP  176 (197)
T ss_pred             HHHhCCcEEEECCCCCCHHHHHHHHHHcCCCEEEEccccccCHHHHHHHHHHHH-HcCCCCCCEEEEEChh
Confidence            44557888865433        567778999999999876532  244566777 2222445666554433

This model describes a subfamily of the B12 binding domain (pfam02607, pfam02310) proteins. Members of the seed alignment include corrinoid proteins specific to four different, mutally non-homologous enzymes of the genus Methanosarcina. Three of the four cognate enzymes (trimethylamine, dimethylamine, and monomethylamine methyltransferases) all have the unusual, ribosomally incorporated amino acid pyrrolysine at the active site. All act in systems in which a methyl group is transferred to the corrinoid protein to create methylcobalamin, from which the methyl group is later transferred elsewhere.

>PF13528 Glyco_trans_1_3: Glycosyl transferase family 1

Probab=85.11  E-value=2  Score=25.17  Aligned_cols=38  Identities=21%  Similarity=0.302  Sum_probs=24.5

Q ss_pred             HHhhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCc
Q 039883           28 EEVHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENI   76 (82)
Q Consensus        28 ~~~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~   76 (82)
                      +.++..+||+||.|....      .....+     ...+|+|.++....
T Consensus        88 ~~l~~~~pDlVIsD~~~~------~~~aa~-----~~giP~i~i~~~~~  125 (318)
T PF13528_consen   88 RWLREFRPDLVISDFYPL------AALAAR-----RAGIPVIVISNQYW  125 (318)
T ss_pred             HHHHhcCCCEEEEcChHH------HHHHHH-----hcCCCEEEEEehHH
Confidence            446677899999996444      122223     55688888886543

>PLN02775 Probable dihydrodipicolinate reductase

Probab=84.56  E-value=4.5  Score=24.21  Aligned_cols=47  Identities=15%  Similarity=0.163  Sum_probs=29.2

Q ss_pred             hhHHhhcc---CccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCchh
Q 039883           26 DTEEVHVL---AVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENILA   78 (82)
Q Consensus        26 ~~~~~~~~---~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~~~   78 (82)
                      ..+.+...   .|++|++|...|.. ..+.++...     ...+|+++-|...+.+
T Consensus        68 l~~~l~~~~~~~~~~VvIDFT~P~a-~~~~~~~~~-----~~g~~~VvGTTG~~~e  117 (286)
T PLN02775         68 REAVLSSVKAEYPNLIVVDYTLPDA-VNDNAELYC-----KNGLPFVMGTTGGDRD  117 (286)
T ss_pred             HHHHHHHhhccCCCEEEEECCChHH-HHHHHHHHH-----HCCCCEEEECCCCCHH
Confidence            33455444   79999999999983 355555544     2345666666555444

>PRK06843 inosine 5-monophosphate dehydrogenase; Validated

Probab=84.25  E-value=4.4  Score=25.47  Aligned_cols=39  Identities=26%  Similarity=0.334  Sum_probs=28.7

Q ss_pred             HhhccCccEEEEeCCCCC-CCHHHHHHHHHhhcCCCCCccEEE
Q 039883           29 EVHVLAVDLIITDYCMPG-MTGCELIKKIKLQSFTFREIPTVI   70 (82)
Q Consensus        29 ~~~~~~~d~vi~d~~~~~-~~~~~~~~~l~~~~~~~~~~~vi~   70 (82)
                      .+....+|+|.+|...+. ....++++++|   ...+..++|+
T Consensus       160 ~lv~aGvDvI~iD~a~g~~~~~~~~v~~ik---~~~p~~~vi~  199 (404)
T PRK06843        160 ELVKAHVDILVIDSAHGHSTRIIELVKKIK---TKYPNLDLIA  199 (404)
T ss_pred             HHHhcCCCEEEEECCCCCChhHHHHHHHHH---hhCCCCcEEE
Confidence            344457999999999874 45567888888   5666777655

>cd02069 methionine_synthase_B12_BD B12 binding domain of methionine synthase

Probab=84.13  E-value=5.8  Score=22.55  Aligned_cols=60  Identities=13%  Similarity=0.101  Sum_probs=38.5

Q ss_pred             hcCCCceeeecChh--------HHhhccCccEEEEeCCCCCC--CHHHHHHHHHhhcCCCCCccEEEEeeCCc
Q 039883           14 SDGSDGFDLSPTDT--------EEVHVLAVDLIITDYCMPGM--TGCELIKKIKLQSFTFREIPTVIISSENI   76 (82)
Q Consensus        14 ~~~~~~~~~~~~~~--------~~~~~~~~d~vi~d~~~~~~--~~~~~~~~l~~~~~~~~~~~vi~ls~~~~   76 (82)
                      .+...||++..-+.        +++...+||+|.+...++..  ...++++.++   .....++|++--...+
T Consensus       111 ~l~~~G~~Vi~LG~~vp~e~~v~~~~~~~~~~V~lS~~~~~~~~~~~~~i~~L~---~~~~~~~i~vGG~~~~  180 (213)
T cd02069         111 ILSNNGYEVIDLGVMVPIEKILEAAKEHKADIIGLSGLLVPSLDEMVEVAEEMN---RRGIKIPLLIGGAATS  180 (213)
T ss_pred             HHHhCCCEEEECCCCCCHHHHHHHHHHcCCCEEEEccchhccHHHHHHHHHHHH---hcCCCCeEEEEChhcC
Confidence            44457787755433        56677799999999888753  2344667777   3455677666554433

This domain binds methylcobalamin, which it uses as an intermediate methyl carrier from methyltetrahydrofolate (CH3H4folate) to homocysteine (Hcy).

>cd02068 radical_SAM_B12_BD B12 binding domain_like associated with radical SAM domain

Probab=83.78  E-value=2.7  Score=21.46  Aligned_cols=41  Identities=17%  Similarity=0.192  Sum_probs=27.4

Q ss_pred             Hhhc-cCccEEEEeCCCCCC-CHHHHHHHHHhhcCCCCCccEEEEe
Q 039883           29 EVHV-LAVDLIITDYCMPGM-TGCELIKKIKLQSFTFREIPTVIIS   72 (82)
Q Consensus        29 ~~~~-~~~d~vi~d~~~~~~-~~~~~~~~l~~~~~~~~~~~vi~ls   72 (82)
                      .+.. .+||+|.+.+..... ...++++.+|   ...+++++++--
T Consensus        33 ~~~~~~~pdiv~~S~~~~~~~~~~~~~~~ik---~~~p~~~iv~GG   75 (127)
T cd02068          33 DIKELLKPDVVGISLMTSAIYEALELAKIAK---EVLPNVIVVVGG   75 (127)
T ss_pred             HHHHhcCCCEEEEeeccccHHHHHHHHHHHH---HHCCCCEEEECC
Confidence            3444 689999998865544 3466788888   456666666543

This domain shows similarity with B12 (adenosylcobamide) binding domains found in several enzymes, such as glutamate mutase, methionine synthase and methylmalonyl-CoA mutase, but it lacks the signature motif Asp-X-His-X-X-Gly, which contains the histidine that acts as a cobalt ligand. The function of this domain remains unclear.

>cd02070 corrinoid_protein_B12-BD B12 binding domain of corrinoid proteins

Probab=83.66  E-value=5.8  Score=22.17  Aligned_cols=60  Identities=15%  Similarity=0.132  Sum_probs=36.3

Q ss_pred             hcCCCceeeecChh--------HHhhccCccEEEEeCCCCCC--CHHHHHHHHHhhcCCCCCccEEEEeeC
Q 039883           14 SDGSDGFDLSPTDT--------EEVHVLAVDLIITDYCMPGM--TGCELIKKIKLQSFTFREIPTVIISSE   74 (82)
Q Consensus        14 ~~~~~~~~~~~~~~--------~~~~~~~~d~vi~d~~~~~~--~~~~~~~~l~~~~~~~~~~~vi~ls~~   74 (82)
                      .....||++..-+.        +++...+||+|-+...+...  ...++++.++ .......++|++--..
T Consensus       105 ~l~~~G~~vi~lG~~~p~~~l~~~~~~~~~d~v~lS~~~~~~~~~~~~~i~~lr-~~~~~~~~~i~vGG~~  174 (201)
T cd02070         105 MLEANGFEVIDLGRDVPPEEFVEAVKEHKPDILGLSALMTTTMGGMKEVIEALK-EAGLRDKVKVMVGGAP  174 (201)
T ss_pred             HHHHCCCEEEECCCCCCHHHHHHHHHHcCCCEEEEeccccccHHHHHHHHHHHH-HCCCCcCCeEEEECCc
Confidence            34457777764322        45667799999999877653  3345667777 2222226666665443

A family of small methanogenic corrinoid proteins that bind methyl-Co(III) 5-hydroxybenzimidazolylcobamide as a cofactor. They play a role on the methanogenesis from trimethylamine, dimethylamine or monomethylamine, which is initiated by a series of corrinoid-dependent methyltransferases.

>cd05014 SIS_Kpsf KpsF-like protein

Probab=80.99  E-value=5.5  Score=20.11  Aligned_cols=39  Identities=18%  Similarity=0.167  Sum_probs=22.7

Q ss_pred             ccEEE-EeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCchh
Q 039883           35 VDLII-TDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENILA   78 (82)
Q Consensus        35 ~d~vi-~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~~~   78 (82)
                      -|++| +...-...+-.+.++..+     ....++|.+|+..+..
T Consensus        48 ~d~vi~iS~sG~t~~~~~~~~~a~-----~~g~~vi~iT~~~~s~   87 (128)
T cd05014          48 GDVVIAISNSGETDELLNLLPHLK-----RRGAPIIAITGNPNST   87 (128)
T ss_pred             CCEEEEEeCCCCCHHHHHHHHHHH-----HCCCeEEEEeCCCCCc
Confidence            34433 333333334456666666     3468999999876544

KpsF is an arabinose-5-phosphate isomerase which contains SIS (Sugar ISomerase) domains. SIS domains are found in many phosphosugar isomerases and phosphosugar binding proteins. KpsF catalyzes the reversible reaction of ribulose 5-phosphate to arabinose 5-phosphate. This is the second step in the CMP-Kdo biosynthesis pathway.

>COG4594 FecB ABC-type Fe3+-citrate transport system, periplasmic component [Inorganic ion transport and metabolism]

Probab=80.81  E-value=3.1  Score=24.72  Aligned_cols=27  Identities=33%  Similarity=0.422  Sum_probs=19.8

Q ss_pred             CceeeecChh----HHhhccCccEEEEeCCC
Q 039883           18 DGFDLSPTDT----EEVHVLAVDLIITDYCM   44 (82)
Q Consensus        18 ~~~~~~~~~~----~~~~~~~~d~vi~d~~~   44 (82)
                      .+|+.+.+..    |.+...+||+||-|..=
T Consensus        91 ~~ytSVGTRsQPslE~Is~LKPDLIIAD~sR  121 (310)
T COG4594          91 DPYTSVGTRSQPSLEAISALKPDLIIADSSR  121 (310)
T ss_pred             CCcccccCCCCCCHHHHhccCCCeEEecchh
Confidence            4455555443    78999999999998753

>PRK05458 guanosine 5'-monophosphate oxidoreductase; Provisional

Probab=80.21  E-value=4.3  Score=24.75  Aligned_cols=35  Identities=17%  Similarity=0.114  Sum_probs=26.7

Q ss_pred             CccEEEEeCCCCCC-CHHHHHHHHHhhcCCCCCccEEEE
Q 039883           34 AVDLIITDYCMPGM-TGCELIKKIKLQSFTFREIPTVII   71 (82)
Q Consensus        34 ~~d~vi~d~~~~~~-~~~~~~~~l~~~~~~~~~~~vi~l   71 (82)
                      .+|+|.+|...+.. ...++++++|   ...+.+|||+-
T Consensus       111 ~~d~i~iD~a~gh~~~~~e~I~~ir---~~~p~~~vi~g  146 (326)
T PRK05458        111 TPEYITIDIAHGHSDSVINMIQHIK---KHLPETFVIAG  146 (326)
T ss_pred             CCCEEEEECCCCchHHHHHHHHHHH---hhCCCCeEEEE
Confidence            35999999999764 3466888888   56777887773

>PRK10558 alpha-dehydro-beta-deoxy-D-glucarate aldolase; Provisional

Probab=80.12  E-value=9.7  Score=22.34  Aligned_cols=46  Identities=13%  Similarity=0.101  Sum_probs=32.9

Q ss_pred             HHhhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeC
Q 039883           28 EEVHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSE   74 (82)
Q Consensus        28 ~~~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~   74 (82)
                      +.+....+|.|++|+.....+-.++...++ .-......|++-+...
T Consensus        34 e~~a~~G~D~v~iD~EHg~~~~~~~~~~i~-a~~~~g~~~lVRvp~~   79 (256)
T PRK10558         34 EVLGLAGFDWLVLDGEHAPNDVSTFIPQLM-ALKGSASAPVVRVPTN   79 (256)
T ss_pred             HHHHhcCCCEEEEccccCCCCHHHHHHHHH-HHhhcCCCcEEECCCC
Confidence            667777899999999999998888777776 3223444555555543

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	82
3h1g_A	129	Crystal Structure Of Chey Mutant T84a Of Helicobact		2e-04
3gwg_A	129	Crystal Structure Of Chey Of Helicobacter Pylori Le		2e-04

>pdb|3H1G|A Chain A, Crystal Structure Of Chey Mutant T84a Of Helicobacter Pylori Length = 129

Iteration: 1
 Score = 41.2 bits (95), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 18/44 (40%), Positives = 31/44 (70%), Gaps = 1/44 (2%)
Query: 37 LIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENILARI 80
          ++ITD+ MP M G +L+KK++  S  F+EIP ++I++E   A +
Sbjct: 54 VLITDWNMPEMNGLDLVKKVRSDS-RFKEIPIIMITAEGGKAEV 96

>pdb|3GWG|A Chain A, Crystal Structure Of Chey Of Helicobacter Pylori Length = 129

Iteration: 1
 Score = 40.8 bits (94), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 18/44 (40%), Positives = 31/44 (70%), Gaps = 1/44 (2%)
Query: 37 LIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENILARI 80
          ++ITD+ MP M G +L+KK++  S  F+EIP ++I++E   A +
Sbjct: 54 VLITDWNMPEMNGLDLVKKVRSDS-RFKEIPIIMITTEGGKAEV 96

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	82
3cu5_A	141	Two component transcriptional regulator, ARAC FAM;	7e-08
3bre_A	358	Probable two-component response regulator; protein	8e-08
1w25_A	459	Stalked-cell differentiation controlling protein;	2e-07
1w25_A	459	Stalked-cell differentiation controlling protein;	3e-07
1jbe_A	128	Chemotaxis protein CHEY; signaling protein; 1.08A	3e-07
2rjn_A	154	Response regulator receiver:metal-dependent phosph	5e-07
3hdg_A	137	Uncharacterized protein; two-component sensor acti	6e-07
3hv2_A	153	Response regulator/HD domain protein; PSI-2, NYSGX	8e-07
2jk1_A	139	HUPR, hydrogenase transcriptional regulatory prote	9e-07
3luf_A	259	Two-component system response regulator/ggdef doma	2e-06
3luf_A	259	Two-component system response regulator/ggdef doma	6e-06
3h1g_A	129	Chemotaxis protein CHEY homolog; sulfate-bound CHE	3e-06
3kcn_A	151	Adenylate cyclase homolog; SGX, PSI 2, structural	4e-06
3jte_A	143	Response regulator receiver protein; structural ge	5e-06
3dzd_A	368	Transcriptional regulator (NTRC family); sigma43 a	5e-06
1p6q_A	129	CHEY2; chemotaxis, signal transduction, response r	6e-06
3eq2_A	394	Probable two-component response regulator; adaptor	6e-06
1ny5_A	387	Transcriptional regulator (NTRC family); AAA+ ATPa	6e-06
3hdv_A	136	Response regulator; PSI-II, structural genomics, P	1e-05
1qkk_A	155	DCTD, C4-dicarboxylate transport transcriptional r	2e-05
3cfy_A	137	Putative LUXO repressor protein; structural genomi	2e-05
1dc7_A	124	NTRC, nitrogen regulation protein; receiver domain	2e-05
1srr_A	124	SPO0F, sporulation response regulatory protein; as	2e-05
1i3c_A	149	Response regulator RCP1; phytochrome, signaling pr	4e-05
3cnb_A	143	DNA-binding response regulator, MERR family; signa	8e-05
3heb_A	152	Response regulator receiver domain protein (CHEY);	1e-04
1k66_A	149	Phytochrome response regulator RCPB; CHEY homologu	1e-04
4dad_A	146	Putative pilus assembly-related protein; response	2e-04
1a2o_A	349	CHEB methylesterase; bacterial chemotaxis, adaptat	2e-04
3nhm_A	133	Response regulator; protein structure initiative I	2e-04
2zay_A	147	Response regulator receiver protein; structural ge	4e-04
2qxy_A	142	Response regulator; regulation of transcription, N	5e-04
3ilh_A	146	Two component response regulator; NYSGXRC, PSI-II,	5e-04
2qvg_A	143	Two component response regulator; NYSGXRC, PSI-2,	5e-04
3n53_A	140	Response regulator receiver modulated diguanylate;	6e-04
3grc_A	140	Sensor protein, kinase; protein structure initiati	6e-04

>3cu5_A Two component transcriptional regulator, ARAC FAM; structural genomics, protein structure initiative; 2.60A {Clostridium phytofermentans isdg} Length = 141

 Score = 45.2 bits (108), Expect = 7e-08
 Identities = 12/59 (20%), Positives = 23/59 (38%), Gaps = 10/59 (16%)

Query: 14 SDGSDGFDLSPTDTEEVHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIIS 72
           DG +   +             ++++TD  MP M G EL+  I      + +   + +S
Sbjct: 36 DDGINAIQI-------ALKHPPNVLLTDVRMPRMDGIELVDNILKL---YPDCSVIFMS 84

>3bre_A Probable two-component response regulator; protein-nucleotide complex, signaling protein; HET: C2E; 2.40A {Pseudomonas aeruginosa} PDB: 3i5a_A* Length = 358

 Score = 46.6 bits (111), Expect = 8e-08
 Identities = 12/41 (29%), Positives = 23/41 (56%), Gaps = 1/41 (2%)

Query: 35  VDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSEN 75
             +I+ D  MPG+ G  L+   +    T R+IP +++S++ 
Sbjct: 64  PTVILQDLVMPGVDGLTLLAAYRGNPAT-RDIPIIVLSTKE 103

>1w25_A Stalked-cell differentiation controlling protein; two-component system, ggdef domain, cyclic dinucleotide, cyclic-digmp; HET: C2E; 2.70A {Caulobacter vibrioides} SCOP: c.23.1.1 c.23.1.1 d.58.29.2 PDB: 2v0n_A* 2wb4_A* Length = 459

 Score = 45.6 bits (108), Expect = 2e-07
 Identities = 20/77 (25%), Positives = 36/77 (46%), Gaps = 8/77 (10%)

Query: 4  TNGVLLSRLMSDGSDGFDLSPTDT-----EEVHVLAVDLIITDYCMPGMTGCELIKKIKL 58
           N  LL   ++  ++ +++S                 D+I+ D  MPGM G  + +K+K 
Sbjct: 12 ANVRLLEAKLT--AEYYEVSTAMDGPTALAMAARDLPDIILLDVMMPGMDGFTVCRKLK- 68

Query: 59 QSFTFREIPTVIISSEN 75
             T R IP V+I++ +
Sbjct: 69 DDPTTRHIPVVLITALD 85

>1w25_A Stalked-cell differentiation controlling protein; two-component system, ggdef domain, cyclic dinucleotide, cyclic-digmp; HET: C2E; 2.70A {Caulobacter vibrioides} SCOP: c.23.1.1 c.23.1.1 d.58.29.2 PDB: 2v0n_A* 2wb4_A* Length = 459

 Score = 45.2 bits (107), Expect = 3e-07
 Identities = 9/69 (13%), Positives = 23/69 (33%), Gaps = 1/69 (1%)

Query: 7   VLLSRLMSDGSDGFDLSPTDTEEVHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREI 66
            + + L  +     +  P   +      VDL+I +       G      ++      R++
Sbjct: 167 RVAAELGVEHRPVIESDPEKAKISAGGPVDLVIVNAAAKNFDGLRFTAALR-SEERTRQL 225

Query: 67  PTVIISSEN 75
           P + +   +
Sbjct: 226 PVLAMVDPD 234

>1jbe_A Chemotaxis protein CHEY; signaling protein; 1.08A {Escherichia coli} SCOP: c.23.1.1 PDB: 3chy_A 1a0o_A 1cey_A 1bdj_A 1eay_A 1f4v_A 1ffg_A 1ffs_A 1ffw_A 1fqw_A 2b1j_A 1chn_A 1djm_A 1kmi_Y* 1d4z_A 3olx_A 3olw_A 1cye_A 2che_A 2chf_A ... Length = 128

 Score = 43.4 bits (103), Expect = 3e-07
 Identities = 12/41 (29%), Positives = 23/41 (56%), Gaps = 1/41 (2%)

Query: 35 VDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSEN 75
             +I+D+ MP M G EL+K I+        +P +++++E 
Sbjct: 50 YGFVISDWNMPNMDGLELLKTIR-AXXAMSALPVLMVTAEA 89

>2rjn_A Response regulator receiver:metal-dependent phosphohydrolase, HD subdomain; structural genomics, oceanospirillum SP. MED92; 2.10A {Neptuniibacter caesariensis} Length = 154

 Score = 43.4 bits (103), Expect = 5e-07
 Identities = 12/38 (31%), Positives = 21/38 (55%), Gaps = 3/38 (7%)

Query: 35 VDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIIS 72
          V L+I+D  MP M G   ++++      + +I  V+IS
Sbjct: 52 VQLVISDMRMPEMGGEVFLEQVAKS---YPDIERVVIS 86

>3hdg_A Uncharacterized protein; two-component sensor activity, response regulator, PSI-II, 11227F, NYSGXRC, structural genomics; 2.27A {Wolinella succinogenes} Length = 137

 Score = 42.9 bits (102), Expect = 6e-07
 Identities = 18/59 (30%), Positives = 28/59 (47%), Gaps = 10/59 (16%)

Query: 14 SDGSDGFDLSPTDTEEVHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIIS 72
           DG +G  L         + A D+IITD  MP + G E++ +IK       +   ++IS
Sbjct: 38 GDGEEGERL-------FGLHAPDVIITDIRMPKLGGLEMLDRIKAGG---AKPYVIVIS 86

>3hv2_A Response regulator/HD domain protein; PSI-2, NYSGXRC, structural genomics, protein structure initiative; 1.50A {Pseudomonas fluorescens pf-5} Length = 153

 Score = 43.0 bits (102), Expect = 8e-07
 Identities = 10/38 (26%), Positives = 20/38 (52%), Gaps = 3/38 (7%)

Query: 35 VDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIIS 72
          VDL+I+   +P M G  L+ +I  Q   +     ++++
Sbjct: 59 VDLVISAAHLPQMDGPTLLARIHQQ---YPSTTRILLT 93

>2jk1_A HUPR, hydrogenase transcriptional regulatory protein HU; nucleotide-binding, transcription regulation; 2.10A {Rhodobacter capsulatus} PDB: 2vui_B 2vuh_B Length = 139

 Score = 42.5 bits (101), Expect = 9e-07
 Identities = 12/38 (31%), Positives = 21/38 (55%), Gaps = 3/38 (7%)

Query: 35 VDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIIS 72
          V +II D  MPG TG + + +++ +     E   +II+
Sbjct: 45 VQVIICDQRMPGRTGVDFLTEVRERW---PETVRIIIT 79

>3luf_A Two-component system response regulator/ggdef domain protein; structural genomics, ASA_2441, PSI-2, protein structure initiative; HET: MSE; 1.76A {Aeromonas salmonicida} PDB: 3mf4_A* Length = 259

 Score = 42.3 bits (100), Expect = 2e-06
 Identities = 11/73 (15%), Positives = 26/73 (35%), Gaps = 8/73 (10%)

Query: 4  TNGVLLSRLMSDGSDGFDLSPTDTEEVHVLA---VDLIITDYCMPGMTGCELIKKIKLQS 60
          T   +L + ++  +     +    E           + + D  +P     E +K +    
Sbjct: 15 TIRRMLIQAIAQQTGLEIDAFDTLEGARHCQGDEYVVALVDLTLPDAPSGEAVKVLLE-- 72

Query: 61 FTFREIPTVIISS 73
             R +P VI+++
Sbjct: 73 ---RGLPVVILTA 82

>3luf_A Two-component system response regulator/ggdef domain protein; structural genomics, ASA_2441, PSI-2, protein structure initiative; HET: MSE; 1.76A {Aeromonas salmonicida} PDB: 3mf4_A* Length = 259

 Score = 41.1 bits (97), Expect = 6e-06
 Identities = 9/41 (21%), Positives = 25/41 (60%), Gaps = 1/41 (2%)

Query: 35  VDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSEN 75
           + L++ DY MP + G  L++ ++ + ++ +++  + IS  +
Sbjct: 170 IRLVLVDYYMPEIDGISLVRMLR-ERYSKQQLAIIGISVSD 209

>3h1g_A Chemotaxis protein CHEY homolog; sulfate-bound CHEY, cytoplasm, flagellar rotatio magnesium, metal-binding, phosphoprotein; 1.70A {Helicobacter pylori} PDB: 3gwg_A 3h1e_A 3h1f_A Length = 129

 Score = 40.9 bits (97), Expect = 3e-06
 Identities = 16/40 (40%), Positives = 28/40 (70%), Gaps = 1/40 (2%)

Query: 35 VDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSE 74
            ++ITD+ MP M G +L+KK++  S   +EIP ++I++E
Sbjct: 52 TKVLITDWNMPEMNGLDLVKKVRSDSRF-KEIPIIMITAE 90

>3kcn_A Adenylate cyclase homolog; SGX, PSI 2, structural genomics, protein structure initiative; 2.45A {Rhodopirellula baltica} Length = 151

 Score = 41.0 bits (97), Expect = 4e-06
 Identities = 12/38 (31%), Positives = 21/38 (55%), Gaps = 3/38 (7%)

Query: 35 VDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIIS 72
            +I+ D  MPGM G E+I+K +L S        ++++
Sbjct: 49 FSVIMVDMRMPGMEGTEVIQKARLIS---PNSVYLMLT 83

>3jte_A Response regulator receiver protein; structural genomics, nysgrc, response regulator receiver domain, target 11226E, PSI-2; 1.90A {Clostridium thermocellum atcc 27405} Length = 143

 Score = 40.6 bits (96), Expect = 5e-06
 Identities = 10/42 (23%), Positives = 27/42 (64%), Gaps = 3/42 (7%)

Query: 31 HVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIIS 72
          +  ++D++ITD  MP ++G +++++IK  +     +  +I++
Sbjct: 46 NCNSIDVVITDMKMPKLSGMDILREIKKIT---PHMAVIILT 84

>3dzd_A Transcriptional regulator (NTRC family); sigma43 activator, AAA+ ATPase, response regulator, transcriptional activator, ATP-binding; HET: ADP; 2.40A {Aquifex aeolicus} PDB: 1zit_A 2jrl_A Length = 368

 Score = 41.3 bits (98), Expect = 5e-06
 Identities = 9/38 (23%), Positives = 15/38 (39%), Gaps = 3/38 (7%)

Query: 35 VDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIIS 72
            +I+ D  MP   G   I  IK       +   ++I+
Sbjct: 45 FPVIVLDVWMPDGDGVNFIDFIKEN---SPDSVVIVIT 79

>1p6q_A CHEY2; chemotaxis, signal transduction, response regulator, structural proteomics in europe, spine, structural genomics; NMR {Sinorhizobium meliloti} SCOP: c.23.1.1 PDB: 1p6u_A Length = 129

 Score = 40.2 bits (95), Expect = 6e-06
 Identities = 9/40 (22%), Positives = 24/40 (60%), Gaps = 1/40 (2%)

Query: 35 VDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSE 74
            L+I+D+ MP M G  L++ ++  +   ++   +I++++
Sbjct: 52 HHLVISDFNMPKMDGLGLLQAVR-ANPATKKAAFIILTAQ 90

>3eq2_A Probable two-component response regulator; adaptor sigmas, signaling protein; 3.40A {Pseudomonas aeruginosa} PDB: 3f7a_A Length = 394

 Score = 41.4 bits (97), Expect = 6e-06
 Identities = 14/48 (29%), Positives = 26/48 (54%), Gaps = 3/48 (6%)

Query: 35 VDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENILARIDR 82
           DL+I D  MP + G ELI++I+  +    E P +++S   +++    
Sbjct: 50 PDLVICDLRMPQIDGLELIRRIRQTA---SETPIIVLSGAGVMSDAVE 94

>1ny5_A Transcriptional regulator (NTRC family); AAA+ ATPase, sigma54 activator, bacterial transcription, DIM transcription; HET: ADP; 2.40A {Aquifex aeolicus} SCOP: c.23.1.1 c.37.1.20 PDB: 1ny6_A* 3m0e_A* 1zy2_A* Length = 387

 Score = 41.3 bits (98), Expect = 6e-06
 Identities = 10/39 (25%), Positives = 22/39 (56%), Gaps = 3/39 (7%)

Query: 34 AVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIIS 72
            ++++ D  +P + G E++K IK +S    E   ++I+
Sbjct: 44 HFNVVLLDLLLPDVNGLEILKWIKERS---PETEVIVIT 79

>3hdv_A Response regulator; PSI-II, structural genomics, Pro structure initiative, NEW YORK SGX research center for STRU genomics, nysgxrc; 2.09A {Pseudomonas putida} Length = 136

 Score = 39.1 bits (92), Expect = 1e-05
 Identities = 10/39 (25%), Positives = 20/39 (51%), Gaps = 2/39 (5%)

Query: 34 AVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIIS 72
           + L+ITD  M   +G +LI+ I+        +  +++S
Sbjct: 52 RIGLMITDLRMQPESGLDLIRTIRASERA--ALSIIVVS 88

>1qkk_A DCTD, C4-dicarboxylate transport transcriptional regulatory protein; receiver domain, 2-component signal transduction; 1.7A {Sinorhizobium meliloti} SCOP: c.23.1.1 PDB: 1l5z_A 1l5y_A Length = 155

 Score = 39.4 bits (93), Expect = 2e-05
 Identities = 11/37 (29%), Positives = 21/37 (56%), Gaps = 3/37 (8%)

Query: 36 DLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIIS 72
           ++I+D  MPGM G  L +KI        ++P ++++
Sbjct: 49 GIVISDIRMPGMDGLALFRKILALD---PDLPMILVT 82

>3cfy_A Putative LUXO repressor protein; structural genomics, unknown function, uncharacterized protein, signal receiver domain; 2.50A {Vibrio parahaemolyticus rimd 2210633} Length = 137

 Score = 39.1 bits (92), Expect = 2e-05
 Identities = 9/37 (24%), Positives = 16/37 (43%), Gaps = 3/37 (8%)

Query: 36 DLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIIS 72
           LII D  +P M+G +++  I            +I +
Sbjct: 50 QLIILDLKLPDMSGEDVLDWINQND---IPTSVIIAT 83

>1dc7_A NTRC, nitrogen regulation protein; receiver domain, phosphorylation, signal transduction, conformational rearrangement; NMR {Salmonella typhimurium} SCOP: c.23.1.1 PDB: 1j56_A 1krw_A 1krx_A 1ntr_A 1dc8_A* Length = 124

 Score = 38.6 bits (91), Expect = 2e-05
 Identities = 13/37 (35%), Positives = 24/37 (64%), Gaps = 3/37 (8%)

Query: 36 DLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIIS 72
          D++++D  MPGM G  L+K+IK +      +P +I++
Sbjct: 49 DVLLSDIRMPGMDGLALLKQIKQR---HPMLPVIIMT 82

>1srr_A SPO0F, sporulation response regulatory protein; aspartate pocket, two component system; 1.90A {Bacillus subtilis} SCOP: c.23.1.1 PDB: 1pey_A 3q15_C 2ftk_E* 1fsp_A 1nat_A 1pux_A 2fsp_A 2jvj_A 2jvk_A 2jvi_A 1f51_E Length = 124

 Score = 38.6 bits (91), Expect = 2e-05
 Identities = 12/37 (32%), Positives = 23/37 (62%), Gaps = 3/37 (8%)

Query: 36 DLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIIS 72
          DL++ D  +PGM G E++K++K+       I  +I++
Sbjct: 49 DLVLLDMKIPGMDGIEILKRMKVID---ENIRVIIMT 82

>1i3c_A Response regulator RCP1; phytochrome, signaling protein; 1.90A {Synechocystis SP} SCOP: c.23.1.1 PDB: 1jlk_A Length = 149

 Score = 38.4 bits (90), Expect = 4e-05
 Identities = 14/60 (23%), Positives = 26/60 (43%), Gaps = 1/60 (1%)

Query: 14 SDGSDGFDLSPTDTEEVHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISS 73
           DG           E  +    +LI+ D  +P   G E++ +IK      + IP V++++
Sbjct: 41 RDGLAAMAFLQQQGEYENSPRPNLILLDLNLPKKDGREVLAEIKQNPDL-KRIPVVVLTT 99

>3cnb_A DNA-binding response regulator, MERR family; signal receiver domain, DNA binding protein, protein structu initiative, PSI-2; 2.00A {Colwellia psychrerythraea} Length = 143

 Score = 37.1 bits (87), Expect = 8e-05
 Identities = 13/59 (22%), Positives = 25/59 (42%), Gaps = 8/59 (13%)

Query: 14 SDGSDGFDLSPTDTEEVHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIIS 72
           +  D  DL       +H +  D+++ D  M GM G  +  +IK  +     I  + ++
Sbjct: 41 YNPFDAGDL-------LHTVKPDVVMLDLMMVGMDGFSICHRIK-STPATANIIVIAMT 91

>3heb_A Response regulator receiver domain protein (CHEY); NYSGXRC, PSI-II, respose regulator, structure initiative, structural genomics; 2.40A {Rhodospirillum rubrum} Length = 152

 Score = 36.9 bits (86), Expect = 1e-04
 Identities = 18/62 (29%), Positives = 32/62 (51%), Gaps = 3/62 (4%)

Query: 14 SDGSDGFDLSPTDTEEVHVLAV--DLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVII 71
          +DG+   +    D +   V A    L++ D  +P MTG +++K +K    T R  P VI+
Sbjct: 37 TDGTSALNYLFGDDKSGRVSAGRAQLVLLDLNLPDMTGIDILKLVKENPHT-RRSPVVIL 95

Query: 72 SS 73
          ++
Sbjct: 96 TT 97

>1k66_A Phytochrome response regulator RCPB; CHEY homologue, homodimer, APO-protein, (beta/alpha)5, signaling protein; 1.75A {Tolypothrix SP} SCOP: c.23.1.1 Length = 149

 Score = 36.8 bits (86), Expect = 1e-04
 Identities = 14/63 (22%), Positives = 28/63 (44%), Gaps = 4/63 (6%)

Query: 14  SDGSDGFDL---SPTDTEEVHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVI 70
             G    D    + +           +I+ D  +PG  G E++++IK      ++IP VI
Sbjct: 39  ITGDQALDFLYQTGSYCNPDIAPRPAVILLDLNLPGTDGREVLQEIKQDE-VLKKIPVVI 97

Query: 71  ISS 73
           +++
Sbjct: 98  MTT 100

>4dad_A Putative pilus assembly-related protein; response regulator receiver domain, CHEY-related protein, ST genomics; 2.50A {Burkholderia pseudomallei} PDB: 4dn6_A Length = 146

 Score = 36.6 bits (85), Expect = 2e-04
 Identities = 5/39 (12%), Positives = 15/39 (38%), Gaps = 3/39 (7%)

Query: 34  AVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIIS 72
           A D+++ D           I+K+         +  ++++
Sbjct: 67  AFDILMIDGAALDTAELAAIEKLSRL---HPGLTCLLVT 102

>1a2o_A CHEB methylesterase; bacterial chemotaxis, adaptation, serine hydrolase; 2.40A {Salmonella typhimurium} SCOP: c.23.1.1 c.40.1.1 Length = 349

 Score = 37.1 bits (87), Expect = 2e-04
 Identities = 12/46 (26%), Positives = 23/46 (50%), Gaps = 4/46 (8%)

Query: 28 EEVHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISS 73
          + +     D++  D  MP M G + ++K+       R +P V++SS
Sbjct: 43 DLIKKFNPDVLTLDVEMPRMDGLDFLEKLMRL----RPMPVVMVSS 84

>3nhm_A Response regulator; protein structure initiative II(PSI II), NYSGXRC, structural genomics; 2.19A {Myxococcus xanthus} Length = 133

 Score = 36.4 bits (85), Expect = 2e-04
 Identities = 11/37 (29%), Positives = 19/37 (51%), Gaps = 1/37 (2%)

Query: 36 DLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIIS 72
          D++I+D  M GM G  L    + +    + IP + +S
Sbjct: 49 DVLISDVNMDGMDGYALCGHFRSEPTL-KHIPVIFVS 84

>2zay_A Response regulator receiver protein; structural genomics, NYSGXRC, target 11006U, protein structure initiative; 2.00A {Desulfuromonas acetoxidans} Length = 147

 Score = 35.3 bits (82), Expect = 4e-04
 Identities = 13/37 (35%), Positives = 20/37 (54%), Gaps = 1/37 (2%)

Query: 36 DLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIIS 72
           LIIT+  MP ++G +L   +K    T   IP + +S
Sbjct: 54 HLIITEANMPKISGMDLFNSLKKNPQT-ASIPVIALS 89

>2qxy_A Response regulator; regulation of transcription, NYSGXRC, protein structure initiative II (PSI II), structural genomics; 1.95A {Thermotoga maritima} Length = 142

 Score = 35.2 bits (82), Expect = 5e-04
 Identities = 9/38 (23%), Positives = 18/38 (47%), Gaps = 4/38 (10%)

Query: 35 VDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIIS 72
          +DL+  D    G     LI++I+ +   F +    ++S
Sbjct: 49 IDLVFVDV-FEGEESLNLIRRIREE---FPDTKVAVLS 82

>3ilh_A Two component response regulator; NYSGXRC, PSI-II, protein S initiative, structural genomics; 2.59A {Cytophaga hutchinsonii} Length = 146

 Score = 35.4 bits (82), Expect = 5e-04
 Identities = 12/39 (30%), Positives = 17/39 (43%), Gaps = 1/39 (2%)

Query: 36  DLIITDYCMPGMTGCELIKKIK-LQSFTFREIPTVIISS 73
            +I  D  MPG+ G ELI   K        +    ++SS
Sbjct: 62  SIICIDINMPGINGWELIDLFKQHFQPMKNKSIVCLLSS 100

>2qvg_A Two component response regulator; NYSGXRC, PSI-2, structural genomics, protein structure initiative; 1.50A {Legionella pneumophila subsp} Length = 143

 Score = 35.3 bits (82), Expect = 5e-04
 Identities = 10/38 (26%), Positives = 22/38 (57%), Gaps = 1/38 (2%)

Query: 36 DLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISS 73
           LI+ D  +P M G E +K+++    +F +I   ++++
Sbjct: 61 KLILLDINIPKMNGIEFLKELR-DDSSFTDIEVFVLTA 97

>3n53_A Response regulator receiver modulated diguanylate; diguanylate cyclase, protein structure I II(PSI II), NYSGXRC, structural genomics; 2.20A {Pelobacter carbinolicus} Length = 140

 Score = 34.8 bits (81), Expect = 6e-04
 Identities = 10/36 (27%), Positives = 16/36 (44%), Gaps = 3/36 (8%)

Query: 36 DLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVII 71
          DL+I D  + G     L  K+K      + +P  +I
Sbjct: 48 DLVILDMDIIGENSPNLCLKLKRSKGL-KNVP--LI 80

>3grc_A Sensor protein, kinase; protein structure initiative II(PSI II), NYSGXRC, 11025B, structural genomics; 2.21A {Polaromonas SP} Length = 140

 Score = 34.9 bits (81), Expect = 6e-04
 Identities = 10/37 (27%), Positives = 19/37 (51%), Gaps = 1/37 (2%)

Query: 36 DLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIIS 72
            +  D  +P   G  LI+ ++  S T R++  V++S
Sbjct: 52 AAMTVDLNLPDQDGVSLIRALRRDSRT-RDLAIVVVS 87

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	82
3to5_A	134	CHEY homolog; alpha(5)beta(5), chemotaxis, FLIM, p	99.68
2lpm_A	123	Two-component response regulator; transcription re	99.52
3gl9_A	122	Response regulator; beta-sheet, surrounded by alph	99.5
3t6k_A	136	Response regulator receiver; flavodoxin-like, stru	99.42
3f6p_A	120	Transcriptional regulatory protein YYCF; unphospho	99.37
3rqi_A	184	Response regulator protein; structural genomics, s	99.34
3gt7_A	154	Sensor protein; structural genomics, signal receiv	99.33
1srr_A	124	SPO0F, sporulation response regulatory protein; as	99.32
3n0r_A	286	Response regulator; sigma factor, receiver, two-co	99.32
3m6m_D	143	Sensory/regulatory protein RPFC; RPFF, REC, enoyl-	99.32
1dbw_A	126	Transcriptional regulatory protein FIXJ; doubly wo	99.32
3eq2_A	394	Probable two-component response regulator; adaptor	99.31
3hv2_A	153	Response regulator/HD domain protein; PSI-2, NYSGX	99.31
3r0j_A	250	Possible two component system response transcript	99.3
3h1g_A	129	Chemotaxis protein CHEY homolog; sulfate-bound CHE	99.3
2pl1_A	121	Transcriptional regulatory protein PHOP; CHEY-like	99.28
3f6c_A	134	Positive transcription regulator EVGA; structural	99.28
1yio_A	208	Response regulatory protein; transcription regulat	99.28
3i42_A	127	Response regulator receiver domain protein (CHEY-	99.28
2r25_B	133	Osmosensing histidine protein kinase SLN1; alpha5-	99.28
3cfy_A	137	Putative LUXO repressor protein; structural genomi	99.27
3kto_A	136	Response regulator receiver protein; PSI-II,struct	99.27
1mb3_A	124	Cell division response regulator DIVK; signal tran	99.26
1p6q_A	129	CHEY2; chemotaxis, signal transduction, response r	99.26
3grc_A	140	Sensor protein, kinase; protein structure initiati	99.26
3crn_A	132	Response regulator receiver domain protein, CHEY-;	99.26
3luf_A	259	Two-component system response regulator/ggdef doma	99.26
3c3m_A	138	Response regulator receiver protein; structural ge	99.26
3dzd_A	368	Transcriptional regulator (NTRC family); sigma43 a	99.25
3eod_A	130	Protein HNR; response regulator, phosphoprotein, t	99.25
3b2n_A	133	Uncharacterized protein Q99UF4; structural genomic	99.24
3a10_A	116	Response regulator; phosphoacceptor, signaling pro	99.24
3nhm_A	133	Response regulator; protein structure initiative I	99.24
1zgz_A	122	Torcad operon transcriptional regulatory protein;	99.24
1w25_A	459	Stalked-cell differentiation controlling protein;	99.23
3hdg_A	137	Uncharacterized protein; two-component sensor acti	99.23
1tmy_A	120	CHEY protein, TMY; chemotaxis, phosphoryl transfer	99.23
4e7p_A	150	Response regulator; DNA binding, cytosol, transcri	99.23
1kgs_A	225	DRRD, DNA binding response regulator D; DNA-bindin	99.22
3hdv_A	136	Response regulator; PSI-II, structural genomics, P	99.22
3snk_A	135	Response regulator CHEY-like protein; P-loop conta	99.22
1i3c_A	149	Response regulator RCP1; phytochrome, signaling pr	99.22
1jbe_A	128	Chemotaxis protein CHEY; signaling protein; 1.08A	99.21
3mm4_A	206	Histidine kinase homolog; receiver domain, CKI1, c	99.21
3ilh_A	146	Two component response regulator; NYSGXRC, PSI-II,	99.21
1ys7_A	233	Transcriptional regulatory protein PRRA; response	99.21
3jte_A	143	Response regulator receiver protein; structural ge	99.21
1a04_A	215	Nitrate/nitrite response regulator protein NARL; s	99.21
2jba_A	127	Phosphate regulon transcriptional regulatory PROT;	99.21
2jk1_A	139	HUPR, hydrogenase transcriptional regulatory prote	99.21
1mvo_A	136	PHOP response regulator; phosphate regulon, transc	99.2
3cg4_A	142	Response regulator receiver domain protein (CHEY-;	99.2
3n53_A	140	Response regulator receiver modulated diguanylate;	99.2
3cu5_A	141	Two component transcriptional regulator, ARAC FAM;	99.2
3bre_A	358	Probable two-component response regulator; protein	99.2
3hzh_A	157	Chemotaxis response regulator (CHEY-3); phosphatas	99.2
1xhf_A	123	DYE resistance, aerobic respiration control protei	99.2
3lua_A	140	Response regulator receiver protein; two-component	99.2
2rjn_A	154	Response regulator receiver:metal-dependent phosph	99.2
3q9s_A	249	DNA-binding response regulator; DNA binding protei	99.2
1dz3_A	130	Stage 0 sporulation protein A; response regulator,	99.19
3kht_A	144	Response regulator; PSI-II, 11023K, structural gen	99.19
1ny5_A	387	Transcriptional regulator (NTRC family); AAA+ ATPa	99.18
2qzj_A	136	Two-component response regulator; 11017X, PSI-II,	99.18
1s8n_A	205	Putative antiterminator; RV1626, structural genomi	99.17
2b4a_A	138	BH3024; flavodoxin-like fold, structural genomics,	99.17
2zay_A	147	Response regulator receiver protein; structural ge	99.16
3heb_A	152	Response regulator receiver domain protein (CHEY);	99.16
2a9o_A	120	Response regulator; essential protein, YYCF/YYCG h	99.16
3cnb_A	143	DNA-binding response regulator, MERR family; signa	99.15
2rdm_A	132	Response regulator receiver protein; structural ge	99.15
3h5i_A	140	Response regulator/sensory box protein/ggdef domai	99.15
2ayx_A	254	Sensor kinase protein RCSC; two independent struct	99.15
3cz5_A	153	Two-component response regulator, LUXR family; str	99.15
2qr3_A	140	Two-component system response regulator; structura	99.15
1k68_A	140	Phytochrome response regulator RCPA; phosphorylate	99.15
3kcn_A	151	Adenylate cyclase homolog; SGX, PSI 2, structural	99.14
3eul_A	152	Possible nitrate/nitrite response transcriptional	99.13
1zh2_A	121	KDP operon transcriptional regulatory protein KDPE	99.13
4dad_A	146	Putative pilus assembly-related protein; response	99.13
2qxy_A	142	Response regulator; regulation of transcription, N	99.12
1qkk_A	155	DCTD, C4-dicarboxylate transport transcriptional r	99.12
3klo_A	225	Transcriptional regulator VPST; REC domain, HTH do	99.12
1k66_A	149	Phytochrome response regulator RCPB; CHEY homologu	99.11
2gwr_A	238	DNA-binding response regulator MTRA; two-component	99.1
3lte_A	132	Response regulator; structural genomics, PSI, prot	99.1
3c3w_A	225	Two component transcriptional regulatory protein;	99.08
2j48_A	119	Two-component sensor kinase; pseudo-receiver, circ	99.06
2oqr_A	230	Sensory transduction protein REGX3; response regul	99.05
3c97_A	140	Signal transduction histidine kinase; structural g	99.04
3cg0_A	140	Response regulator receiver modulated diguanylate	99.04
3eqz_A	135	Response regulator; structural genomics, unknown f	99.03
3luf_A	259	Two-component system response regulator/ggdef doma	99.01
2gkg_A	127	Response regulator homolog; social motility, recei	99.0
2qvg_A	143	Two component response regulator; NYSGXRC, PSI-2,	98.99
3sy8_A	400	ROCR; TIM barrel phosphodiesterase-A, transcriptio	98.97
3t8y_A	164	CHEB, chemotaxis response regulator protein-glutam	98.96
1dc7_A	124	NTRC, nitrogen regulation protein; receiver domain	98.96
1p2f_A	220	Response regulator; DRRB, OMPR/PHOB, transcription	98.96
3kyj_B	145	CHEY6 protein, putative histidine protein kinase;	98.95
2qv0_A	143	Protein MRKE; structural genomics, transcription,	98.94
1qo0_D	196	AMIR; binding protein, gene regulator, receptor; 2	98.93
1a2o_A	349	CHEB methylesterase; bacterial chemotaxis, adaptat	98.93
2qsj_A	154	DNA-binding response regulator, LUXR family; struc	98.89
1dcf_A	136	ETR1 protein; beta-alpha five sandwich, transferas	98.88
2vyc_A	755	Biodegradative arginine decarboxylase; pyridoxal p	98.71
2hqr_A	223	Putative transcriptional regulator; phosporylation	98.7
2pln_A	137	HP1043, response regulator; signaling protein; 1.8	98.63
3cwo_X	237	Beta/alpha-barrel protein based on 1THF and 1TMY;	98.48
1w25_A	459	Stalked-cell differentiation controlling protein;	97.78
3n75_A	715	LDC, lysine decarboxylase, inducible; pyridoxal-5'	95.88
1g5t_A	196	COB(I)alamin adenosyltransferase; P-loop protein,	86.74
3md9_A	255	Hemin-binding periplasmic protein HMUT; transport	84.66
4h08_A	200	Putative hydrolase; GDSL-like lipase/acylhydrolase	84.07
2r7a_A	256	Bacterial heme binding protein; periplasmic bindin	80.26

>3to5_A CHEY homolog; alpha(5)beta(5), chemotaxis, FLIM, phosphorylation, motor AC signaling protein; 1.65A {Vibrio cholerae}

Probab=99.68  E-value=8.6e-17  Score=82.81  Aligned_cols=78  Identities=22%  Similarity=0.353  Sum_probs=57.2

Q ss_pred             CchhHHHHHHHHhcCCCcee---eecChhHH---hhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCC
Q 039883            2 TTTNGVLLSRLMSDGSDGFD---LSPTDTEE---VHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSEN   75 (82)
Q Consensus         2 d~~~~~~~~~~~~~~~~~~~---~~~~~~~~---~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~   75 (82)
                      |+++..+......+...||+   .+.++.++   +...+||+||+|+.||+++|+++++.+| .....+.+|||++|+..
T Consensus        19 DD~~~~r~~l~~~L~~~G~~~v~~a~~g~~al~~~~~~~~DlillD~~MP~mdG~el~~~ir-~~~~~~~ipvI~lTa~~   97 (134)
T 3to5_A           19 DDFSTMRRIVKNLLRDLGFNNTQEADDGLTALPMLKKGDFDFVVTDWNMPGMQGIDLLKNIR-ADEELKHLPVLMITAEA   97 (134)
T ss_dssp             CSCHHHHHHHHHHHHHTTCCCEEEESSHHHHHHHHHHHCCSEEEEESCCSSSCHHHHHHHHH-HSTTTTTCCEEEEESSC
T ss_pred             eCCHHHHHHHHHHHHHcCCcEEEEECCHHHHHHHHHhCCCCEEEEcCCCCCCCHHHHHHHHH-hCCCCCCCeEEEEECCC
Confidence            45555554444444455554   34455544   4566899999999999999999999999 55567889999999987


Q ss_pred             chhhh
Q 039883           76 ILARI   80 (82)
Q Consensus        76 ~~~~~   80 (82)
                      +.+..
T Consensus        98 ~~~~~  102 (134)
T 3to5_A           98 KREQI  102 (134)
T ss_dssp             CHHHH
T ss_pred             CHHHH
Confidence            76543

>2lpm_A Two-component response regulator; transcription regulator; NMR {Sinorhizobium meliloti}

Probab=99.52  E-value=9.8e-16  Score=77.85  Aligned_cols=71  Identities=11%  Similarity=0.124  Sum_probs=49.6

Q ss_pred             chhHHHHHHHHhcCCCceeee---cChhHH---hhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCc
Q 039883            3 TTNGVLLSRLMSDGSDGFDLS---PTDTEE---VHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENI   76 (82)
Q Consensus         3 ~~~~~~~~~~~~~~~~~~~~~---~~~~~~---~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~   76 (82)
                      |++..+......+...||++.   .++.++   +...+||++|+|+.||+++|+++++.+| .    ..+|+|++|+..+
T Consensus        16 D~~~~~~~l~~~L~~~G~~v~~~a~~g~eAl~~~~~~~~DlvllDi~mP~~~G~el~~~lr-~----~~ipvI~lTa~~~   90 (123)
T 2lpm_A           16 DESMIAMLIEDTLCELGHEVAATASRMQEALDIARKGQFDIAIIDVNLDGEPSYPVADILA-E----RNVPFIFATGYGS   90 (123)
T ss_dssp             SSTTTSHHHHHHHHHHCCCCCBCSCCHHHHHHHHHHCCSSEEEECSSSSSCCSHHHHHHHH-H----TCCSSCCBCTTCT
T ss_pred             CCHHHHHHHHHHHHHCCCEEEEEECCHHHHHHHHHhCCCCEEEEecCCCCCCHHHHHHHHH-c----CCCCEEEEecCcc
Confidence            333333333333344566653   344444   4566899999999999999999999999 2    3589999998765


Q ss_pred             hh
Q 039883           77 LA   78 (82)
Q Consensus        77 ~~   78 (82)
                      ..
T Consensus        91 ~~   92 (123)
T 2lpm_A           91 KG   92 (123)
T ss_dssp             TS
T ss_pred             HH
Confidence            44

>3gl9_A Response regulator; beta-sheet, surrounded by alpha helices, BOTH sides, signaling protein; HET: BFD; 1.80A {Thermotoga maritima} SCOP: c.23.1.0 PDB: 3dgf_C 3dge_C

Probab=99.50  E-value=9.2e-14  Score=69.79  Aligned_cols=77  Identities=16%  Similarity=0.309  Sum_probs=52.1

Q ss_pred             CchhHHHHHHHHhcCCCceeee--cChhHH---hhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCc
Q 039883            2 TTTNGVLLSRLMSDGSDGFDLS--PTDTEE---VHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENI   76 (82)
Q Consensus         2 d~~~~~~~~~~~~~~~~~~~~~--~~~~~~---~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~   76 (82)
                      |+++.............+|++.  .++.++   +...+||++|+|+.||+++|+++++.++ .....+.+|+|++|+..+
T Consensus         9 dd~~~~~~~l~~~l~~~g~~v~~~~~~~~al~~l~~~~~dlvllD~~~p~~~g~~~~~~l~-~~~~~~~~pii~~s~~~~   87 (122)
T 3gl9_A            9 DDSAVLRKIVSFNLKKEGYEVIEAENGQIALEKLSEFTPDLIVLXIMMPVMDGFTVLKKLQ-EKEEWKRIPVIVLTAKGG   87 (122)
T ss_dssp             CSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHHTTBCCSEEEECSCCSSSCHHHHHHHHH-TSTTTTTSCEEEEESCCS
T ss_pred             eCCHHHHHHHHHHHHHCCcEEEEeCCHHHHHHHHHhcCCCEEEEeccCCCCcHHHHHHHHH-hcccccCCCEEEEecCCc
Confidence            3344433333333333455554  444444   4566899999999999999999999998 333457899999998776


Q ss_pred             hhh
Q 039883           77 LAR   79 (82)
Q Consensus        77 ~~~   79 (82)
                      .+.
T Consensus        88 ~~~   90 (122)
T 3gl9_A           88 EED   90 (122)
T ss_dssp             HHH
T ss_pred             hHH
Confidence            544

>3t6k_A Response regulator receiver; flavodoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative; HET: MSE; 1.86A {Chloroflexus aurantiacus} SCOP: c.23.1.0

Probab=99.42  E-value=5e-13  Score=68.18  Aligned_cols=61  Identities=20%  Similarity=0.474  Sum_probs=46.4

Q ss_pred             Cceee--ecChhHH---hhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCchhh
Q 039883           18 DGFDL--SPTDTEE---VHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENILAR   79 (82)
Q Consensus        18 ~~~~~--~~~~~~~---~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~~~~   79 (82)
                      .+|++  +.++.++   +...+||+||+|+.||+++|+++++.++ .....+.+|+|++|+..+...
T Consensus        27 ~g~~v~~~~~~~~al~~~~~~~~dlvl~D~~lp~~~g~~~~~~lr-~~~~~~~~pii~~t~~~~~~~   92 (136)
T 3t6k_A           27 AGYEVRRAASGEEALQQIYKNLPDALICDVLLPGIDGYTLCKRVR-QHPLTKTLPILMLTAQGDISA   92 (136)
T ss_dssp             TTCEEEEESSHHHHHHHHHHSCCSEEEEESCCSSSCHHHHHHHHH-HSGGGTTCCEEEEECTTCHHH
T ss_pred             CCCEEEEeCCHHHHHHHHHhCCCCEEEEeCCCCCCCHHHHHHHHH-cCCCcCCccEEEEecCCCHHH
Confidence            44554  4444444   4566899999999999999999999999 333467889999998876543

>3f6p_A Transcriptional regulatory protein YYCF; unphosphorelated, receiver domain, cytoplasm, DNA-binding, phosphoprotein, transcription regulation; 1.95A {Bacillus subtilis} SCOP: c.23.1.1 PDB: 2zwm_A

Probab=99.37  E-value=1.6e-12  Score=64.96  Aligned_cols=58  Identities=21%  Similarity=0.500  Sum_probs=44.3

Q ss_pred             Cceee--ecChhHH---hhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCchhh
Q 039883           18 DGFDL--SPTDTEE---VHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENILAR   79 (82)
Q Consensus        18 ~~~~~--~~~~~~~---~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~~~~   79 (82)
                      .+|++  +.++.++   +...+||++|+|+.||+++|+++++.++   . ....|+|++|+..+...
T Consensus        25 ~g~~v~~~~~~~~al~~~~~~~~dlii~D~~~p~~~g~~~~~~lr---~-~~~~~ii~~t~~~~~~~   87 (120)
T 3f6p_A           25 EGYEVHCAHDGNEAVEMVEELQPDLILLDIMLPNKDGVEVCREVR---K-KYDMPIIMLTAKDSEID   87 (120)
T ss_dssp             TTCEEEEESSHHHHHHHHHTTCCSEEEEETTSTTTHHHHHHHHHH---T-TCCSCEEEEEESSCHHH
T ss_pred             CCEEEEEeCCHHHHHHHHhhCCCCEEEEeCCCCCCCHHHHHHHHH---h-cCCCCEEEEECCCChHH
Confidence            34444  4444444   4566899999999999999999999999   3 34689999998876543

>3rqi_A Response regulator protein; structural genomics, seattle structural genomics center for infectious disease, ssgcid; HET: PHD CIT; 1.70A {Burkholderia pseudomallei}

Probab=99.34  E-value=3.3e-13  Score=72.08  Aligned_cols=75  Identities=9%  Similarity=0.083  Sum_probs=51.9

Q ss_pred             CchhHHHHHHHHhcCCCceee--ecChhHH---hhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCc
Q 039883            2 TTTNGVLLSRLMSDGSDGFDL--SPTDTEE---VHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENI   76 (82)
Q Consensus         2 d~~~~~~~~~~~~~~~~~~~~--~~~~~~~---~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~   76 (82)
                      |+++.............+|++  +.++.++   +...+||+||+|+.||+++|+++++.++   ...+.+|+|++|+..+
T Consensus        14 dd~~~~~~~l~~~L~~~g~~v~~~~~~~~al~~~~~~~~dlvl~D~~lp~~~g~~~~~~l~---~~~~~~~ii~lt~~~~   90 (184)
T 3rqi_A           14 DDNEVFAGTLARGLERRGYAVRQAHNKDEALKLAGAEKFEFITVXLHLGNDSGLSLIAPLC---DLQPDARILVLTGYAS   90 (184)
T ss_dssp             CSCHHHHHHHHHHHHHTTCEEEEECSHHHHHHHHTTSCCSEEEECSEETTEESHHHHHHHH---HHCTTCEEEEEESSCC
T ss_pred             cCCHHHHHHHHHHHHHCCCEEEEeCCHHHHHHHHhhCCCCEEEEeccCCCccHHHHHHHHH---hcCCCCCEEEEeCCCC
Confidence            344444433333232344554  4445544   4456799999999999999999999999   4567899999999877


Q ss_pred             hhh
Q 039883           77 LAR   79 (82)
Q Consensus        77 ~~~   79 (82)
                      .+.
T Consensus        91 ~~~   93 (184)
T 3rqi_A           91 IAT   93 (184)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            654

>3gt7_A Sensor protein; structural genomics, signal receiver domain, kinase, PSI-2, protein structure initiative; 2.30A {Syntrophus aciditrophicus SB}

Probab=99.33  E-value=9.5e-12  Score=64.58  Aligned_cols=76  Identities=21%  Similarity=0.256  Sum_probs=51.8

Q ss_pred             chhHHHHHHHHhcCCCceee--ecChhHH---hhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCch
Q 039883            3 TTNGVLLSRLMSDGSDGFDL--SPTDTEE---VHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENIL   77 (82)
Q Consensus         3 ~~~~~~~~~~~~~~~~~~~~--~~~~~~~---~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~~   77 (82)
                      ++..............+|.+  +.++.++   +...+||+||+|+.+|+.+|+++++.++ .....+.+|+|++|+..+.
T Consensus        15 d~~~~~~~l~~~L~~~g~~v~~~~~~~~al~~l~~~~~dlii~D~~l~~~~g~~~~~~lr-~~~~~~~~pii~~s~~~~~   93 (154)
T 3gt7_A           15 DSPTQAEHLKHILEETGYQTEHVRNGREAVRFLSLTRPDLIISDVLMPEMDGYALCRWLK-GQPDLRTIPVILLTILSDP   93 (154)
T ss_dssp             SCHHHHHHHHHHHHTTTCEEEEESSHHHHHHHHTTCCCSEEEEESCCSSSCHHHHHHHHH-HSTTTTTSCEEEEECCCSH
T ss_pred             CCHHHHHHHHHHHHHCCCEEEEeCCHHHHHHHHHhCCCCEEEEeCCCCCCCHHHHHHHHH-hCCCcCCCCEEEEECCCCh
Confidence            33333333333333345554  4444444   4456899999999999999999999999 3334578999999987765


Q ss_pred             hh
Q 039883           78 AR   79 (82)
Q Consensus        78 ~~   79 (82)
                      +.
T Consensus        94 ~~   95 (154)
T 3gt7_A           94 RD   95 (154)
T ss_dssp             HH
T ss_pred             HH
Confidence            44

>1srr_A SPO0F, sporulation response regulatory protein; aspartate pocket, two component system; 1.90A {Bacillus subtilis} SCOP: c.23.1.1 PDB: 1pey_A 3q15_C 2ftk_E* 1fsp_A 1nat_A 1pux_A 2fsp_A 2jvj_A 2jvk_A 2jvi_A 1f51_E

Probab=99.32  E-value=5e-12  Score=63.26  Aligned_cols=60  Identities=25%  Similarity=0.444  Sum_probs=45.2

Q ss_pred             CCceeee--cChhHH---hhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCchhh
Q 039883           17 SDGFDLS--PTDTEE---VHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENILAR   79 (82)
Q Consensus        17 ~~~~~~~--~~~~~~---~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~~~~   79 (82)
                      ..+|.+.  .++.++   +...+||++|+|+.+|+.+|+++++.++   ...+.+|+|++|+..+.+.
T Consensus        25 ~~~~~v~~~~~~~~a~~~~~~~~~dlvl~D~~l~~~~g~~~~~~l~---~~~~~~~ii~~s~~~~~~~   89 (124)
T 1srr_A           25 KEGYQTFQAANGLQALDIVTKERPDLVLLDMKIPGMDGIEILKRMK---VIDENIRVIIMTAYGELDM   89 (124)
T ss_dssp             TTTCEEEEESSHHHHHHHHHHHCCSEEEEESCCTTCCHHHHHHHHH---HHCTTCEEEEEESSCCHHH
T ss_pred             HCCcEEEEeCCHHHHHHHHhccCCCEEEEecCCCCCCHHHHHHHHH---HhCCCCCEEEEEccCchHH
Confidence            3455543  344443   4456899999999999999999999999   3467899999998766543

>3n0r_A Response regulator; sigma factor, receiver, two-component SI transduction, signaling protein; HET: MSE GOL; 1.25A {Caulobacter vibrioides} PDB: 3t0y_A

Probab=99.32  E-value=7.6e-13  Score=75.29  Aligned_cols=71  Identities=18%  Similarity=0.251  Sum_probs=50.7

Q ss_pred             CchhHHHHHHHHhcCCCceeee---cChhHH---hhccCccEEEEeCCCC-CCCHHHHHHHHHhhcCCCCCccEEEEeeC
Q 039883            2 TTTNGVLLSRLMSDGSDGFDLS---PTDTEE---VHVLAVDLIITDYCMP-GMTGCELIKKIKLQSFTFREIPTVIISSE   74 (82)
Q Consensus         2 d~~~~~~~~~~~~~~~~~~~~~---~~~~~~---~~~~~~d~vi~d~~~~-~~~~~~~~~~l~~~~~~~~~~~vi~ls~~   74 (82)
                      |+++.........+...||.+.   .++.++   +...+||+||+|+.|| +++|+++++.+| .  .. .+|||++|+.
T Consensus       167 dD~~~~~~~l~~~L~~~g~~v~~~a~~g~eAl~~~~~~~~dlvl~D~~MPd~mdG~e~~~~ir-~--~~-~~piI~lT~~  242 (286)
T 3n0r_A          167 EDEPVIAADIEALVRELGHDVTDIAATRGEALEAVTRRTPGLVLADIQLADGSSGIDAVKDIL-G--RM-DVPVIFITAF  242 (286)
T ss_dssp             CCSHHHHHHHHHHHHHTTCEEEEEESSHHHHHHHHHHCCCSEEEEESCCTTSCCTTTTTHHHH-H--HT-TCCEEEEESC
T ss_pred             cCCHHHHHHHHHHhhccCceEEEEeCCHHHHHHHHHhCCCCEEEEcCCCCCCCCHHHHHHHHH-h--cC-CCCEEEEeCC
Confidence            4455555444444444566554   445544   4456899999999999 799999999999 3  23 8999999997


Q ss_pred             Cc
Q 039883           75 NI   76 (82)
Q Consensus        75 ~~   76 (82)
                      .+
T Consensus       243 ~~  244 (286)
T 3n0r_A          243 PE  244 (286)
T ss_dssp             GG
T ss_pred             HH
Confidence            53

>3m6m_D Sensory/regulatory protein RPFC; RPFF, REC, enoyl-COA hydratase, lyase-transferase COMP; 2.50A {Xanthomonas campestris PV}

Probab=99.32  E-value=1e-11  Score=63.77  Aligned_cols=78  Identities=18%  Similarity=0.287  Sum_probs=50.5

Q ss_pred             CchhHHHHHHHHhcCCCceee--ecChhH---HhhccCccEEEEeCCCCCCCHHHHHHHHHhh-cCCCCCccEEEEeeCC
Q 039883            2 TTTNGVLLSRLMSDGSDGFDL--SPTDTE---EVHVLAVDLIITDYCMPGMTGCELIKKIKLQ-SFTFREIPTVIISSEN   75 (82)
Q Consensus         2 d~~~~~~~~~~~~~~~~~~~~--~~~~~~---~~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~-~~~~~~~~vi~ls~~~   75 (82)
                      |++..............++.+  +.++.+   .+...+||+||+|+.||+++|+++++.++.. ....+.+|+|++|+..
T Consensus        21 dd~~~~~~~l~~~L~~~g~~v~~~~~~~~al~~~~~~~~dlvl~D~~mp~~~g~~~~~~lr~~~~~~~~~~pii~~s~~~  100 (143)
T 3m6m_D           21 DDHEANRMVLQRLLEKAGHKVLCVNGAEQVLDAMAEEDYDAVIVDLHMPGMNGLDMLKQLRVMQASGMRYTPVVVLSADV  100 (143)
T ss_dssp             CSSHHHHHHHHHHHHC--CEEEEESSHHHHHHHHHHSCCSEEEEESCCSSSCHHHHHHHHHHHHHTTCCCCCEEEEESCC
T ss_pred             eCCHHHHHHHHHHHHHcCCeEEEeCCHHHHHHHHhcCCCCEEEEeCCCCCCCHHHHHHHHHhchhccCCCCeEEEEeCCC
Confidence            334444433333333445554  444444   3456689999999999999999999999821 1345678999999877


Q ss_pred             chhh
Q 039883           76 ILAR   79 (82)
Q Consensus        76 ~~~~   79 (82)
                      +.+.
T Consensus       101 ~~~~  104 (143)
T 3m6m_D          101 TPEA  104 (143)
T ss_dssp             CHHH
T ss_pred             CHHH
Confidence            6544

>1dbw_A Transcriptional regulatory protein FIXJ; doubly wound five-stranded beta/alpha fold, nitrogen fixatio regulation; HET: 15P; 1.60A {Sinorhizobium meliloti} SCOP: c.23.1.1 PDB: 1dck_A* 1dcm_A 1d5w_A*

Probab=99.32  E-value=4.7e-12  Score=63.59  Aligned_cols=58  Identities=19%  Similarity=0.350  Sum_probs=44.2

Q ss_pred             ceeeecChhHH---hhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCchhh
Q 039883           19 GFDLSPTDTEE---VHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENILAR   79 (82)
Q Consensus        19 ~~~~~~~~~~~---~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~~~~   79 (82)
                      .+....++.++   +...+||++|+|+.+|+++|+++++.++   ...+.+|+|++|+..+...
T Consensus        29 ~v~~~~~~~~~~~~~~~~~~dlvi~D~~l~~~~g~~~~~~l~---~~~~~~~ii~~s~~~~~~~   89 (126)
T 1dbw_A           29 AVKMHQSAEAFLAFAPDVRNGVLVTDLRMPDMSGVELLRNLG---DLKINIPSIVITGHGDVPM   89 (126)
T ss_dssp             EEEEESCHHHHHHHGGGCCSEEEEEECCSTTSCHHHHHHHHH---HTTCCCCEEEEECTTCHHH
T ss_pred             EEEEeCCHHHHHHHHhcCCCCEEEEECCCCCCCHHHHHHHHH---hcCCCCCEEEEECCCCHHH
Confidence            33334444443   4455799999999999999999999999   4567899999998876543

>3eq2_A Probable two-component response regulator; adaptor sigmas, signaling protein; 3.40A {Pseudomonas aeruginosa} PDB: 3f7a_A

Probab=99.31  E-value=2.3e-12  Score=75.69  Aligned_cols=75  Identities=24%  Similarity=0.343  Sum_probs=51.3

Q ss_pred             CchhHHHHHHHHhcCCCceeeecC--hhHH---hhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCc
Q 039883            2 TTTNGVLLSRLMSDGSDGFDLSPT--DTEE---VHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENI   76 (82)
Q Consensus         2 d~~~~~~~~~~~~~~~~~~~~~~~--~~~~---~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~   76 (82)
                      |++..............+|++..+  +.++   +...+||+||+|+.||+++|+++++.+|   ...+.+|+|++|+..+
T Consensus        12 dD~~~~~~~l~~~L~~~g~~v~~a~~~~~al~~~~~~~~dlvllD~~mp~~~G~~~~~~lr---~~~~~~pii~lt~~~~   88 (394)
T 3eq2_A           12 DDDEVVRESLAAYLEDSNFKVLQALNGLQGLQIFESEQPDLVICDLRMPQIDGLELIRRIR---QTASETPIIVLSGAGV   88 (394)
T ss_dssp             CSCHHHHHHHHHHHHHTTEEEEECSSHHHHHHHHHHSCCSEEEECCCSSSSCTHHHHHHHH---HTTCCCCEEEC---CH
T ss_pred             eCCHHHHHHHHHHHHhCCCEEEEECCHHHHHHHHhhCCCCEEEEcCCCCCCCHHHHHHHHH---hhCCCCcEEEEEcCCC
Confidence            444444444444444456666544  3344   4566899999999999999999999999   4567899999998876


Q ss_pred             hhh
Q 039883           77 LAR   79 (82)
Q Consensus        77 ~~~   79 (82)
                      .+.
T Consensus        89 ~~~   91 (394)
T 3eq2_A           89 MSD   91 (394)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            554

>3hv2_A Response regulator/HD domain protein; PSI-2, NYSGXRC, structural genomics, protein structure initiative; 1.50A {Pseudomonas fluorescens pf-5}

Probab=99.31  E-value=7.3e-12  Score=64.85  Aligned_cols=75  Identities=17%  Similarity=0.231  Sum_probs=52.9

Q ss_pred             CchhHHHHHHHHhcCCCceeeec--ChhH---HhhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCc
Q 039883            2 TTTNGVLLSRLMSDGSDGFDLSP--TDTE---EVHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENI   76 (82)
Q Consensus         2 d~~~~~~~~~~~~~~~~~~~~~~--~~~~---~~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~   76 (82)
                      |++..............+|.+..  +..+   .+...+||+||+|+.+|+++|+++++.++   ...+.+|+|++|+..+
T Consensus        21 dd~~~~~~~l~~~L~~~g~~v~~~~~~~~a~~~l~~~~~dlvi~D~~l~~~~g~~~~~~l~---~~~~~~~ii~~s~~~~   97 (153)
T 3hv2_A           21 DSQEVILQRLQQLLSPLPYTLHFARDATQALQLLASREVDLVISAAHLPQMDGPTLLARIH---QQYPSTTRILLTGDPD   97 (153)
T ss_dssp             CSCHHHHHHHHHHHTTSSCEEEEESSHHHHHHHHHHSCCSEEEEESCCSSSCHHHHHHHHH---HHCTTSEEEEECCCCC
T ss_pred             CCCHHHHHHHHHHhcccCcEEEEECCHHHHHHHHHcCCCCEEEEeCCCCcCcHHHHHHHHH---hHCCCCeEEEEECCCC
Confidence            34444444444444444565543  4444   44566899999999999999999999999   4567899999998776


Q ss_pred             hhh
Q 039883           77 LAR   79 (82)
Q Consensus        77 ~~~   79 (82)
                      .+.
T Consensus        98 ~~~  100 (153)
T 3hv2_A           98 LKL  100 (153)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            544

>3r0j_A Possible two component system response transcript positive regulator PHOP; beta-alpha fold, winged helix-turn-helix; 2.50A {Mycobacterium tuberculosis}

Probab=99.30  E-value=5.4e-12  Score=70.13  Aligned_cols=75  Identities=17%  Similarity=0.350  Sum_probs=51.7

Q ss_pred             CchhHHHHHHHHhcCCCceee--ecChhHH---hhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCc
Q 039883            2 TTTNGVLLSRLMSDGSDGFDL--SPTDTEE---VHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENI   76 (82)
Q Consensus         2 d~~~~~~~~~~~~~~~~~~~~--~~~~~~~---~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~   76 (82)
                      |++..............+|++  +.++.++   +...+||+||+|+.||+++|+++++.++   ...+.+|+|++|+..+
T Consensus        30 dd~~~~~~~l~~~L~~~g~~v~~~~~~~~al~~~~~~~~dlvllD~~lp~~~g~~~~~~lr---~~~~~~~ii~lt~~~~  106 (250)
T 3r0j_A           30 DDEANIVELLSVSLKFQGFEVYTATNGAQALDRARETRPDAVILDVXMPGMDGFGVLRRLR---ADGIDAPALFLTARDS  106 (250)
T ss_dssp             CSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHHHHHCCSEEEEESCCSSSCHHHHHHHHH---HTTCCCCEEEEECSTT
T ss_pred             ECCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHHhCCCCEEEEeCCCCCCCHHHHHHHHH---hcCCCCCEEEEECCCC
Confidence            334444333333233345555  4444444   4456899999999999999999999999   4567899999999876


Q ss_pred             hhh
Q 039883           77 LAR   79 (82)
Q Consensus        77 ~~~   79 (82)
                      .+.
T Consensus       107 ~~~  109 (250)
T 3r0j_A          107 LQD  109 (250)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            554

>3h1g_A Chemotaxis protein CHEY homolog; sulfate-bound CHEY, cytoplasm, flagellar rotatio magnesium, metal-binding, phosphoprotein; 1.70A {Helicobacter pylori} SCOP: c.23.1.1 PDB: 3gwg_A 3h1e_A 3h1f_A

Probab=99.30  E-value=9.3e-12  Score=62.81  Aligned_cols=45  Identities=38%  Similarity=0.709  Sum_probs=38.5

Q ss_pred             CccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCchhh
Q 039883           34 AVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENILAR   79 (82)
Q Consensus        34 ~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~~~~   79 (82)
                      +||++|+|+.||+++|+++++.++ .....+.+|+|++|+..+...
T Consensus        51 ~~dlvi~D~~~p~~~g~~~~~~lr-~~~~~~~~pii~~s~~~~~~~   95 (129)
T 3h1g_A           51 DTKVLITDWNMPEMNGLDLVKKVR-SDSRFKEIPIIMITAEGGKAE   95 (129)
T ss_dssp             TCCEEEECSCCSSSCHHHHHHHHH-TSTTCTTCCEEEEESCCSHHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHH-hcCCCCCCeEEEEeCCCChHH
Confidence            699999999999999999999999 333457899999998876553

>2pl1_A Transcriptional regulatory protein PHOP; CHEY-like fold, response regulator, beryllium fluoride, transcription factor, activated, virulence; 1.90A {Escherichia coli} SCOP: c.23.1.1 PDB: 2pkx_A

Probab=99.28  E-value=1e-11  Score=61.75  Aligned_cols=57  Identities=18%  Similarity=0.306  Sum_probs=43.9

Q ss_pred             ceeeecChhHH---hhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCchh
Q 039883           19 GFDLSPTDTEE---VHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENILA   78 (82)
Q Consensus        19 ~~~~~~~~~~~---~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~~~   78 (82)
                      .+..+.++.++   +...+||++++|+.+|+++|+++++.++   ...+.+|+|++|+..+..
T Consensus        26 ~v~~~~~~~~a~~~~~~~~~dlil~D~~l~~~~g~~~~~~l~---~~~~~~~ii~~s~~~~~~   85 (121)
T 2pl1_A           26 QVDDAEDAKEADYYLNEHIPDIAIVDLGLPDEDGLSLIRRWR---SNDVSLPILVLTARESWQ   85 (121)
T ss_dssp             EEEEESSHHHHHHHHHHSCCSEEEECSCCSSSCHHHHHHHHH---HTTCCSCEEEEESCCCHH
T ss_pred             EEEEeCCHHHHHHHHhccCCCEEEEecCCCCCCHHHHHHHHH---hcCCCCCEEEEecCCCHH
Confidence            33334444443   4456899999999999999999999999   456788999999876654

>3f6c_A Positive transcription regulator EVGA; structural genomics, PSI-2, protein structure initiative, PO transcription regulator EVGA; 1.45A {Escherichia coli k-12}

Probab=99.28  E-value=8.6e-12  Score=63.09  Aligned_cols=73  Identities=15%  Similarity=0.185  Sum_probs=49.2

Q ss_pred             chhHHHHHHHHhcCCCceeee---cChh---HHhhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCc
Q 039883            3 TTNGVLLSRLMSDGSDGFDLS---PTDT---EEVHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENI   76 (82)
Q Consensus         3 ~~~~~~~~~~~~~~~~~~~~~---~~~~---~~~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~   76 (82)
                      ++..............++++.   .+..   +.+...+||+||+|+.+|+.+|+++++.++   ...+.+|+|++|+..+
T Consensus         9 d~~~~~~~l~~~L~~~g~~v~~~~~~~~~a~~~~~~~~~dlii~d~~l~~~~g~~~~~~l~---~~~~~~~ii~~s~~~~   85 (134)
T 3f6c_A            9 DHPLAIAAIRNLLIKNDIEILAELTEGGSAVQRVETLKPDIVIIDVDIPGVNGIQVLETLR---KRQYSGIIIIVSAKND   85 (134)
T ss_dssp             CCHHHHHHHHHHHHHTTEEEEEEESSSTTHHHHHHHHCCSEEEEETTCSSSCHHHHHHHHH---HTTCCSEEEEEECC--
T ss_pred             CCHHHHHHHHHHHhhCCcEEEEEcCCHHHHHHHHHhcCCCEEEEecCCCCCChHHHHHHHH---hcCCCCeEEEEeCCCC
Confidence            333333333333333456654   2333   345566899999999999999999999999   5577899999998766


Q ss_pred             hh
Q 039883           77 LA   78 (82)
Q Consensus        77 ~~   78 (82)
                      .+
T Consensus        86 ~~   87 (134)
T 3f6c_A           86 HF   87 (134)
T ss_dssp             -C
T ss_pred             hH
Confidence            54

>1yio_A Response regulatory protein; transcription regulation, DNA binding protein; 2.20A {Pseudomonas fluorescens} SCOP: a.4.6.2 c.23.1.1 PDB: 1zn2_A

Probab=99.28  E-value=6.7e-12  Score=67.84  Aligned_cols=74  Identities=22%  Similarity=0.244  Sum_probs=51.2

Q ss_pred             CchhHHHHHHHHhcCCCceee--ecChhHHhh---ccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCc
Q 039883            2 TTTNGVLLSRLMSDGSDGFDL--SPTDTEEVH---VLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENI   76 (82)
Q Consensus         2 d~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~---~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~   76 (82)
                      |+++.............+|++  +.++.+++.   ..+||++|+|+.||+++|+++++.++   ...+.+|+|++|+..+
T Consensus        11 dd~~~~~~~l~~~L~~~g~~v~~~~~~~~al~~~~~~~~dlvl~D~~lp~~~g~~~~~~l~---~~~~~~~ii~ls~~~~   87 (208)
T 1yio_A           11 DDDMSVREGLRNLLRSAGFEVETFDCASTFLEHRRPEQHGCLVLDMRMPGMSGIELQEQLT---AISDGIPIVFITAHGD   87 (208)
T ss_dssp             CSCHHHHHHHHHHHHTTTCEEEEESSHHHHHHHCCTTSCEEEEEESCCSSSCHHHHHHHHH---HTTCCCCEEEEESCTT
T ss_pred             cCCHHHHHHHHHHHHhCCceEEEcCCHHHHHHhhhccCCCEEEEeCCCCCCCHHHHHHHHH---hcCCCCCEEEEeCCCC
Confidence            344444433333333345555  344445443   45799999999999999999999999   4567899999998766


Q ss_pred             hh
Q 039883           77 LA   78 (82)
Q Consensus        77 ~~   78 (82)
                      .+
T Consensus        88 ~~   89 (208)
T 1yio_A           88 IP   89 (208)
T ss_dssp             SC
T ss_pred             HH
Confidence            43

>3i42_A Response regulator receiver domain protein (CHEY- like); structural genomics, PSI-2, protein structure initiative; 2.15A {Methylobacillus flagellatus KT} SCOP: c.23.1.0

Probab=99.28  E-value=1.8e-11  Score=61.41  Aligned_cols=61  Identities=18%  Similarity=0.219  Sum_probs=45.6

Q ss_pred             CCceee--ecChhH---HhhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCchh
Q 039883           17 SDGFDL--SPTDTE---EVHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENILA   78 (82)
Q Consensus        17 ~~~~~~--~~~~~~---~~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~~~   78 (82)
                      ..+|++  +.++.+   .+...+||+||+|+.+|+.+|+++++.++ .....+.+|+|++|+..+..
T Consensus        25 ~~g~~v~~~~~~~~a~~~l~~~~~dlii~D~~l~~~~g~~~~~~l~-~~~~~~~~~ii~~s~~~~~~   90 (127)
T 3i42_A           25 MLGFQADYVMSGTDALHAMSTRGYDAVFIDLNLPDTSGLALVKQLR-ALPMEKTSKFVAVSGFAKND   90 (127)
T ss_dssp             HTTEEEEEESSHHHHHHHHHHSCCSEEEEESBCSSSBHHHHHHHHH-HSCCSSCCEEEEEECC-CTT
T ss_pred             HcCCCEEEECCHHHHHHHHHhcCCCEEEEeCCCCCCCHHHHHHHHH-hhhccCCCCEEEEECCcchh
Confidence            345555  444444   44566899999999999999999999999 33337889999999876654

>2r25_B Osmosensing histidine protein kinase SLN1; alpha5-BETA5, response regulator, four helix bundle, histidine phosphotransfer (HPT) protein; 1.70A {Saccharomyces cerevisiae} SCOP: c.23.1.1 PDB: 1oxk_B 1oxb_B

Probab=99.28  E-value=9.6e-12  Score=63.16  Aligned_cols=45  Identities=20%  Similarity=0.173  Sum_probs=37.3

Q ss_pred             cCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCchhh
Q 039883           33 LAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENILAR   79 (82)
Q Consensus        33 ~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~~~~   79 (82)
                      .+||++|+|+.||+++|+++++.++ .. ..+.+|+|++|+..+...
T Consensus        51 ~~~dlvllD~~mp~~~G~~~~~~lr-~~-~~~~~~ii~lt~~~~~~~   95 (133)
T 2r25_B           51 ENYNMIFMDVQMPKVDGLLSTKMIR-RD-LGYTSPIVALTAFADDSN   95 (133)
T ss_dssp             CCCSEEEECSCCSSSCHHHHHHHHH-HH-SCCCSCEEEEESCCSHHH
T ss_pred             CCCCEEEEeCCCCCCChHHHHHHHH-hh-cCCCCCEEEEECCCCHHH
Confidence            5799999999999999999999998 21 244679999998876543

>3cfy_A Putative LUXO repressor protein; structural genomics, unknown function, uncharacterized protein, signal receiver domain; 2.50A {Vibrio parahaemolyticus rimd 2210633}

Probab=99.27  E-value=1.3e-11  Score=63.02  Aligned_cols=64  Identities=17%  Similarity=0.240  Sum_probs=47.1

Q ss_pred             HhcCCCceeeec--ChhHH---hhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCchhh
Q 039883           13 MSDGSDGFDLSP--TDTEE---VHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENILAR   79 (82)
Q Consensus        13 ~~~~~~~~~~~~--~~~~~---~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~~~~   79 (82)
                      ......+|++..  ++.++   +...+||++|+|+.+|+.+|+++++.++   ...+.+|+|++|+..+.+.
T Consensus        22 ~~L~~~g~~v~~~~~~~~a~~~l~~~~~dlvllD~~l~~~~g~~l~~~l~---~~~~~~~ii~ls~~~~~~~   90 (137)
T 3cfy_A           22 QYVKDEPYDIFHVETGRDAIQFIERSKPQLIILDLKLPDMSGEDVLDWIN---QNDIPTSVIIATAHGSVDL   90 (137)
T ss_dssp             HHTTTSSSEEEEESSHHHHHHHHHHHCCSEEEECSBCSSSBHHHHHHHHH---HTTCCCEEEEEESSCCHHH
T ss_pred             HHHHhcCceEEEeCCHHHHHHHHHhcCCCEEEEecCCCCCCHHHHHHHHH---hcCCCCCEEEEEecCcHHH
Confidence            333344565543  34443   4456899999999999999999999999   4567889999998766543

>3kto_A Response regulator receiver protein; PSI-II,structural genomics, protein structure initiative; 1.98A {Pseudoalteromonas atlantica T6C} SCOP: c.23.1.0

Probab=99.27  E-value=4.1e-12  Score=64.64  Aligned_cols=75  Identities=9%  Similarity=0.036  Sum_probs=52.9

Q ss_pred             CchhHHHHHHHHhcCCCceeeec--ChhHHhh---ccCccEEEEeCCCCC--CCHHHHHHHHHhhcCCCCCccEEEEeeC
Q 039883            2 TTTNGVLLSRLMSDGSDGFDLSP--TDTEEVH---VLAVDLIITDYCMPG--MTGCELIKKIKLQSFTFREIPTVIISSE   74 (82)
Q Consensus         2 d~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~---~~~~d~vi~d~~~~~--~~~~~~~~~l~~~~~~~~~~~vi~ls~~   74 (82)
                      |++..............+|++..  ++.+++.   ..+||+||+|+.+|+  .+|+++++.++   ...+.+|+|++|+.
T Consensus        13 dd~~~~~~~l~~~L~~~g~~v~~~~~~~~a~~~l~~~~~dlvi~D~~l~~~~~~g~~~~~~l~---~~~~~~~ii~~s~~   89 (136)
T 3kto_A           13 DHQKDARAALSKLLSPLDVTIQCFASAESFMRQQISDDAIGMIIEAHLEDKKDSGIELLETLV---KRGFHLPTIVMASS   89 (136)
T ss_dssp             CSCHHHHHHHHHHHTTSSSEEEEESSHHHHTTSCCCTTEEEEEEETTGGGBTTHHHHHHHHHH---HTTCCCCEEEEESS
T ss_pred             cCCHHHHHHHHHHHHHCCcEEEEeCCHHHHHHHHhccCCCEEEEeCcCCCCCccHHHHHHHHH---hCCCCCCEEEEEcC
Confidence            34444444444444445666543  4445543   457999999999999  99999999999   45688999999988


Q ss_pred             Cchhh
Q 039883           75 NILAR   79 (82)
Q Consensus        75 ~~~~~   79 (82)
                      .+.+.
T Consensus        90 ~~~~~   94 (136)
T 3kto_A           90 SDIPT   94 (136)
T ss_dssp             CCHHH
T ss_pred             CCHHH
Confidence            76543

>1mb3_A Cell division response regulator DIVK; signal transduction protein, structural proteomics in europe, spine, structural genomics; 1.41A {Caulobacter vibrioides} SCOP: c.23.1.1 PDB: 1m5u_A 1mav_A 1mb0_A 1m5t_A

Probab=99.26  E-value=9.8e-12  Score=62.06  Aligned_cols=60  Identities=22%  Similarity=0.384  Sum_probs=40.8

Q ss_pred             Cceee--ecChhHH---hhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCchh
Q 039883           18 DGFDL--SPTDTEE---VHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENILA   78 (82)
Q Consensus        18 ~~~~~--~~~~~~~---~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~~~   78 (82)
                      .++.+  +.++.++   +...+||++|+|+.||+++|+++++.++ .....+.+|+|++|+..+..
T Consensus        24 ~~~~v~~~~~~~~a~~~~~~~~~dlvi~D~~l~~~~g~~~~~~l~-~~~~~~~~~ii~~s~~~~~~   88 (124)
T 1mb3_A           24 QGYETLQTREGLSALSIARENKPDLILMDIQLPEISGLEVTKWLK-EDDDLAHIPVVAVTAFAMKG   88 (124)
T ss_dssp             TTCEEEEESCHHHHHHHHHHHCCSEEEEESBCSSSBHHHHHHHHH-HSTTTTTSCEEEEC------
T ss_pred             cCcEEEEeCCHHHHHHHHhcCCCCEEEEeCCCCCCCHHHHHHHHH-cCccccCCcEEEEECCCCHH
Confidence            34444  3344443   4456899999999999999999999999 33345688999999875543

>1p6q_A CHEY2; chemotaxis, signal transduction, response regulator, structural proteomics in europe, spine, structural genomics; NMR {Sinorhizobium meliloti} SCOP: c.23.1.1 PDB: 1p6u_A

Probab=99.26  E-value=2.5e-11  Score=60.99  Aligned_cols=50  Identities=20%  Similarity=0.343  Sum_probs=40.2

Q ss_pred             HhhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCchhh
Q 039883           29 EVHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENILAR   79 (82)
Q Consensus        29 ~~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~~~~   79 (82)
                      .+...+||++++|+.+|+++|+++++.++ .....+.+|+|++|+..+...
T Consensus        46 ~~~~~~~dlvl~D~~l~~~~g~~~~~~l~-~~~~~~~~~ii~~s~~~~~~~   95 (129)
T 1p6q_A           46 IMAQNPHHLVISDFNMPKMDGLGLLQAVR-ANPATKKAAFIILTAQGDRAL   95 (129)
T ss_dssp             HHHTSCCSEEEECSSSCSSCHHHHHHHHT-TCTTSTTCEEEECCSCCCHHH
T ss_pred             HHHcCCCCEEEEeCCCCCCCHHHHHHHHh-cCccccCCCEEEEeCCCCHHH
Confidence            34456899999999999999999999999 322357889999998766543

>3grc_A Sensor protein, kinase; protein structure initiative II(PSI II), NYSGXRC, 11025B, structural genomics; 2.21A {Polaromonas SP}

Probab=99.26  E-value=1.5e-11  Score=62.67  Aligned_cols=61  Identities=16%  Similarity=0.287  Sum_probs=46.0

Q ss_pred             CceeeecChhH---HhhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCchhh
Q 039883           18 DGFDLSPTDTE---EVHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENILAR   79 (82)
Q Consensus        18 ~~~~~~~~~~~---~~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~~~~   79 (82)
                      ..+..+.++.+   .+...+||+||+|+.+|+.+|+++++.++ .....+.+|+|++|+..+...
T Consensus        31 ~~v~~~~~~~~a~~~l~~~~~dlvi~d~~l~~~~g~~~~~~l~-~~~~~~~~~ii~~s~~~~~~~   94 (140)
T 3grc_A           31 FDSDMVHSAAQALEQVARRPYAAMTVDLNLPDQDGVSLIRALR-RDSRTRDLAIVVVSANAREGE   94 (140)
T ss_dssp             CEEEEECSHHHHHHHHHHSCCSEEEECSCCSSSCHHHHHHHHH-TSGGGTTCEEEEECTTHHHHH
T ss_pred             CeEEEECCHHHHHHHHHhCCCCEEEEeCCCCCCCHHHHHHHHH-hCcccCCCCEEEEecCCChHH
Confidence            33444445544   44566899999999999999999999999 322678899999998765543

>3crn_A Response regulator receiver domain protein, CHEY-; structural genomics, signal regulator receiver domain; HET: PHD; 1.58A {Methanospirillum hungatei jf-1}

Probab=99.26  E-value=8e-12  Score=63.28  Aligned_cols=59  Identities=19%  Similarity=0.349  Sum_probs=44.6

Q ss_pred             Cceee--ecChhHH---hhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCchhh
Q 039883           18 DGFDL--SPTDTEE---VHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENILAR   79 (82)
Q Consensus        18 ~~~~~--~~~~~~~---~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~~~~   79 (82)
                      .+|.+  +.++.++   +...+||++|+|+.+|+++|+++++.++   ...+.+|+|++|+..+...
T Consensus        26 ~g~~v~~~~~~~~al~~~~~~~~dlvl~D~~l~~~~g~~~~~~l~---~~~~~~~ii~~s~~~~~~~   89 (132)
T 3crn_A           26 EGYEVEIAATAGEGLAKIENEFFNLALFXIKLPDMEGTELLEKAH---KLRPGMKKIMVTGYASLEN   89 (132)
T ss_dssp             TTCEEEEESSHHHHHHHHHHSCCSEEEECSBCSSSBHHHHHHHHH---HHCTTSEEEEEESCCCHHH
T ss_pred             CCceEEEeCCHHHHHHHHhcCCCCEEEEecCCCCCchHHHHHHHH---hhCCCCcEEEEeccccHHH
Confidence            34444  4444443   4456899999999999999999999998   3456899999998766543

>3luf_A Two-component system response regulator/ggdef domain protein; structural genomics, ASA_2441, PSI-2, protein structure initiative; HET: MSE; 1.76A {Aeromonas salmonicida} PDB: 3mf4_A*

Probab=99.26  E-value=1.6e-11  Score=68.81  Aligned_cols=77  Identities=14%  Similarity=0.290  Sum_probs=51.0

Q ss_pred             CchhHHHHHHHHhcCCCceee--ecChhHHhh---cc-CccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCC
Q 039883            2 TTTNGVLLSRLMSDGSDGFDL--SPTDTEEVH---VL-AVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSEN   75 (82)
Q Consensus         2 d~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~---~~-~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~   75 (82)
                      |++..............++.+  +.++.+++.   .. .||+||+|+.||+++|+++++.+| .......+|+|++|+..
T Consensus       131 DD~~~~~~~l~~~L~~~~~~v~~a~~~~eal~~l~~~~~~dlvllD~~mP~~dG~~l~~~lr-~~~~~~~~~ii~~s~~~  209 (259)
T 3luf_A          131 DDSRTSRHRTMAQLRKQLLQVHEASHAREALATLEQHPAIRLVLVDYYMPEIDGISLVRMLR-ERYSKQQLAIIGISVSD  209 (259)
T ss_dssp             CSCHHHHHHHHHHHHTTTCEEEEESSHHHHHHHHHHCTTEEEEEECSCCSSSCHHHHHHHHH-HHCCTTTSEEEEEECSS
T ss_pred             eCCHHHHHHHHHHHHHcCcEEEEeCCHHHHHHHHhcCCCCCEEEEcCCCCCCCHHHHHHHHH-hccCCCCCeEEEEEccC
Confidence            344444433333333445554  445555443   34 389999999999999999999999 33345578999999876


Q ss_pred             chhh
Q 039883           76 ILAR   79 (82)
Q Consensus        76 ~~~~   79 (82)
                      +...
T Consensus       210 ~~~~  213 (259)
T 3luf_A          210 KRGL  213 (259)
T ss_dssp             SSSH
T ss_pred             CHHH
Confidence            6543

>3c3m_A Response regulator receiver protein; structural genomics, unknown function, PSI-2, protein struct initiative; HET: MSE; 1.70A {Methanoculleus marisnigri JR1}

Probab=99.26  E-value=3.5e-11  Score=61.33  Aligned_cols=58  Identities=24%  Similarity=0.464  Sum_probs=43.3

Q ss_pred             Cceee--ecChhHH---hhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCc
Q 039883           18 DGFDL--SPTDTEE---VHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENI   76 (82)
Q Consensus        18 ~~~~~--~~~~~~~---~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~   76 (82)
                      .+|.+  +.++.++   +...+||++|+|+.+|+++|+++++.++ .....+.+|+|++|+..+
T Consensus        26 ~g~~v~~~~~~~~al~~l~~~~~dlvi~D~~l~~~~g~~~~~~l~-~~~~~~~~~ii~ls~~~~   88 (138)
T 3c3m_A           26 GGYRPITAFSGEECLEALNATPPDLVLLDIMMEPMDGWETLERIK-TDPATRDIPVLMLTAKPL   88 (138)
T ss_dssp             TTCEEEEESSHHHHHHHHHHSCCSEEEEESCCSSSCHHHHHHHHH-HSTTTTTSCEEEEESSCC
T ss_pred             cCceEEEeCCHHHHHHHHhccCCCEEEEeCCCCCCCHHHHHHHHH-cCcccCCCCEEEEECCCC
Confidence            34544  3344443   4456899999999999999999999999 333456789999998653

>3dzd_A Transcriptional regulator (NTRC family); sigma43 activator, AAA+ ATPase, response regulator, transcriptional activator, ATP-binding; HET: ADP; 2.40A {Aquifex aeolicus} PDB: 1zit_A 2jrl_A

Probab=99.25  E-value=1.3e-12  Score=76.52  Aligned_cols=75  Identities=19%  Similarity=0.226  Sum_probs=53.2

Q ss_pred             CchhHHHHHHHHhcCCCceee--ecChhHH---hhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCc
Q 039883            2 TTTNGVLLSRLMSDGSDGFDL--SPTDTEE---VHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENI   76 (82)
Q Consensus         2 d~~~~~~~~~~~~~~~~~~~~--~~~~~~~---~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~   76 (82)
                      |+++.............+|.+  +.++.++   +...+||+||+|+.||+++|+++++.++   ...+.+|||++|+..+
T Consensus         7 DDd~~~~~~l~~~L~~~g~~v~~a~~~~eal~~l~~~~~DlvllDi~mP~~dG~ell~~lr---~~~~~~pvI~lT~~~~   83 (368)
T 3dzd_A            7 DDEESITSSLSAILEEEGYHPDTAKTLREAEKKIKELFFPVIVLDVWMPDGDGVNFIDFIK---ENSPDSVVIVITGHGS   83 (368)
T ss_dssp             CSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHHHHBCCSEEEEESEETTEETTTHHHHHH---HHCTTCEEEEEECSSC
T ss_pred             eCCHHHHHHHHHHHHHcCCEEEEECCHHHHHHHHHhCCCCEEEEeCCCCCCCHHHHHHHHH---hhCCCCeEEEEeCCCC
Confidence            455555444433333344544  4445444   4566899999999999999999999999   4567899999999876


Q ss_pred             hhh
Q 039883           77 LAR   79 (82)
Q Consensus        77 ~~~   79 (82)
                      .+.
T Consensus        84 ~~~   86 (368)
T 3dzd_A           84 VDT   86 (368)
T ss_dssp             CHH
T ss_pred             HHH
Confidence            544

>3eod_A Protein HNR; response regulator, phosphoprotein, two-component regulatory system, signaling protein; 1.75A {Escherichia coli K12}

Probab=99.25  E-value=8e-12  Score=62.96  Aligned_cols=59  Identities=25%  Similarity=0.403  Sum_probs=40.6

Q ss_pred             CceeeecChhHH---hhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCchhh
Q 039883           18 DGFDLSPTDTEE---VHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENILAR   79 (82)
Q Consensus        18 ~~~~~~~~~~~~---~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~~~~   79 (82)
                      ..+..+.++.++   +...+||+||+|+.+|+.+|+++++.++   ...+.+|+|++|+..+...
T Consensus        32 ~~v~~~~~~~~a~~~l~~~~~dlvi~d~~l~~~~g~~~~~~l~---~~~~~~~ii~~t~~~~~~~   93 (130)
T 3eod_A           32 ATTVLAADGVDALELLGGFTPDLMICDIAMPRMNGLKLLEHIR---NRGDQTPVLVISATENMAD   93 (130)
T ss_dssp             CEEEEESCHHHHHHHHTTCCCSEEEECCC-----CHHHHHHHH---HTTCCCCEEEEECCCCHHH
T ss_pred             ceEEEeCCHHHHHHHHhcCCCCEEEEecCCCCCCHHHHHHHHH---hcCCCCCEEEEEcCCCHHH
Confidence            333334444444   4456899999999999999999999999   4577899999998876653

>3b2n_A Uncharacterized protein Q99UF4; structural genomics, PSI-2, protein structure initiative, NE SGX research center for structural genomics; 2.04A {Staphylococcus aureus}

Probab=99.24  E-value=1.5e-11  Score=62.39  Aligned_cols=54  Identities=22%  Similarity=0.384  Sum_probs=43.0

Q ss_pred             ecChhHH---hhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCchhh
Q 039883           23 SPTDTEE---VHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENILAR   79 (82)
Q Consensus        23 ~~~~~~~---~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~~~~   79 (82)
                      +.++.++   +...+||++|+|+.||+++|+++++.++   ...+.+|+|++|+..+...
T Consensus        35 ~~~~~~al~~~~~~~~dlvilD~~lp~~~g~~~~~~l~---~~~~~~~ii~ls~~~~~~~   91 (133)
T 3b2n_A           35 TDNGLDAMKLIEEYNPNVVILDIEMPGMTGLEVLAEIR---KKHLNIKVIIVTTFKRPGY   91 (133)
T ss_dssp             ESCHHHHHHHHHHHCCSEEEECSSCSSSCHHHHHHHHH---HTTCSCEEEEEESCCCHHH
T ss_pred             cCCHHHHHHHHhhcCCCEEEEecCCCCCCHHHHHHHHH---HHCCCCcEEEEecCCCHHH
Confidence            3444444   4456899999999999999999999999   4567899999998876543

>3a10_A Response regulator; phosphoacceptor, signaling protein; HET: MSE PG4; 1.63A {Thermotoga maritima} PDB: 3a0r_B* 3a0u_A*

Probab=99.24  E-value=2.2e-11  Score=60.20  Aligned_cols=57  Identities=21%  Similarity=0.448  Sum_probs=43.1

Q ss_pred             Cceee--ecChhHH---hhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCch
Q 039883           18 DGFDL--SPTDTEE---VHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENIL   77 (82)
Q Consensus        18 ~~~~~--~~~~~~~---~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~~   77 (82)
                      .++.+  +.++.++   +...+||++++|+.+|+.+|.++++.++   ...+.+|+|++|+..+.
T Consensus        24 ~~~~v~~~~~~~~a~~~~~~~~~dlvl~D~~l~~~~g~~~~~~l~---~~~~~~~ii~~s~~~~~   85 (116)
T 3a10_A           24 EGYEIDTAENGEEALKKFFSGNYDLVILDIEMPGISGLEVAGEIR---KKKKDAKIILLTAYSHY   85 (116)
T ss_dssp             TTCEEEEESSHHHHHHHHHHSCCSEEEECSCCSSSCHHHHHHHHH---HHCTTCCEEEEESCGGG
T ss_pred             CCCEEEEeCCHHHHHHHHhcCCCCEEEEECCCCCCCHHHHHHHHH---ccCCCCeEEEEECCcch
Confidence            34444  4444443   4456899999999999999999999998   34578899999986543

>3nhm_A Response regulator; protein structure initiative II(PSI II), NYSGXRC, structural genomics; 2.19A {Myxococcus xanthus}

Probab=99.24  E-value=7.3e-11  Score=59.54  Aligned_cols=61  Identities=20%  Similarity=0.298  Sum_probs=44.6

Q ss_pred             CCceeeecChhH---HhhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCchh
Q 039883           17 SDGFDLSPTDTE---EVHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENILA   78 (82)
Q Consensus        17 ~~~~~~~~~~~~---~~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~~~   78 (82)
                      +..+..+.+..+   .+...+||+||+|+.+|+.+|+++++.++ .....+.+|+|++|+..+..
T Consensus        27 ~~~v~~~~~~~~a~~~l~~~~~dlvi~d~~l~~~~g~~~~~~l~-~~~~~~~~pii~~s~~~~~~   90 (133)
T 3nhm_A           27 EFDCTTAADGASGLQQALAHPPDVLISDVNMDGMDGYALCGHFR-SEPTLKHIPVIFVSGYAPRT   90 (133)
T ss_dssp             TSEEEEESSHHHHHHHHHHSCCSEEEECSSCSSSCHHHHHHHHH-HSTTTTTCCEEEEESCCC--
T ss_pred             CcEEEEECCHHHHHHHHhcCCCCEEEEeCCCCCCCHHHHHHHHH-hCCccCCCCEEEEeCCCcHh
Confidence            333344444444   44566899999999999999999999999 43346689999999876543

>1zgz_A Torcad operon transcriptional regulatory protein; two-component system, gene regulation, transcription factor, respiratory system; 1.80A {Escherichia coli} SCOP: c.23.1.1

Probab=99.24  E-value=3.6e-11  Score=59.88  Aligned_cols=46  Identities=17%  Similarity=0.287  Sum_probs=38.9

Q ss_pred             HhhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCchh
Q 039883           29 EVHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENILA   78 (82)
Q Consensus        29 ~~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~~~   78 (82)
                      .+...+||++|+|+.+|+++|+++++.++   . .+.+|+|++|+..+..
T Consensus        41 ~~~~~~~dlvi~d~~l~~~~g~~~~~~l~---~-~~~~~ii~~s~~~~~~   86 (122)
T 1zgz_A           41 IMQNQSVDLILLDINLPDENGLMLTRALR---E-RSTVGIILVTGRSDRI   86 (122)
T ss_dssp             HHHHSCCSEEEEESCCSSSCHHHHHHHHH---T-TCCCEEEEEESSCCHH
T ss_pred             HHhcCCCCEEEEeCCCCCCChHHHHHHHH---h-cCCCCEEEEECCCChh
Confidence            34456899999999999999999999999   4 5678999999876654

>1w25_A Stalked-cell differentiation controlling protein; two-component system, ggdef domain, cyclic dinucleotide, cyclic-digmp; HET: C2E; 2.70A {Caulobacter vibrioides} SCOP: c.23.1.1 c.23.1.1 d.58.29.2 PDB: 2v0n_A* 2wb4_A*

Probab=99.23  E-value=1.8e-11  Score=72.94  Aligned_cols=61  Identities=26%  Similarity=0.349  Sum_probs=46.1

Q ss_pred             CceeeecChhHHh---hccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCchhh
Q 039883           18 DGFDLSPTDTEEV---HVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENILAR   79 (82)
Q Consensus        18 ~~~~~~~~~~~~~---~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~~~~   79 (82)
                      ..+..+.++.+++   ...+||+||+|+.||+++|+++++.++ .....+.+|||++|+..+.+.
T Consensus        26 ~~v~~a~~~~~al~~~~~~~~dlvllD~~mp~~~G~~~~~~l~-~~~~~~~~pii~lt~~~~~~~   89 (459)
T 1w25_A           26 YEVSTAMDGPTALAMAARDLPDIILLDVMMPGMDGFTVCRKLK-DDPTTRHIPVVLITALDGRGD   89 (459)
T ss_dssp             CEEEEESSHHHHHHHHHHHCCSEEEEESCCSSSCHHHHHHHHH-HSTTTTTSCEEEEECSSCHHH
T ss_pred             CEEEEECCHHHHHHHHhcCCCCEEEEcCCCCCCCHHHHHHHHh-cCcccCCCCEEEEECCCCHHH
Confidence            3333444555444   455899999999999999999999999 333456899999999877654

>3hdg_A Uncharacterized protein; two-component sensor activity, response regulator, PSI-II, 11227F, NYSGXRC, structural genomics; 2.27A {Wolinella succinogenes} SCOP: c.23.1.0

Probab=99.23  E-value=2e-11  Score=61.96  Aligned_cols=59  Identities=25%  Similarity=0.247  Sum_probs=45.9

Q ss_pred             CceeeecChhHH---hhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCchhh
Q 039883           18 DGFDLSPTDTEE---VHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENILAR   79 (82)
Q Consensus        18 ~~~~~~~~~~~~---~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~~~~   79 (82)
                      ..+..+.+..++   +...+||+||+|+.+|+.+|+++++.++   ...+.+|+|++|+..+.+.
T Consensus        32 ~~v~~~~~~~~a~~~l~~~~~dlvi~d~~l~~~~g~~~~~~l~---~~~~~~~ii~~s~~~~~~~   93 (137)
T 3hdg_A           32 PEVWSAGDGEEGERLFGLHAPDVIITDIRMPKLGGLEMLDRIK---AGGAKPYVIVISAFSEMKY   93 (137)
T ss_dssp             SCEEEESSHHHHHHHHHHHCCSEEEECSSCSSSCHHHHHHHHH---HTTCCCEEEECCCCCCHHH
T ss_pred             cEEEEECCHHHHHHHHhccCCCEEEEeCCCCCCCHHHHHHHHH---hcCCCCcEEEEecCcChHH
Confidence            334445555543   4556899999999999999999999999   4568899999998876543

>1tmy_A CHEY protein, TMY; chemotaxis, phosphoryl transfer, signal transduction; 1.90A {Thermotoga maritima} SCOP: c.23.1.1 PDB: 2tmy_A 3tmy_A 4tmy_A 1u0s_Y

Probab=99.23  E-value=1.2e-11  Score=61.46  Aligned_cols=59  Identities=24%  Similarity=0.356  Sum_probs=44.9

Q ss_pred             CCceee---ecChhHH---hhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCchh
Q 039883           17 SDGFDL---SPTDTEE---VHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENILA   78 (82)
Q Consensus        17 ~~~~~~---~~~~~~~---~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~~~   78 (82)
                      ..+|++   +.++.++   +...+||++++|+.+|+.+|.++++.++   ...+.+|+|++|+..+..
T Consensus        24 ~~g~~vv~~~~~~~~a~~~~~~~~~dlil~D~~l~~~~g~~~~~~l~---~~~~~~~ii~~s~~~~~~   88 (120)
T 1tmy_A           24 KAGYEVAGEATNGREAVEKYKELKPDIVTMDITMPEMNGIDAIKEIM---KIDPNAKIIVCSAMGQQA   88 (120)
T ss_dssp             HTTCEEEEEESSHHHHHHHHHHHCCSEEEEECSCGGGCHHHHHHHHH---HHCTTCCEEEEECTTCHH
T ss_pred             hcCcEEEEEECCHHHHHHHHHhcCCCEEEEeCCCCCCcHHHHHHHHH---hhCCCCeEEEEeCCCCHH
Confidence            445653   3344443   4456899999999999999999999998   345788999999876654

>4e7p_A Response regulator; DNA binding, cytosol, transcription regulator; 1.89A {Streptococcus pneumoniae} PDB: 4e7o_A

Probab=99.23  E-value=4.8e-11  Score=61.57  Aligned_cols=54  Identities=24%  Similarity=0.266  Sum_probs=43.8

Q ss_pred             ecChhHH---hhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCchhh
Q 039883           23 SPTDTEE---VHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENILAR   79 (82)
Q Consensus        23 ~~~~~~~---~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~~~~   79 (82)
                      +.+..++   +...+||+||+|+.+|+.+|+++++.++   ...+.+|+|++|+..+.+.
T Consensus        52 ~~~~~~al~~l~~~~~dlii~D~~l~~~~g~~~~~~l~---~~~~~~~ii~ls~~~~~~~  108 (150)
T 4e7p_A           52 AKNGQEAIQLLEKESVDIAILDVEMPVKTGLEVLEWIR---SEKLETKVVVVTTFKRAGY  108 (150)
T ss_dssp             ESSHHHHHHHHTTSCCSEEEECSSCSSSCHHHHHHHHH---HTTCSCEEEEEESCCCHHH
T ss_pred             ECCHHHHHHHhhccCCCEEEEeCCCCCCcHHHHHHHHH---HhCCCCeEEEEeCCCCHHH
Confidence            4444444   4566899999999999999999999999   4578899999998876543

>1kgs_A DRRD, DNA binding response regulator D; DNA-binding protein, ALPH-beta sandwich, winged-helix, helix helix, DNA binding protein; HET: DNA MSE; 1.50A {Thermotoga maritima} SCOP: a.4.6.1 c.23.1.1 PDB: 3nnn_A*

Probab=99.22  E-value=2.6e-11  Score=66.15  Aligned_cols=59  Identities=17%  Similarity=0.274  Sum_probs=45.5

Q ss_pred             Cceee--ecChhHH---hhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCchhh
Q 039883           18 DGFDL--SPTDTEE---VHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENILAR   79 (82)
Q Consensus        18 ~~~~~--~~~~~~~---~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~~~~   79 (82)
                      .++++  +.++.++   +...+||++|+|+.+|+++|+++++.++   ...+.+|+|++|+..+.+.
T Consensus        25 ~g~~v~~~~~~~~a~~~~~~~~~dlvllD~~l~~~~g~~~~~~lr---~~~~~~~ii~ls~~~~~~~   88 (225)
T 1kgs_A           25 EMFTVDVCYDGEEGMYMALNEPFDVVILDIMLPVHDGWEILKSMR---ESGVNTPVLMLTALSDVEY   88 (225)
T ss_dssp             TTCEEEEESSHHHHHHHHHHSCCSEEEEESCCSSSCHHHHHHHHH---HTTCCCCEEEEESSCHHHH
T ss_pred             CCCEEEEECCHHHHHHHHhcCCCCEEEEeCCCCCCCHHHHHHHHH---hcCCCCCEEEEeCCCCHHH
Confidence            44544  4444444   4456899999999999999999999999   4567899999998876543

>3hdv_A Response regulator; PSI-II, structural genomics, Pro structure initiative, NEW YORK SGX research center for STRU genomics, nysgxrc; 2.09A {Pseudomonas putida} SCOP: c.23.1.0

Probab=99.22  E-value=2.8e-11  Score=61.34  Aligned_cols=59  Identities=20%  Similarity=0.292  Sum_probs=44.1

Q ss_pred             CceeeecChhHH---hhccC-ccEEEEeCCCCCCCHHHHHHHHHhhcCC-CCCccEEEEeeCCchhh
Q 039883           18 DGFDLSPTDTEE---VHVLA-VDLIITDYCMPGMTGCELIKKIKLQSFT-FREIPTVIISSENILAR   79 (82)
Q Consensus        18 ~~~~~~~~~~~~---~~~~~-~d~vi~d~~~~~~~~~~~~~~l~~~~~~-~~~~~vi~ls~~~~~~~   79 (82)
                      ..+..+.+..++   +.... ||+||+|+.+|+.+|+++++.++   .. .+.+|+|++|+..+.+.
T Consensus        32 ~~v~~~~~~~~a~~~~~~~~~~dlvi~D~~l~~~~g~~~~~~l~---~~~~~~~~ii~~s~~~~~~~   95 (136)
T 3hdv_A           32 IDAVGADGAEEARLYLHYQKRIGLMITDLRMQPESGLDLIRTIR---ASERAALSIIVVSGDTDVEE   95 (136)
T ss_dssp             CCEEEESSHHHHHHHHHHCTTEEEEEECSCCSSSCHHHHHHHHH---TSTTTTCEEEEEESSCCHHH
T ss_pred             ceEEEeCCHHHHHHHHHhCCCCcEEEEeccCCCCCHHHHHHHHH---hcCCCCCCEEEEeCCCChHH
Confidence            333334444443   33444 99999999999999999999999   44 68899999998876543

>3snk_A Response regulator CHEY-like protein; P-loop containing nucleoside triphosphate hydrolases, struct genomics; 2.02A {Mesorhizobium loti}

Probab=99.22  E-value=2.3e-12  Score=65.50  Aligned_cols=74  Identities=14%  Similarity=0.076  Sum_probs=51.1

Q ss_pred             chhHHHHHHHHhcCCCc-eeeec--ChhHHh---hccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCc
Q 039883            3 TTNGVLLSRLMSDGSDG-FDLSP--TDTEEV---HVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENI   76 (82)
Q Consensus         3 ~~~~~~~~~~~~~~~~~-~~~~~--~~~~~~---~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~   76 (82)
                      ++..............+ |++..  ++.+++   ...+||+||+|+.+|+.+|+++++.++   ...+.+|+|++|+..+
T Consensus        22 d~~~~~~~l~~~L~~~g~~~v~~~~~~~~a~~~l~~~~~dlvi~D~~l~~~~g~~~~~~l~---~~~~~~~ii~~s~~~~   98 (135)
T 3snk_A           22 SDPNFKRDVATRLDALAIYDVRVSETDDFLKGPPADTRPGIVILDLGGGDLLGKPGIVEAR---ALWATVPLIAVSDELT   98 (135)
T ss_dssp             SCHHHHHHHHHHHHHTSSEEEEEECGGGGGGCCCTTCCCSEEEEEEETTGGGGSTTHHHHH---GGGTTCCEEEEESCCC
T ss_pred             CCHHHHHHHHHHHhhcCCeEEEEeccHHHHHHHHhccCCCEEEEeCCCCCchHHHHHHHHH---hhCCCCcEEEEeCCCC
Confidence            33343333333333345 65543  334444   455799999999999999999999999   4566899999999876


Q ss_pred             hhh
Q 039883           77 LAR   79 (82)
Q Consensus        77 ~~~   79 (82)
                      .+.
T Consensus        99 ~~~  101 (135)
T 3snk_A           99 SEQ  101 (135)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            544

>1i3c_A Response regulator RCP1; phytochrome, signaling protein; 1.90A {Synechocystis SP} SCOP: c.23.1.1 PDB: 1jlk_A

Probab=99.22  E-value=7.5e-11  Score=60.81  Aligned_cols=46  Identities=26%  Similarity=0.453  Sum_probs=38.1

Q ss_pred             cCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCchhh
Q 039883           33 LAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENILAR   79 (82)
Q Consensus        33 ~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~~~~   79 (82)
                      .+||++|+|+.||+++|+++++.++ .....+.+|+|++|+..+...
T Consensus        60 ~~~dlillD~~lp~~~g~~l~~~l~-~~~~~~~~piiils~~~~~~~  105 (149)
T 1i3c_A           60 PRPNLILLDLNLPKKDGREVLAEIK-QNPDLKRIPVVVLTTSHNEDD  105 (149)
T ss_dssp             CCCSEEEECSCCSSSCHHHHHHHHH-HCTTTTTSCEEEEESCCCHHH
T ss_pred             CCCCEEEEeCCCCCCcHHHHHHHHH-hCcCcCCCeEEEEECCCChHH
Confidence            4699999999999999999999999 333346889999998776543

>1jbe_A Chemotaxis protein CHEY; signaling protein; 1.08A {Escherichia coli} SCOP: c.23.1.1 PDB: 3chy_A 1a0o_A 1cey_A 1bdj_A 1eay_A 1f4v_A 1ffg_A 1ffs_A 1ffw_A 1fqw_A 2b1j_A 1chn_A 1djm_A 1kmi_Y* 1d4z_A 3olx_A 3olw_A 1cye_A 2che_A 2chf_A ...

Probab=99.21  E-value=4.8e-11  Score=59.89  Aligned_cols=59  Identities=20%  Similarity=0.474  Sum_probs=44.0

Q ss_pred             eeeecChhHHh---hccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCchhh
Q 039883           20 FDLSPTDTEEV---HVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENILAR   79 (82)
Q Consensus        20 ~~~~~~~~~~~---~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~~~~   79 (82)
                      +..+.++.+++   ...+||++++|+.+|+++|+++++.++ .....+.+|+|++|+..+.+.
T Consensus        32 v~~~~~~~~a~~~~~~~~~dlvi~D~~l~~~~g~~l~~~l~-~~~~~~~~~ii~~s~~~~~~~   93 (128)
T 1jbe_A           32 VEEAEDGVDALNKLQAGGYGFVISDWNMPNMDGLELLKTIR-AXXAMSALPVLMVTAEAKKEN   93 (128)
T ss_dssp             EEEESSHHHHHHHHTTCCCCEEEEESCCSSSCHHHHHHHHH-C--CCTTCCEEEEESSCCHHH
T ss_pred             EEeeCCHHHHHHHHHhcCCCEEEEeCCCCCCCHHHHHHHHH-hhcccCCCcEEEEecCccHHH
Confidence            34444555443   455799999999999999999999999 322457889999998766543

>3mm4_A Histidine kinase homolog; receiver domain, CKI1, cytokinin signaling, ROS fold, CHEY-like, transferase; 2.00A {Arabidopsis thaliana} PDB: 3mmn_A

Probab=99.21  E-value=2.4e-11  Score=66.01  Aligned_cols=42  Identities=26%  Similarity=0.377  Sum_probs=35.6

Q ss_pred             CccEEEEeCCCCCCCHHHHHHHHHhhc-CCCCCccEEEEeeCC
Q 039883           34 AVDLIITDYCMPGMTGCELIKKIKLQS-FTFREIPTVIISSEN   75 (82)
Q Consensus        34 ~~d~vi~d~~~~~~~~~~~~~~l~~~~-~~~~~~~vi~ls~~~   75 (82)
                      +||+||+|+.||+++|+++++.++... ...+.+|+|++|+..
T Consensus       119 ~~dlillD~~lp~~~G~el~~~lr~~~~~~~~~~piI~ls~~~  161 (206)
T 3mm4_A          119 PFDYIFMDCQMPEMDGYEATREIRKVEKSYGVRTPIIAVSGHD  161 (206)
T ss_dssp             SCSEEEEESCCSSSCHHHHHHHHHHHHHTTTCCCCEEEEESSC
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhhhhhcCCCCcEEEEECCC
Confidence            799999999999999999999999211 125789999999876

>3ilh_A Two component response regulator; NYSGXRC, PSI-II, protein S initiative, structural genomics; 2.59A {Cytophaga hutchinsonii}

Probab=99.21  E-value=4.7e-11  Score=60.99  Aligned_cols=46  Identities=30%  Similarity=0.323  Sum_probs=39.1

Q ss_pred             cCccEEEEeCCCCCCCHHHHHHHHHhhcC--CCCCccEEEEeeCCchhh
Q 039883           33 LAVDLIITDYCMPGMTGCELIKKIKLQSF--TFREIPTVIISSENILAR   79 (82)
Q Consensus        33 ~~~d~vi~d~~~~~~~~~~~~~~l~~~~~--~~~~~~vi~ls~~~~~~~   79 (82)
                      .+||+||+|+.+|+++|+++++.++ ...  ..+.+|+|++|+..+...
T Consensus        59 ~~~dlvi~D~~l~~~~g~~~~~~l~-~~~~~~~~~~~ii~~t~~~~~~~  106 (146)
T 3ilh_A           59 RWPSIICIDINMPGINGWELIDLFK-QHFQPMKNKSIVCLLSSSLDPRD  106 (146)
T ss_dssp             CCCSEEEEESSCSSSCHHHHHHHHH-HHCGGGTTTCEEEEECSSCCHHH
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHH-HhhhhccCCCeEEEEeCCCChHH
Confidence            7799999999999999999999999 322  568899999998876544

>1ys7_A Transcriptional regulatory protein PRRA; response regulator, DNA binding domain, phosphorylation; 1.58A {Mycobacterium tuberculosis} SCOP: a.4.6.1 c.23.1.1 PDB: 1ys6_A

Probab=99.21  E-value=4.1e-11  Score=65.66  Aligned_cols=58  Identities=19%  Similarity=0.409  Sum_probs=44.9

Q ss_pred             Cceee--ecChhHH---hhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCchh
Q 039883           18 DGFDL--SPTDTEE---VHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENILA   78 (82)
Q Consensus        18 ~~~~~--~~~~~~~---~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~~~   78 (82)
                      .++++  +.++.++   +...+||++|+|+.+|+++|+++++.++   ...+.+|+|++|+..+.+
T Consensus        30 ~g~~v~~~~~~~~a~~~~~~~~~dlvllD~~l~~~~g~~~~~~l~---~~~~~~~ii~lt~~~~~~   92 (233)
T 1ys7_A           30 SGFEVATAVDGAEALRSATENRPDAIVLDINMPVLDGVSVVTALR---AMDNDVPVCVLSARSSVD   92 (233)
T ss_dssp             TTCEEEEESSHHHHHHHHHHSCCSEEEEESSCSSSCHHHHHHHHH---HTTCCCCEEEEECCCTTT
T ss_pred             CCCEEEEECCHHHHHHHHHhCCCCEEEEeCCCCCCCHHHHHHHHH---hcCCCCCEEEEEcCCCHH
Confidence            34544  3344444   4456899999999999999999999999   446789999999876654

>3jte_A Response regulator receiver protein; structural genomics, nysgrc, response regulator receiver DOM target 11226E, PSI-2; 1.90A {Clostridium thermocellum atcc 27405}

Probab=99.21  E-value=3.1e-11  Score=61.66  Aligned_cols=45  Identities=24%  Similarity=0.506  Sum_probs=39.1

Q ss_pred             ccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCchhh
Q 039883           32 VLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENILAR   79 (82)
Q Consensus        32 ~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~~~~   79 (82)
                      ..+||+||+|+.+|+.+|+++++.++   ...+.+|+|++|+..+.+.
T Consensus        47 ~~~~dlvi~d~~l~~~~g~~~~~~l~---~~~~~~~ii~ls~~~~~~~   91 (143)
T 3jte_A           47 CNSIDVVITDMKMPKLSGMDILREIK---KITPHMAVIILTGHGDLDN   91 (143)
T ss_dssp             TTTCCEEEEESCCSSSCHHHHHHHHH---HHCTTCEEEEEECTTCHHH
T ss_pred             CCCCCEEEEeCCCCCCcHHHHHHHHH---HhCCCCeEEEEECCCCHHH
Confidence            45899999999999999999999999   4567899999998876543

>1a04_A Nitrate/nitrite response regulator protein NARL; signal transduction protein, response regulators, two- component systems; 2.20A {Escherichia coli} SCOP: a.4.6.2 c.23.1.1 PDB: 1rnl_A

Probab=99.21  E-value=7.4e-11  Score=64.07  Aligned_cols=75  Identities=20%  Similarity=0.186  Sum_probs=52.2

Q ss_pred             CchhHHHHHHHHhcCCC-ceee---ecChhHH---hhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeC
Q 039883            2 TTTNGVLLSRLMSDGSD-GFDL---SPTDTEE---VHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSE   74 (82)
Q Consensus         2 d~~~~~~~~~~~~~~~~-~~~~---~~~~~~~---~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~   74 (82)
                      |+++............. ++.+   +.++.++   +...+||++|+|+.||+++|+++++.++   ...+.+|+|++|+.
T Consensus        12 dd~~~~~~~l~~~L~~~~~~~vv~~~~~~~~al~~~~~~~~dlvllD~~lp~~~g~~~~~~lr---~~~~~~~ii~ls~~   88 (215)
T 1a04_A           12 DDHPMLRTGVKQLISMAPDITVVGEASNGEQGIELAESLDPDLILLDLNMPGMNGLETLDKLR---EKSLSGRIVVFSVS   88 (215)
T ss_dssp             CSCHHHHHHHHHHHTTCTTEEEEEEESSHHHHHHHHHHHCCSEEEEETTSTTSCHHHHHHHHH---HSCCCSEEEEEECC
T ss_pred             CCCHHHHHHHHHHHhcCCCcEEEEEeCCHHHHHHHHHhcCCCEEEEeCCCCCCcHHHHHHHHH---HhCCCCcEEEEECC
Confidence            44444444333333333 4655   3344444   4456899999999999999999999999   45678999999988


Q ss_pred             Cchhh
Q 039883           75 NILAR   79 (82)
Q Consensus        75 ~~~~~   79 (82)
                      .+.+.
T Consensus        89 ~~~~~   93 (215)
T 1a04_A           89 NHEED   93 (215)
T ss_dssp             CCHHH
T ss_pred             CCHHH
Confidence            76543

>2jba_A Phosphate regulon transcriptional regulatory PROT; transcription factor, sensory transduction, phosphate regula transcription regulation; 1.45A {Escherichia coli} PDB: 2jba_B 1b00_A 2iyn_A 2jb9_A 1zes_A

Probab=99.21  E-value=1.7e-11  Score=61.36  Aligned_cols=60  Identities=25%  Similarity=0.452  Sum_probs=44.4

Q ss_pred             ceee--ecChhHHhh---ccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCchhh
Q 039883           19 GFDL--SPTDTEEVH---VLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENILAR   79 (82)
Q Consensus        19 ~~~~--~~~~~~~~~---~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~~~~   79 (82)
                      ++.+  ..++.+++.   ..+||++|+|+.+|+.+|+++++.++ .....+.+|+|++|+..+.+.
T Consensus        26 g~~v~~~~~~~~a~~~~~~~~~dlvi~D~~l~~~~g~~~~~~l~-~~~~~~~~~ii~~s~~~~~~~   90 (127)
T 2jba_A           26 GFQPVEAEDYDSAVNQLNEPWPDLILLAWMLPGGSGIQFIKHLR-RESMTRDIPVVMLTARGEEED   90 (127)
T ss_dssp             TCEEEEECSHHHHHTTCSSSCCSEEEEESEETTEEHHHHHHHHH-TSTTTTTSCEEEEEETTHHHH
T ss_pred             CceEEEeCCHHHHHHHHhccCCCEEEEecCCCCCCHHHHHHHHH-hCcccCCCCEEEEeCCCCHHH
Confidence            4444  444445443   44799999999999999999999999 322337899999998876543

>2jk1_A HUPR, hydrogenase transcriptional regulatory protein HU; nucleotide-binding, transcription regulation; 2.10A {Rhodobacter capsulatus} PDB: 2vui_B 2vuh_B

Probab=99.21  E-value=3.3e-11  Score=61.40  Aligned_cols=57  Identities=23%  Similarity=0.294  Sum_probs=43.2

Q ss_pred             ceeeecChhHH---hhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCchh
Q 039883           19 GFDLSPTDTEE---VHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENILA   78 (82)
Q Consensus        19 ~~~~~~~~~~~---~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~~~   78 (82)
                      .+..+.++.++   +...+||++|+|+.||+++|+++++.++   ...+..|+|++|+..+..
T Consensus        26 ~v~~~~~~~~a~~~~~~~~~dlvl~D~~lp~~~g~~~~~~l~---~~~~~~~ii~~s~~~~~~   85 (139)
T 2jk1_A           26 DVLTAQGAEAAIAILEEEWVQVIICDQRMPGRTGVDFLTEVR---ERWPETVRIIITGYTDSA   85 (139)
T ss_dssp             CEEEESSHHHHHHHHHHSCEEEEEEESCCSSSCHHHHHHHHH---HHCTTSEEEEEESCTTCH
T ss_pred             eEEEcCCHHHHHHHHhcCCCCEEEEeCCCCCCcHHHHHHHHH---HhCCCCcEEEEeCCCChH
Confidence            33334444443   4456899999999999999999999999   346678999999876543

>1mvo_A PHOP response regulator; phosphate regulon, transcriptional regulatory protein, alpha/beta doubly wound fold, phosphorylation; 1.60A {Bacillus subtilis} SCOP: c.23.1.1

Probab=99.20  E-value=4.6e-11  Score=60.49  Aligned_cols=57  Identities=21%  Similarity=0.434  Sum_probs=43.4

Q ss_pred             Cceee--ecChhHH---hhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCch
Q 039883           18 DGFDL--SPTDTEE---VHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENIL   77 (82)
Q Consensus        18 ~~~~~--~~~~~~~---~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~~   77 (82)
                      .+|.+  +.++.++   +...+||++|+|+.+|+++|+++++.++   ...+.+|+|++|+..+.
T Consensus        26 ~g~~v~~~~~~~~a~~~~~~~~~dlvl~D~~l~~~~g~~~~~~l~---~~~~~~~ii~~s~~~~~   87 (136)
T 1mvo_A           26 SGYDVITASDGEEALKKAETEKPDLIVLDVMLPKLDGIEVCKQLR---QQKLMFPILMLTAKDEE   87 (136)
T ss_dssp             TTCEEEEESSHHHHHHHHHHHCCSEEEEESSCSSSCHHHHHHHHH---HTTCCCCEEEEECTTCC
T ss_pred             CCcEEEEecCHHHHHHHHhhcCCCEEEEecCCCCCCHHHHHHHHH---cCCCCCCEEEEECCCCH
Confidence            34444  4444444   4455899999999999999999999999   44567899999987654

>3cg4_A Response regulator receiver domain protein (CHEY-; structural genomics, unknown function; HET: MSE; 1.61A {Methanospirillum hungatei jf-1}

Probab=99.20  E-value=6.5e-11  Score=60.32  Aligned_cols=59  Identities=22%  Similarity=0.387  Sum_probs=45.0

Q ss_pred             ceee--ecChhH---HhhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCchh
Q 039883           19 GFDL--SPTDTE---EVHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENILA   78 (82)
Q Consensus        19 ~~~~--~~~~~~---~~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~~~   78 (82)
                      +|++  +.+..+   .+...+||++|+|+.+|+.+|+++++.++ .....+.+|+|++|+..+.+
T Consensus        31 g~~v~~~~~~~~a~~~l~~~~~dlii~d~~l~~~~g~~~~~~l~-~~~~~~~~pii~~s~~~~~~   94 (142)
T 3cg4_A           31 GFHIISADSGGQCIDLLKKGFSGVVLLDIMMPGMDGWDTIRAIL-DNSLEQGIAIVMLTAKNAPD   94 (142)
T ss_dssp             TCEEEEESSHHHHHHHHHTCCCEEEEEESCCSSSCHHHHHHHHH-HTTCCTTEEEEEEECTTCCC
T ss_pred             CeEEEEeCCHHHHHHHHHhcCCCEEEEeCCCCCCCHHHHHHHHH-hhcccCCCCEEEEECCCCHH
Confidence            4444  444444   34566899999999999999999999999 32367889999999876543

>3n53_A Response regulator receiver modulated diguanylate; diguanylate cyclase, protein structure I II(PSI II), NYSGXRC, structural genomics; 2.20A {Pelobacter carbinolicus} SCOP: c.23.1.0

Probab=99.20  E-value=5.6e-11  Score=60.57  Aligned_cols=58  Identities=22%  Similarity=0.279  Sum_probs=35.6

Q ss_pred             eeecChhH---HhhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCchhh
Q 039883           21 DLSPTDTE---EVHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENILAR   79 (82)
Q Consensus        21 ~~~~~~~~---~~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~~~~   79 (82)
                      ..+.+..+   .+...+||+||+|+.+|+.+|+++++.++ .....+.+|+|++|+..+.+.
T Consensus        30 ~~~~~~~~a~~~~~~~~~dlvi~D~~l~~~~g~~~~~~l~-~~~~~~~~~ii~~s~~~~~~~   90 (140)
T 3n53_A           30 IESKNEKEALEQIDHHHPDLVILDMDIIGENSPNLCLKLK-RSKGLKNVPLILLFSSEHKEA   90 (140)
T ss_dssp             EEESSHHHHHHHHHHHCCSEEEEETTC------CHHHHHH-TSTTCTTCCEEEEECC----C
T ss_pred             EEeCCHHHHHHHHhcCCCCEEEEeCCCCCCcHHHHHHHHH-cCcccCCCCEEEEecCCCHHH
Confidence            33444444   34566899999999999999999999999 322238899999998766543

>3cu5_A Two component transcriptional regulator, ARAC FAM; structural genomics, protein structure initiative; 2.60A {Clostridium phytofermentans isdg}

Probab=99.20  E-value=5.1e-11  Score=61.00  Aligned_cols=46  Identities=22%  Similarity=0.322  Sum_probs=38.8

Q ss_pred             hhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCchh
Q 039883           30 VHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENILA   78 (82)
Q Consensus        30 ~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~~~   78 (82)
                      +...+||++|+|+.||+++|+++++.++   ...+.+|+|++|+..+.+
T Consensus        45 ~~~~~~dlvllD~~lp~~~g~~l~~~l~---~~~~~~~ii~ls~~~~~~   90 (141)
T 3cu5_A           45 ALKHPPNVLLTDVRMPRMDGIELVDNIL---KLYPDCSVIFMSGYSDKE   90 (141)
T ss_dssp             HTTSCCSEEEEESCCSSSCHHHHHHHHH---HHCTTCEEEEECCSTTTC
T ss_pred             HhcCCCCEEEEeCCCCCCCHHHHHHHHH---hhCCCCcEEEEeCCCcHH
Confidence            3455799999999999999999999999   446788999999876543

>3bre_A Probable two-component response regulator; protein-nucleotide complex, signaling protein; HET: C2E; 2.40A {Pseudomonas aeruginosa} PDB: 3i5a_A*

Probab=99.20  E-value=4.6e-11  Score=69.18  Aligned_cols=77  Identities=18%  Similarity=0.302  Sum_probs=52.8

Q ss_pred             CchhHHHHHHHHhcC-CCceeee--cChhHH---hhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCC
Q 039883            2 TTTNGVLLSRLMSDG-SDGFDLS--PTDTEE---VHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSEN   75 (82)
Q Consensus         2 d~~~~~~~~~~~~~~-~~~~~~~--~~~~~~---~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~   75 (82)
                      |+++........... ..++.+.  .++.++   +...+||+||+|+.||+++|+++++.++ .....+.+|+|++|+..
T Consensus        25 dD~~~~~~~l~~~l~~~~~~~v~~~~~~~~al~~~~~~~~dlvl~D~~mp~~~G~~~~~~l~-~~~~~~~~~ii~~s~~~  103 (358)
T 3bre_A           25 DDQAMIGEAVRRSLASEAGIDFHFCSDPQQAVAVANQIKPTVILQDLVMPGVDGLTLLAAYR-GNPATRDIPIIVLSTKE  103 (358)
T ss_dssp             CSCTTHHHHHHTTSSSCTTEEEEEECCHHHHHHHHHHHCCSEEEEESBCSSSBHHHHHHHHT-TSTTTTTSCEEEEESSC
T ss_pred             ECCHHHHHHHHHHHHhccCcEEEEeCCHHHHHHHHHhCCCCEEEEeCCCCCCCHHHHHHHHh-cCcccCCCcEEEEeCCC
Confidence            344444444443332 3466654  344444   4455899999999999999999999999 32335689999999887


Q ss_pred             chhh
Q 039883           76 ILAR   79 (82)
Q Consensus        76 ~~~~   79 (82)
                      +.+.
T Consensus       104 ~~~~  107 (358)
T 3bre_A          104 EPTV  107 (358)
T ss_dssp             CHHH
T ss_pred             CHHH
Confidence            6554

>3hzh_A Chemotaxis response regulator (CHEY-3); phosphatase, complex, response regulator, receiver domain, two-component signal transduction; HET: BFD; 1.96A {Borrelia burgdorferi}

Probab=99.20  E-value=2.5e-11  Score=63.19  Aligned_cols=60  Identities=20%  Similarity=0.295  Sum_probs=45.9

Q ss_pred             CCceeee---cChhH---Hhhcc--CccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCchhh
Q 039883           17 SDGFDLS---PTDTE---EVHVL--AVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENILAR   79 (82)
Q Consensus        17 ~~~~~~~---~~~~~---~~~~~--~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~~~~   79 (82)
                      ..+|++.   .+..+   .+...  +||+||+|+.+++++|+++++.++   ...+.+|+|++|+..+.+.
T Consensus        58 ~~g~~v~~~~~~~~~al~~l~~~~~~~dliilD~~l~~~~g~~~~~~lr---~~~~~~~ii~ls~~~~~~~  125 (157)
T 3hzh_A           58 SEGFNIIDTAADGEEAVIKYKNHYPNIDIVTLXITMPKMDGITCLSNIM---EFDKNARVIMISALGKEQL  125 (157)
T ss_dssp             HTTCEEEEEESSHHHHHHHHHHHGGGCCEEEECSSCSSSCHHHHHHHHH---HHCTTCCEEEEESCCCHHH
T ss_pred             hCCCeEEEEECCHHHHHHHHHhcCCCCCEEEEeccCCCccHHHHHHHHH---hhCCCCcEEEEeccCcHHH
Confidence            3456544   34443   34455  789999999999999999999999   4568899999998866554

>1xhf_A DYE resistance, aerobic respiration control protein ARCA; two-component system, gene regulation, transcription factor, anoxic redox control; 2.15A {Escherichia coli} SCOP: c.23.1.1 PDB: 1xhe_A

Probab=99.20  E-value=4.8e-11  Score=59.50  Aligned_cols=58  Identities=17%  Similarity=0.448  Sum_probs=43.5

Q ss_pred             CCceeee--cChhH---HhhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCchh
Q 039883           17 SDGFDLS--PTDTE---EVHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENILA   78 (82)
Q Consensus        17 ~~~~~~~--~~~~~---~~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~~~   78 (82)
                      ..+|++.  .++.+   .+...+||++|+|+.+|+.+|+++++.++ .  . +.+|+|++|+..+..
T Consensus        25 ~~~~~v~~~~~~~~a~~~~~~~~~dlvi~D~~l~~~~g~~~~~~l~-~--~-~~~~ii~~s~~~~~~   87 (123)
T 1xhf_A           25 AEGYDVFEATDGAEMHQILSEYDINLVIMDINLPGKNGLLLARELR-E--Q-ANVALMFLTGRDNEV   87 (123)
T ss_dssp             TTTCEEEEESSHHHHHHHHHHSCCSEEEECSSCSSSCHHHHHHHHH-H--H-CCCEEEEEESCCSHH
T ss_pred             hCCcEEEEeCCHHHHHHHHhcCCCCEEEEcCCCCCCCHHHHHHHHH-h--C-CCCcEEEEECCCChH
Confidence            3455543  34443   34456899999999999999999999999 2  2 578999999876654

>3lua_A Response regulator receiver protein; two-component signal transduction system, histidine kinase, phosphorelay, receiver domain, nysgxrc; 2.40A {Clostridium thermocellum}

Probab=99.20  E-value=9.8e-12  Score=63.41  Aligned_cols=62  Identities=18%  Similarity=0.208  Sum_probs=46.9

Q ss_pred             CCceeeecChhHH---hhc-cCccEEEEeCCCC-CCCHHHHHHHHHhhcCCCCCccEEEEeeCCchhh
Q 039883           17 SDGFDLSPTDTEE---VHV-LAVDLIITDYCMP-GMTGCELIKKIKLQSFTFREIPTVIISSENILAR   79 (82)
Q Consensus        17 ~~~~~~~~~~~~~---~~~-~~~d~vi~d~~~~-~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~~~~   79 (82)
                      +..+..+.++.++   +.. .+||+||+|+.+| +.+|+++++.++ .....+.+|+|++|+..+.+.
T Consensus        29 ~~~v~~~~~~~~a~~~l~~~~~~dlvi~D~~l~~~~~g~~~~~~l~-~~~~~~~~~ii~ls~~~~~~~   95 (140)
T 3lua_A           29 EYDFIEVENLKKFYSIFKDLDSITLIIMDIAFPVEKEGLEVLSAIR-NNSRTANTPVIIATKSDNPGY   95 (140)
T ss_dssp             CCEEEEECSHHHHHTTTTTCCCCSEEEECSCSSSHHHHHHHHHHHH-HSGGGTTCCEEEEESCCCHHH
T ss_pred             CccEEEECCHHHHHHHHhcCCCCcEEEEeCCCCCCCcHHHHHHHHH-hCcccCCCCEEEEeCCCCHHH
Confidence            3333434445444   445 7899999999999 999999999999 333678999999998876544

>2rjn_A Response regulator receiver:metal-dependent phosphohydrolase, HD subdomain; structural genomics, oceanospirillum SP. MED92; 2.10A {Neptuniibacter caesariensis}

Probab=99.20  E-value=4.8e-11  Score=61.76  Aligned_cols=58  Identities=22%  Similarity=0.369  Sum_probs=44.7

Q ss_pred             Cceee--ecChhHH---hhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCchh
Q 039883           18 DGFDL--SPTDTEE---VHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENILA   78 (82)
Q Consensus        18 ~~~~~--~~~~~~~---~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~~~   78 (82)
                      .+|++  +.+..++   +...+||+||+|+.+|+.+|+++++.++   ...+.+|+|++|+..+..
T Consensus        30 ~g~~v~~~~~~~~a~~~l~~~~~dlvi~d~~l~~~~g~~~~~~l~---~~~~~~~ii~ls~~~~~~   92 (154)
T 2rjn_A           30 LGCNIITFTSPLDALEALKGTSVQLVISDMRMPEMGGEVFLEQVA---KSYPDIERVVISGYADAQ   92 (154)
T ss_dssp             TTCEEEEESCHHHHHHHHTTSCCSEEEEESSCSSSCHHHHHHHHH---HHCTTSEEEEEECGGGHH
T ss_pred             cCCeEEEeCCHHHHHHHHhcCCCCEEEEecCCCCCCHHHHHHHHH---HhCCCCcEEEEecCCCHH
Confidence            45555  4444444   4455799999999999999999999999   446789999999876644

>3q9s_A DNA-binding response regulator; DNA binding protein; 2.40A {Deinococcus radiodurans}

Probab=99.20  E-value=2.6e-11  Score=67.58  Aligned_cols=74  Identities=12%  Similarity=0.310  Sum_probs=51.4

Q ss_pred             CchhHHHHHHHHhcCCCceee--ecChhHH---hhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCc
Q 039883            2 TTTNGVLLSRLMSDGSDGFDL--SPTDTEE---VHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENI   76 (82)
Q Consensus         2 d~~~~~~~~~~~~~~~~~~~~--~~~~~~~---~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~   76 (82)
                      |++..............++.+  +.++.++   +...+||+||+|+.||+++|+++++.++   . .+.+|||++|+..+
T Consensus        44 dd~~~~~~~l~~~L~~~g~~v~~~~~~~~al~~~~~~~~DlvllD~~lp~~~G~~l~~~lr---~-~~~~~iI~lt~~~~  119 (249)
T 3q9s_A           44 EDDHDIANVLRMDLTDAGYVVDHADSAMNGLIKAREDHPDLILLDLGLPDFDGGDVVQRLR---K-NSALPIIVLTARDT  119 (249)
T ss_dssp             CSCHHHHHHHHHHHHTTTCEEEEESSHHHHHHHHHHSCCSEEEEECCSCHHHHHHHHHHHH---T-TCCCCEEEEESCCS
T ss_pred             ECCHHHHHHHHHHHHHCCCEEEEeCCHHHHHHHHhcCCCCEEEEcCCCCCCCHHHHHHHHH---c-CCCCCEEEEECCCC
Confidence            344444433333333445544  4444444   4456899999999999999999999999   3 56789999999876


Q ss_pred             hhh
Q 039883           77 LAR   79 (82)
Q Consensus        77 ~~~   79 (82)
                      .+.
T Consensus       120 ~~~  122 (249)
T 3q9s_A          120 VEE  122 (249)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            554

>1dz3_A Stage 0 sporulation protein A; response regulator, domain swapping; 1.65A {Bacillus stearothermophilus} SCOP: c.23.1.1 PDB: 1qmp_A*

Probab=99.19  E-value=7.1e-11  Score=59.50  Aligned_cols=59  Identities=10%  Similarity=0.223  Sum_probs=43.9

Q ss_pred             ceeee---cChhHH---hhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCchhh
Q 039883           19 GFDLS---PTDTEE---VHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENILAR   79 (82)
Q Consensus        19 ~~~~~---~~~~~~---~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~~~~   79 (82)
                      ++.+.   .++.++   +...+||++|+|+.||+++|+++++.++ .. ..+..|+|++|+..+.+.
T Consensus        27 ~~~~~~~~~~~~~a~~~~~~~~~dlvllD~~l~~~~g~~~~~~l~-~~-~~~~~~ii~ls~~~~~~~   91 (130)
T 1dz3_A           27 DMEVIGTAYNGQDCLQMLEEKRPDILLLDIIMPHLDGLAVLERIR-AG-FEHQPNVIMLTAFGQEDV   91 (130)
T ss_dssp             TEEEEEEESSHHHHHHHHHHHCCSEEEEESCCSSSCHHHHHHHHH-HH-CSSCCEEEEEEETTCHHH
T ss_pred             CceEEEEeCCHHHHHHHHhcCCCCEEEEecCCCCCCHHHHHHHHH-hc-CCCCCcEEEEecCCCHHH
Confidence            66543   344443   4456899999999999999999999999 21 246778999998766543

>3kht_A Response regulator; PSI-II, 11023K, structural genomics, Pro structure initiative, NEW YORK SGX research center for STRU genomics, nysgxrc; 2.10A {Hahella chejuensis} SCOP: c.23.1.0

Probab=99.19  E-value=3.5e-11  Score=61.57  Aligned_cols=59  Identities=22%  Similarity=0.352  Sum_probs=45.5

Q ss_pred             eeeecChhHH---hhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCchhh
Q 039883           20 FDLSPTDTEE---VHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENILAR   79 (82)
Q Consensus        20 ~~~~~~~~~~---~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~~~~   79 (82)
                      +..+.+..++   +...+||+||+|+.+|+.+|+++++.++ .....+.+|+|++|+..+.+.
T Consensus        34 v~~~~~~~~a~~~l~~~~~dlii~D~~l~~~~g~~~~~~lr-~~~~~~~~pii~~s~~~~~~~   95 (144)
T 3kht_A           34 LEFVDNGAKALYQVQQAKYDLIILDIGLPIANGFEVMSAVR-KPGANQHTPIVILTDNVSDDR   95 (144)
T ss_dssp             EEEESSHHHHHHHHTTCCCSEEEECTTCGGGCHHHHHHHHH-SSSTTTTCCEEEEETTCCHHH
T ss_pred             EEEECCHHHHHHHhhcCCCCEEEEeCCCCCCCHHHHHHHHH-hcccccCCCEEEEeCCCCHHH
Confidence            3334455544   4456899999999999999999999999 323678899999998776554

>1ny5_A Transcriptional regulator (NTRC family); AAA+ ATPase, sigma54 activator, bacterial transcription, DIM transcription; HET: ADP; 2.40A {Aquifex aeolicus} SCOP: c.23.1.1 c.37.1.20 PDB: 1ny6_A* 3m0e_A* 1zy2_A*

Probab=99.18  E-value=1.9e-11  Score=72.00  Aligned_cols=75  Identities=15%  Similarity=0.185  Sum_probs=51.6

Q ss_pred             CchhHHHHHHHHhcCCCceee--ecChhHH---hhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCc
Q 039883            2 TTTNGVLLSRLMSDGSDGFDL--SPTDTEE---VHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENI   76 (82)
Q Consensus         2 d~~~~~~~~~~~~~~~~~~~~--~~~~~~~---~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~   76 (82)
                      |++..............+|++  +.++.++   +...+||+||+|+.||+++|+++++.++   ...+.+|+|++|+..+
T Consensus         7 DDd~~~~~~l~~~L~~~g~~v~~a~~~~eal~~l~~~~~DlvllD~~mp~~dG~ell~~lr---~~~~~~pvIvlT~~~~   83 (387)
T 1ny5_A            7 EDDKVFRGLLEEYLSMKGIKVESAERGKEAYKLLSEKHFNVVLLDLLLPDVNGLEILKWIK---ERSPETEVIVITGHGT   83 (387)
T ss_dssp             CCCHHHHHHHHHHHHHHTCEEEEESSHHHHHHHHHHSCCSEEEEESBCSSSBHHHHHHHHH---HHCTTSEEEEEEETTC
T ss_pred             ECCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHHhCCCCEEEEeCCCCCCCHHHHHHHHH---hhCCCCcEEEEeCCCC
Confidence            344444433333222334444  4444444   4456899999999999999999999999   4567899999999876


Q ss_pred             hhh
Q 039883           77 LAR   79 (82)
Q Consensus        77 ~~~   79 (82)
                      .+.
T Consensus        84 ~~~   86 (387)
T 1ny5_A           84 IKT   86 (387)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            554

>2qzj_A Two-component response regulator; 11017X, PSI-II, structural genomics; 2.89A {Clostridium difficile}

Probab=99.18  E-value=4.5e-11  Score=60.85  Aligned_cols=57  Identities=23%  Similarity=0.246  Sum_probs=43.1

Q ss_pred             Cceee--ecChhHH---hhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCchh
Q 039883           18 DGFDL--SPTDTEE---VHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENILA   78 (82)
Q Consensus        18 ~~~~~--~~~~~~~---~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~~~   78 (82)
                      .++.+  +.++.++   +...+||++|+|+.+|+++|+++++.++   ... .+|+|++|+..+.+
T Consensus        27 ~g~~v~~~~~~~~al~~~~~~~~dlvllD~~l~~~~g~~l~~~l~---~~~-~~~ii~ls~~~~~~   88 (136)
T 2qzj_A           27 KGISIDLAYNCEEAIGKIFSNKYDLIFLEIILSDGDGWTLCKKIR---NVT-TCPIVYMTYINEDQ   88 (136)
T ss_dssp             TTCEEEEESSHHHHHHHHHHCCCSEEEEESEETTEEHHHHHHHHH---TTC-CCCEEEEESCCCHH
T ss_pred             CCCEEEEECCHHHHHHHHHhcCCCEEEEeCCCCCCCHHHHHHHHc---cCC-CCCEEEEEcCCCHH
Confidence            44544  4444444   4456899999999999999999999999   333 78999999876654

>1s8n_A Putative antiterminator; RV1626, structural genomics, transcriptional antiterminator, component system, PSI; 1.48A {Mycobacterium tuberculosis} SCOP: c.23.1.1 PDB: 1sd5_A

Probab=99.17  E-value=9e-11  Score=63.37  Aligned_cols=73  Identities=16%  Similarity=0.201  Sum_probs=48.8

Q ss_pred             chhHHHHHHHHhcCCCceeee---cChhHH---hhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCc
Q 039883            3 TTNGVLLSRLMSDGSDGFDLS---PTDTEE---VHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENI   76 (82)
Q Consensus         3 ~~~~~~~~~~~~~~~~~~~~~---~~~~~~---~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~   76 (82)
                      ++..............+|++.   .++.++   +...+||+||+|+.||+++|+++++.++   ...+ .|+|++|+..+
T Consensus        21 d~~~~~~~l~~~L~~~g~~v~~~~~~~~~al~~~~~~~~dlvi~D~~~p~~~g~~~~~~l~---~~~~-~pii~lt~~~~   96 (205)
T 1s8n_A           21 DEALIRMDLAEMLREEGYEIVGEAGDGQEAVELAELHKPDLVIMDVKMPRRDGIDAASEIA---SKRI-APIVVLTAFSQ   96 (205)
T ss_dssp             SSHHHHHHHHHHHHHTTCEEEEEESSHHHHHHHHHHHCCSEEEEESSCSSSCHHHHHHHHH---HTTC-SCEEEEEEGGG
T ss_pred             CCHHHHHHHHHHHHHCCCEEEEEeCCHHHHHHHHhhcCCCEEEEeCCCCCCChHHHHHHHH---hcCC-CCEEEEecCCC
Confidence            344433333333333456554   344443   4456899999999999999999999999   2333 49999998876


Q ss_pred             hhh
Q 039883           77 LAR   79 (82)
Q Consensus        77 ~~~   79 (82)
                      .+.
T Consensus        97 ~~~   99 (205)
T 1s8n_A           97 RDL   99 (205)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            544

>2b4a_A BH3024; flavodoxin-like fold, structural genomics, joint center for structural genomics, JCSG, protein structure initiative; 2.42A {Bacillus halodurans} SCOP: c.23.1.1

Probab=99.17  E-value=9.8e-11  Score=59.51  Aligned_cols=57  Identities=14%  Similarity=0.202  Sum_probs=42.7

Q ss_pred             CceeeecChhHH---hhc-cCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEe-eCCch
Q 039883           18 DGFDLSPTDTEE---VHV-LAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIIS-SENIL   77 (82)
Q Consensus        18 ~~~~~~~~~~~~---~~~-~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls-~~~~~   77 (82)
                      ..+..+.++.++   +.. ..||++|+|+.+|+.+|+++++.++   ...+.+|+|++| +..+.
T Consensus        40 ~~v~~~~~~~~al~~l~~~~~~dlvilD~~l~~~~g~~~~~~l~---~~~~~~~ii~ls~~~~~~  101 (138)
T 2b4a_A           40 AEVTVHPSGSAFFQHRSQLSTCDLLIVSDQLVDLSIFSLLDIVK---EQTKQPSVLILTTGRHEL  101 (138)
T ss_dssp             CEEEEESSHHHHHHTGGGGGSCSEEEEETTCTTSCHHHHHHHHT---TSSSCCEEEEEESCC--C
T ss_pred             CEEEEeCCHHHHHHHHHhCCCCCEEEEeCCCCCCCHHHHHHHHH---hhCCCCCEEEEECCCCCH
Confidence            333334444443   456 7899999999999999999999999   567789999999 76544

>2zay_A Response regulator receiver protein; structural genomics, NYSGXRC, target 11006U, protein structure initiative; 2.00A {Desulfuromonas acetoxidans}

Probab=99.16  E-value=5.1e-11  Score=61.12  Aligned_cols=61  Identities=26%  Similarity=0.440  Sum_probs=46.0

Q ss_pred             Cceee--ecChhHH---hhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCchhh
Q 039883           18 DGFDL--SPTDTEE---VHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENILAR   79 (82)
Q Consensus        18 ~~~~~--~~~~~~~---~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~~~~   79 (82)
                      .+|++  +.+..++   +...+||+||+|+.+++.+|+++++.++ .....+.+|+|++|+..+...
T Consensus        31 ~g~~v~~~~~~~~a~~~l~~~~~dlii~d~~l~~~~g~~~~~~l~-~~~~~~~~pii~ls~~~~~~~   96 (147)
T 2zay_A           31 EGFDIIQCGNAIEAVPVAVKTHPHLIITEANMPKISGMDLFNSLK-KNPQTASIPVIALSGRATAKE   96 (147)
T ss_dssp             HTEEEEEESSHHHHHHHHHHHCCSEEEEESCCSSSCHHHHHHHHH-TSTTTTTSCEEEEESSCCHHH
T ss_pred             cCCeEEEeCCHHHHHHHHHcCCCCEEEEcCCCCCCCHHHHHHHHH-cCcccCCCCEEEEeCCCCHHH
Confidence            34544  4444443   4456899999999999999999999999 322678899999998776543

>3heb_A Response regulator receiver domain protein (CHEY); NYSGXRC, PSI-II, respose regulator, structure initiative, structural genomics; 2.40A {Rhodospirillum rubrum} SCOP: c.23.1.0

Probab=99.16  E-value=4.7e-10  Score=57.86  Aligned_cols=47  Identities=26%  Similarity=0.448  Sum_probs=40.1

Q ss_pred             ccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCchhh
Q 039883           32 VLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENILAR   79 (82)
Q Consensus        32 ~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~~~~   79 (82)
                      ..+||+||+|+.+|+++|+++++.++ .....+.+|+|++|+..+.+.
T Consensus        57 ~~~~dliilD~~l~~~~g~~~~~~lr-~~~~~~~~pii~~t~~~~~~~  103 (152)
T 3heb_A           57 AGRAQLVLLDLNLPDMTGIDILKLVK-ENPHTRRSPVVILTTTDDQRE  103 (152)
T ss_dssp             TTCBEEEEECSBCSSSBHHHHHHHHH-HSTTTTTSCEEEEESCCCHHH
T ss_pred             cCCCCEEEEeCCCCCCcHHHHHHHHH-hcccccCCCEEEEecCCCHHH
Confidence            45799999999999999999999999 433678899999998876544

>2a9o_A Response regulator; essential protein, YYCF/YYCG homolog, signaling protein; 1.65A {Streptococcus pneumoniae} SCOP: c.23.1.1 PDB: 1nxo_A 1nxs_A 1nxv_A 1nxw_A 1nxx_A 1nxp_A 2a9p_A 2a9q_A 1nxt_A* 2a9r_A*

Probab=99.16  E-value=5.9e-11  Score=58.81  Aligned_cols=56  Identities=23%  Similarity=0.473  Sum_probs=42.6

Q ss_pred             ceee--ecChhHH---hhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCchh
Q 039883           19 GFDL--SPTDTEE---VHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENILA   78 (82)
Q Consensus        19 ~~~~--~~~~~~~---~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~~~   78 (82)
                      +|++  +.++.++   +...+||++++|+.+|+.+|+++++.++ .   .+..|+|++|+..+..
T Consensus        25 ~~~v~~~~~~~~a~~~~~~~~~dlvl~D~~l~~~~g~~~~~~l~-~---~~~~~ii~~s~~~~~~   85 (120)
T 2a9o_A           25 GYEVVTAFNGREALEQFEAEQPDIIILDLMLPEIDGLEVAKTIR-K---TSSVPILMLSAKDSEF   85 (120)
T ss_dssp             TCEEEEESSHHHHHHHHHHHCCSEEEECSSCSSSCHHHHHHHHH-H---HCCCCEEEEESCCSHH
T ss_pred             CcEEEEecCHHHHHHHHHhCCCCEEEEeccCCCCCHHHHHHHHH-h---CCCCCEEEEecCCchH
Confidence            4444  4444443   4455899999999999999999999999 2   3578999999876654

>3cnb_A DNA-binding response regulator, MERR family; signal receiver domain, DNA binding protein, protein structu initiative, PSI-2; 2.00A {Colwellia psychrerythraea}

Probab=99.15  E-value=1.2e-10  Score=59.26  Aligned_cols=58  Identities=17%  Similarity=0.306  Sum_probs=45.3

Q ss_pred             eeeecChhHH---hhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCchh
Q 039883           20 FDLSPTDTEE---VHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENILA   78 (82)
Q Consensus        20 ~~~~~~~~~~---~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~~~   78 (82)
                      +..+.+..++   +...+||+||+|+.+++.+|+++++.++ .....+.+|+|++|+..+..
T Consensus        37 v~~~~~~~~a~~~l~~~~~dlii~d~~l~~~~g~~~~~~l~-~~~~~~~~~ii~~s~~~~~~   97 (143)
T 3cnb_A           37 IKIAYNPFDAGDLLHTVKPDVVMLDLMMVGMDGFSICHRIK-STPATANIIVIAMTGALTDD   97 (143)
T ss_dssp             EEEECSHHHHHHHHHHTCCSEEEEETTCTTSCHHHHHHHHH-TSTTTTTSEEEEEESSCCHH
T ss_pred             EEEECCHHHHHHHHHhcCCCEEEEecccCCCcHHHHHHHHH-hCccccCCcEEEEeCCCCHH
Confidence            4445555543   4556899999999999999999999999 32257889999999877654

>2rdm_A Response regulator receiver protein; structural genomics, unknown function, PSI-2, protein struct initiative; HET: MSE; 1.76A {Sinorhizobium medicae}

Probab=99.15  E-value=9.2e-11  Score=59.04  Aligned_cols=58  Identities=21%  Similarity=0.258  Sum_probs=44.0

Q ss_pred             Cceee--ecChhH---Hhhcc-CccEEEEeCCCCC-CCHHHHHHHHHhhcCCCCCccEEEEeeCCchh
Q 039883           18 DGFDL--SPTDTE---EVHVL-AVDLIITDYCMPG-MTGCELIKKIKLQSFTFREIPTVIISSENILA   78 (82)
Q Consensus        18 ~~~~~--~~~~~~---~~~~~-~~d~vi~d~~~~~-~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~~~   78 (82)
                      .+|++  +.+..+   .+... +||++|+|+.+|+ .+|+++++.++   ...+.+|+|++|+..+..
T Consensus        28 ~g~~v~~~~~~~~a~~~l~~~~~~dlvi~d~~l~~~~~g~~~~~~l~---~~~~~~~ii~~s~~~~~~   92 (132)
T 2rdm_A           28 AGFLVTAVSSGAKAIEMLKSGAAIDGVVTDIRFCQPPDGWQVARVAR---EIDPNMPIVYISGHAALE   92 (132)
T ss_dssp             TTCEEEEESSHHHHHHHHHTTCCCCEEEEESCCSSSSCHHHHHHHHH---HHCTTCCEEEEESSCCTT
T ss_pred             cCCEEEEECCHHHHHHHHHcCCCCCEEEEeeeCCCCCCHHHHHHHHH---hcCCCCCEEEEeCCccHH
Confidence            34444  444443   34555 7999999999997 99999999999   345789999999876654

>3h5i_A Response regulator/sensory box protein/ggdef domain protein; structural genomics, transcription, PSI-2; 1.90A {Carboxydothermus hydrogenoformans z-2901}

Probab=99.15  E-value=8.2e-11  Score=60.04  Aligned_cols=57  Identities=26%  Similarity=0.367  Sum_probs=42.9

Q ss_pred             Cceee--ecChhHH---hhc-cCccEEEEeCCCCC-CCHHHHHHHHHhhcCCCCCccEEEEeeCCchh
Q 039883           18 DGFDL--SPTDTEE---VHV-LAVDLIITDYCMPG-MTGCELIKKIKLQSFTFREIPTVIISSENILA   78 (82)
Q Consensus        18 ~~~~~--~~~~~~~---~~~-~~~d~vi~d~~~~~-~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~~~   78 (82)
                      .+|++  +.++.++   +.. ..||+||+|+.+|+ .+|+++++.++ .   .+.+|+|++|+..+.+
T Consensus        28 ~g~~v~~~~~~~~a~~~l~~~~~~dlvi~D~~l~~~~~g~~~~~~l~-~---~~~~~ii~ls~~~~~~   91 (140)
T 3h5i_A           28 YGYTVEIALTGEAAVEKVSGGWYPDLILMDIELGEGMDGVQTALAIQ-Q---ISELPVVFLTAHTEPA   91 (140)
T ss_dssp             TTCEEEEESSHHHHHHHHHTTCCCSEEEEESSCSSSCCHHHHHHHHH-H---HCCCCEEEEESSSSCC
T ss_pred             cCCEEEEecChHHHHHHHhcCCCCCEEEEeccCCCCCCHHHHHHHHH-h---CCCCCEEEEECCCCHH
Confidence            34554  4444444   344 57999999999985 99999999999 2   2688999999876654

>2ayx_A Sensor kinase protein RCSC; two independent structural domains, transferase; NMR {Escherichia coli} SCOP: c.23.1.1 c.23.1.6 PDB: 2ayz_A 2ayy_A

Probab=99.15  E-value=1.4e-11  Score=68.83  Aligned_cols=59  Identities=15%  Similarity=0.322  Sum_probs=44.9

Q ss_pred             CCceeeecChhHH---hhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCchh
Q 039883           17 SDGFDLSPTDTEE---VHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENILA   78 (82)
Q Consensus        17 ~~~~~~~~~~~~~---~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~~~   78 (82)
                      +..+..+.++.++   +...+||+||+|+.||+++|+++++.+|   ...+.+|||++|+..+.+
T Consensus       153 g~~v~~a~~~~eal~~l~~~~~dlvl~D~~mp~~~G~~l~~~ir---~~~~~~piI~lt~~~~~~  214 (254)
T 2ayx_A          153 GYQCKTANDGVDALNVLSKNHIDIVLSDVNMPNMDGYRLTQRIR---QLGLTLPVIGVTANALAE  214 (254)
T ss_dssp             TSEEEEECCSHHHHHHHHHSCCSEEEEEESSCSSCCHHHHHHHH---HHHCCSCEEEEESSTTSH
T ss_pred             CCEEEEECCHHHHHHHHHhCCCCEEEEcCCCCCCCHHHHHHHHH---hcCCCCcEEEEECCCCHH
Confidence            3344444555544   4456899999999999999999999999   345679999999876544

>3cz5_A Two-component response regulator, LUXR family; structural genomics, protein structure initiative; 2.70A {Aurantimonas SP}

Probab=99.15  E-value=1.8e-10  Score=59.48  Aligned_cols=74  Identities=16%  Similarity=0.100  Sum_probs=51.5

Q ss_pred             chhHHHHHHHHhcCC-Cceeee---cChhH---HhhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCC
Q 039883            3 TTNGVLLSRLMSDGS-DGFDLS---PTDTE---EVHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSEN   75 (82)
Q Consensus         3 ~~~~~~~~~~~~~~~-~~~~~~---~~~~~---~~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~   75 (82)
                      ++............. .+|.+.   .+..+   .+...+||+||+|+.+++.+|.++++.++   ...+.+|+|++|+..
T Consensus        13 d~~~~~~~l~~~L~~~~~~~v~~~~~~~~~a~~~l~~~~~dlii~D~~l~~~~g~~~~~~l~---~~~~~~~ii~ls~~~   89 (153)
T 3cz5_A           13 DHPIVREGYRRLIERRPGYAVVAEAADAGEAYRLYRETTPDIVVMDLTLPGPGGIEATRHIR---QWDGAARILIFTMHQ   89 (153)
T ss_dssp             SCHHHHHHHHHHHTTSTTEEEEEEESSHHHHHHHHHTTCCSEEEECSCCSSSCHHHHHHHHH---HHCTTCCEEEEESCC
T ss_pred             CcHHHHHHHHHHHhhCCCcEEEEEeCCHHHHHHHHhcCCCCEEEEecCCCCCCHHHHHHHHH---HhCCCCeEEEEECCC
Confidence            334444333333333 577654   23333   34566899999999999999999999999   446788999999876


Q ss_pred             chhh
Q 039883           76 ILAR   79 (82)
Q Consensus        76 ~~~~   79 (82)
                      +.+.
T Consensus        90 ~~~~   93 (153)
T 3cz5_A           90 GSAF   93 (153)
T ss_dssp             SHHH
T ss_pred             CHHH
Confidence            6543

>2qr3_A Two-component system response regulator; structural genomics, signal receiver, PSI-2, protein structu initiative; 1.80A {Bacteroides fragilis}

Probab=99.15  E-value=1.2e-10  Score=59.15  Aligned_cols=73  Identities=15%  Similarity=0.236  Sum_probs=49.7

Q ss_pred             chhHHHHHHHHhcCCCceeee--cChhH---HhhccCccEEEEeCCCC-----CCCHHHHHHHHHhhcCCCCCccEEEEe
Q 039883            3 TTNGVLLSRLMSDGSDGFDLS--PTDTE---EVHVLAVDLIITDYCMP-----GMTGCELIKKIKLQSFTFREIPTVIIS   72 (82)
Q Consensus         3 ~~~~~~~~~~~~~~~~~~~~~--~~~~~---~~~~~~~d~vi~d~~~~-----~~~~~~~~~~l~~~~~~~~~~~vi~ls   72 (82)
                      ++..............++++.  .+..+   .+...+||++|+|+.++     +.+|+++++.++   ...+.+|+|++|
T Consensus        11 d~~~~~~~l~~~L~~~g~~v~~~~~~~~a~~~l~~~~~dlvi~d~~~~~~~~~~~~g~~~~~~l~---~~~~~~~ii~ls   87 (140)
T 2qr3_A           11 DNKGVLTAVQLLLKNHFSKVITLSSPVSLSTVLREENPEVVLLDMNFTSGINNGNEGLFWLHEIK---RQYRDLPVVLFT   87 (140)
T ss_dssp             SCHHHHHHHHHHHTTTSSEEEEECCHHHHHHHHHHSCEEEEEEETTTTC-----CCHHHHHHHHH---HHCTTCCEEEEE
T ss_pred             CCHHHHHHHHHHHHhCCcEEEEeCCHHHHHHHHHcCCCCEEEEeCCcCCCCCCCccHHHHHHHHH---hhCcCCCEEEEE
Confidence            333333333333334455554  34443   44566899999999999     999999999999   446789999999


Q ss_pred             eCCchh
Q 039883           73 SENILA   78 (82)
Q Consensus        73 ~~~~~~   78 (82)
                      +..+.+
T Consensus        88 ~~~~~~   93 (140)
T 2qr3_A           88 AYADID   93 (140)
T ss_dssp             EGGGHH
T ss_pred             CCCCHH
Confidence            876654

>1k68_A Phytochrome response regulator RCPA; phosphorylated aspartate, CHEY homologue, homodimer, (beta/alpha)5, signaling protein; HET: PHD; 1.90A {Tolypothrix SP} SCOP: c.23.1.1

Probab=99.15  E-value=1.7e-10  Score=58.36  Aligned_cols=46  Identities=28%  Similarity=0.416  Sum_probs=38.2

Q ss_pred             cCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCchhh
Q 039883           33 LAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENILAR   79 (82)
Q Consensus        33 ~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~~~~   79 (82)
                      ..||++|+|+.+|+.+|+++++.++ .....+.+|+|++|+..+.+.
T Consensus        54 ~~~dlvi~d~~~~~~~g~~~~~~l~-~~~~~~~~pii~ls~~~~~~~   99 (140)
T 1k68_A           54 SRPDLILLXLNLPKKDGREVLAEIK-SDPTLKRIPVVVLSTSINEDD   99 (140)
T ss_dssp             CCCSEEEECSSCSSSCHHHHHHHHH-HSTTGGGSCEEEEESCCCHHH
T ss_pred             CCCcEEEEecCCCcccHHHHHHHHH-cCcccccccEEEEecCCcHHH
Confidence            6799999999999999999999999 322237899999998776543

>3kcn_A Adenylate cyclase homolog; SGX, PSI 2, structural genomics, protein structure initiative; 2.45A {Rhodopirellula baltica}

Probab=99.14  E-value=1.6e-10  Score=59.62  Aligned_cols=58  Identities=22%  Similarity=0.440  Sum_probs=44.0

Q ss_pred             ceee--ecChhHH---hhccC-ccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCchhh
Q 039883           19 GFDL--SPTDTEE---VHVLA-VDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENILAR   79 (82)
Q Consensus        19 ~~~~--~~~~~~~---~~~~~-~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~~~~   79 (82)
                      ++++  +.+..++   +.... ||+||+|+.+|+.+|+++++.++   ...+.+|+|++|+..+.+.
T Consensus        27 ~~~v~~~~~~~~a~~~l~~~~~~dlvi~D~~l~~~~g~~~~~~l~---~~~~~~~ii~~s~~~~~~~   90 (151)
T 3kcn_A           27 DFEVTTCESGPEALACIKKSDPFSVIMVDMRMPGMEGTEVIQKAR---LISPNSVYLMLTGNQDLTT   90 (151)
T ss_dssp             TSEEEEESSHHHHHHHHHHSCCCSEEEEESCCSSSCHHHHHHHHH---HHCSSCEEEEEECGGGHHH
T ss_pred             CceEEEeCCHHHHHHHHHcCCCCCEEEEeCCCCCCcHHHHHHHHH---hcCCCcEEEEEECCCCHHH
Confidence            4554  4444444   33444 59999999999999999999999   4567899999998776543

>3eul_A Possible nitrate/nitrite response transcriptional regulatory protein NARL (DNA-binding...; central beta strand flanked by alpha helices; 1.90A {Mycobacterium tuberculosis}

Probab=99.13  E-value=2.1e-10  Score=59.22  Aligned_cols=54  Identities=20%  Similarity=0.304  Sum_probs=43.9

Q ss_pred             ecChhH---HhhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCchhh
Q 039883           23 SPTDTE---EVHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENILAR   79 (82)
Q Consensus        23 ~~~~~~---~~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~~~~   79 (82)
                      +.+..+   .+...+||+||+|+.+|+.+|+++++.++   ...+.+|+|++|+..+.+.
T Consensus        47 ~~~~~~a~~~l~~~~~dlii~d~~l~~~~g~~~~~~l~---~~~~~~~ii~~s~~~~~~~  103 (152)
T 3eul_A           47 ADDGAAALELIKAHLPDVALLDYRMPGMDGAQVAAAVR---SYELPTRVLLISAHDEPAI  103 (152)
T ss_dssp             ESSHHHHHHHHHHHCCSEEEEETTCSSSCHHHHHHHHH---HTTCSCEEEEEESCCCHHH
T ss_pred             eCCHHHHHHHHHhcCCCEEEEeCCCCCCCHHHHHHHHH---hcCCCCeEEEEEccCCHHH
Confidence            444444   44566899999999999999999999999   4578899999998876554

>1zh2_A KDP operon transcriptional regulatory protein KDPE; two-component system, gene regulation, transcription factor, KDP potassium transport system; 2.00A {Escherichia coli} SCOP: c.23.1.1 PDB: 1zh4_A

Probab=99.13  E-value=1e-10  Score=57.98  Aligned_cols=58  Identities=24%  Similarity=0.427  Sum_probs=43.6

Q ss_pred             CCceeeec--ChhHH---hhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCchh
Q 039883           17 SDGFDLSP--TDTEE---VHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENILA   78 (82)
Q Consensus        17 ~~~~~~~~--~~~~~---~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~~~   78 (82)
                      ..++.+..  ++.++   +...+||++++|+.+|+++|+++++.++   . .+..|+|++|+..+..
T Consensus        23 ~~~~~v~~~~~~~~~~~~~~~~~~dlvi~D~~l~~~~g~~~~~~l~---~-~~~~~ii~~s~~~~~~   85 (121)
T 1zh2_A           23 GDGMRVFEAETLQRGLLEAATRKPDLIILDLGLPDGDGIEFIRDLR---Q-WSAVPVIVLSARSEES   85 (121)
T ss_dssp             TTTCEEEEESSHHHHHHHHHHHCCSEEEEESEETTEEHHHHHHHHH---T-TCCCCEEEEESCCSHH
T ss_pred             cCCCEEEEeCCHHHHHHHHhcCCCCEEEEeCCCCCCcHHHHHHHHH---h-CCCCcEEEEECCCCHH
Confidence            34555543  33443   3455899999999999999999999999   2 4678999999876654

>4dad_A Putative pilus assembly-related protein; response regulator receiver domain, CHEY-related protein, ST genomics; 2.50A {Burkholderia pseudomallei} PDB: 4dn6_A

Probab=99.13  E-value=2.4e-11  Score=62.33  Aligned_cols=44  Identities=11%  Similarity=0.166  Sum_probs=38.8

Q ss_pred             cCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCchhh
Q 039883           33 LAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENILAR   79 (82)
Q Consensus        33 ~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~~~~   79 (82)
                      .+||+||+|+.||+++|+++++.++   ...+.+|+|++|+..+.+.
T Consensus        66 ~~~dlvi~D~~l~~~~g~~~~~~l~---~~~~~~~ii~lt~~~~~~~  109 (146)
T 4dad_A           66 DAFDILMIDGAALDTAELAAIEKLS---RLHPGLTCLLVTTDASSQT  109 (146)
T ss_dssp             TTCSEEEEECTTCCHHHHHHHHHHH---HHCTTCEEEEEESCCCHHH
T ss_pred             CCCCEEEEeCCCCCccHHHHHHHHH---HhCCCCcEEEEeCCCCHHH
Confidence            7899999999999999999999999   4567899999998876544

>2qxy_A Response regulator; regulation of transcription, NYSGXRC, protein structure initiative II (PSI II), structural genomics; 1.95A {Thermotoga maritima}

Probab=99.12  E-value=7.2e-11  Score=60.22  Aligned_cols=59  Identities=22%  Similarity=0.367  Sum_probs=44.5

Q ss_pred             CCceeee--cChhH---HhhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCchhh
Q 039883           17 SDGFDLS--PTDTE---EVHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENILAR   79 (82)
Q Consensus        17 ~~~~~~~--~~~~~---~~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~~~~   79 (82)
                      ..+|++.  .+..+   .+...+||++|+|+ +++.+|+++++.++   ...+.+|+|++|+..+.+.
T Consensus        26 ~~g~~v~~~~~~~~a~~~l~~~~~dlvi~d~-~~~~~g~~~~~~l~---~~~~~~pii~ls~~~~~~~   89 (142)
T 2qxy_A           26 KDGFNVIWAKNEQEAFTFLRREKIDLVFVDV-FEGEESLNLIRRIR---EEFPDTKVAVLSAYVDKDL   89 (142)
T ss_dssp             GGTCEEEEESSHHHHHHHHTTSCCSEEEEEC-TTTHHHHHHHHHHH---HHCTTCEEEEEESCCCHHH
T ss_pred             hCCCEEEEECCHHHHHHHHhccCCCEEEEeC-CCCCcHHHHHHHHH---HHCCCCCEEEEECCCCHHH
Confidence            3455554  34444   34456899999999 99999999999999   4466899999998866543

>1qkk_A DCTD, C4-dicarboxylate transport transcriptional regulatory protein; receiver domain, 2-component signal transduction; 1.7A {Sinorhizobium meliloti} SCOP: c.23.1.1 PDB: 1l5z_A 1l5y_A

Probab=99.12  E-value=8.4e-11  Score=60.87  Aligned_cols=58  Identities=22%  Similarity=0.352  Sum_probs=44.3

Q ss_pred             CceeeecChhHHhh---ccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCchh
Q 039883           18 DGFDLSPTDTEEVH---VLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENILA   78 (82)
Q Consensus        18 ~~~~~~~~~~~~~~---~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~~~   78 (82)
                      ..+..+.+..+++.   ..+||++|+|+.+++.+|+++++.++   ...+.+|+|++|+..+..
T Consensus        28 ~~v~~~~~~~~a~~~l~~~~~dliild~~l~~~~g~~~~~~l~---~~~~~~pii~ls~~~~~~   88 (155)
T 1qkk_A           28 FTVSSFASATEALAGLSADFAGIVISDIRMPGMDGLALFRKIL---ALDPDLPMILVTGHGDIP   88 (155)
T ss_dssp             CEEEEESCHHHHHHTCCTTCCSEEEEESCCSSSCHHHHHHHHH---HHCTTSCEEEEECGGGHH
T ss_pred             cEEEEECCHHHHHHHHHhCCCCEEEEeCCCCCCCHHHHHHHHH---hhCCCCCEEEEECCCChH
Confidence            33333444455544   45799999999999999999999999   446789999999876644

>3klo_A Transcriptional regulator VPST; REC domain, HTH domain, DNA-binding, transcription regulation; HET: C2E TAR; 2.80A {Vibrio cholerae} PDB: 3kln_A*

Probab=99.12  E-value=3.3e-11  Score=66.01  Aligned_cols=45  Identities=13%  Similarity=0.175  Sum_probs=39.1

Q ss_pred             hccCccEEEEeCCCCCCCHHHHHHHHHhhcC-CCCCccEEEEeeCCchh
Q 039883           31 HVLAVDLIITDYCMPGMTGCELIKKIKLQSF-TFREIPTVIISSENILA   78 (82)
Q Consensus        31 ~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~-~~~~~~vi~ls~~~~~~   78 (82)
                      ...+||+||+|+.||+++|+++++.++   . ..+.+|+|++|+..+..
T Consensus        51 ~~~~~dlvllD~~mp~~~G~~~~~~lr---~~~~~~~~ii~lt~~~~~~   96 (225)
T 3klo_A           51 ESRSIQMLVIDYSRISDDVLTDYSSFK---HISCPDAKEVIINCPQDIE   96 (225)
T ss_dssp             GGGGCCEEEEEGGGCCHHHHHHHHHHH---HHHCTTCEEEEEEECTTCC
T ss_pred             hccCCCEEEEeCCCCCCCHHHHHHHHH---HhhCCCCcEEEEECCcchh
Confidence            455799999999999999999999999   4 57789999999887644

>1k66_A Phytochrome response regulator RCPB; CHEY homologue, homodimer, APO-protein, (beta/alpha)5, signaling protein; 1.75A {Tolypothrix SP} SCOP: c.23.1.1

Probab=99.11  E-value=1.8e-10  Score=58.96  Aligned_cols=46  Identities=28%  Similarity=0.502  Sum_probs=38.1

Q ss_pred             cCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCchhh
Q 039883           33 LAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENILAR   79 (82)
Q Consensus        33 ~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~~~~   79 (82)
                      ..||++|+|+.+|+.+|+++++.++ .....+.+|+|++|+..+.+.
T Consensus        61 ~~~dlvi~D~~l~~~~g~~~~~~l~-~~~~~~~~~ii~~t~~~~~~~  106 (149)
T 1k66_A           61 PRPAVILLDLNLPGTDGREVLQEIK-QDEVLKKIPVVIMTTSSNPKD  106 (149)
T ss_dssp             CCCSEEEECSCCSSSCHHHHHHHHT-TSTTGGGSCEEEEESCCCHHH
T ss_pred             CCCcEEEEECCCCCCCHHHHHHHHH-hCcccCCCeEEEEeCCCCHHH
Confidence            6799999999999999999999999 222237899999998776543

>2gwr_A DNA-binding response regulator MTRA; two-component regulatory system, transcription regulation, phosphorylation, OMPR family; 2.10A {Mycobacterium tuberculosis} PDB: 3nhz_A

Probab=99.10  E-value=2.2e-10  Score=63.22  Aligned_cols=57  Identities=26%  Similarity=0.547  Sum_probs=43.4

Q ss_pred             Cceee--ecChhHH---hhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCchh
Q 039883           18 DGFDL--SPTDTEE---VHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENILA   78 (82)
Q Consensus        18 ~~~~~--~~~~~~~---~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~~~   78 (82)
                      .+|++  +.++.++   +...+||++|+|+.+|+++|+++++.++   .. +.+|+|++|+..+..
T Consensus        28 ~g~~v~~~~~~~~al~~l~~~~~dlvilD~~l~~~~g~~~~~~lr---~~-~~~~ii~lt~~~~~~   89 (238)
T 2gwr_A           28 EGFDTAVIGDGTQALTAVRELRPDLVLLDLMLPGMNGIDVCRVLR---AD-SGVPIVMLTAKTDTV   89 (238)
T ss_dssp             TTCEEEEECCGGGHHHHHHHHCCSEEEEESSCSSSCHHHHHHHHH---TT-CCCCEEEEEETTCCS
T ss_pred             CCCEEEEECCHHHHHHHHHhCCCCEEEEeCCCCCCCHHHHHHHHH---hC-CCCcEEEEeCCCCHH
Confidence            34444  4444444   4456899999999999999999999999   33 378999999876654

>3lte_A Response regulator; structural genomics, PSI, protein structure initiative, NYSG YORK structural genomix research consortium, nysgxrc; 2.00A {Bermanella marisrubri}

Probab=99.10  E-value=4.4e-10  Score=56.55  Aligned_cols=58  Identities=12%  Similarity=0.288  Sum_probs=39.7

Q ss_pred             CceeeecChhHH---hhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCc
Q 039883           18 DGFDLSPTDTEE---VHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENI   76 (82)
Q Consensus        18 ~~~~~~~~~~~~---~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~   76 (82)
                      ..+..+.+..++   +...+||+||+|+.+|+.+|.++++.++ .....+.+++++++....
T Consensus        31 ~~v~~~~~~~~a~~~l~~~~~dlii~d~~l~~~~g~~~~~~l~-~~~~~~~~~ii~~~~~~~   91 (132)
T 3lte_A           31 WQVEIAHNGFDAGIKLSTFEPAIMTLDLSMPKLDGLDVIRSLR-QNKVANQPKILVVSGLDK   91 (132)
T ss_dssp             CEEEEESSHHHHHHHHHHTCCSEEEEESCBTTBCHHHHHHHHH-TTTCSSCCEEEEECCSCS
T ss_pred             cEEEEeCCHHHHHHHHHhcCCCEEEEecCCCCCCHHHHHHHHH-hcCccCCCeEEEEeCCCh
Confidence            333344444443   4566899999999999999999999999 322224566666665443

>3c3w_A Two component transcriptional regulatory protein; response regulator, two-component regulatory system, DNA-BIN protein; 2.20A {Mycobacterium tuberculosis}

Probab=99.08  E-value=4.9e-11  Score=65.41  Aligned_cols=75  Identities=19%  Similarity=0.204  Sum_probs=51.8

Q ss_pred             CchhHHHHHHHHhcCCCc-eee---ecChhHH---hhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeC
Q 039883            2 TTTNGVLLSRLMSDGSDG-FDL---SPTDTEE---VHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSE   74 (82)
Q Consensus         2 d~~~~~~~~~~~~~~~~~-~~~---~~~~~~~---~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~   74 (82)
                      |+++.............+ |.+   +.++.++   +...+||+||+|+.||+++|+++++.++   ...+.+|+|++|+.
T Consensus         8 dd~~~~~~~l~~~L~~~~~~~vv~~~~~~~~al~~l~~~~~dlvllD~~lp~~~g~~~~~~lr---~~~~~~~ii~lt~~   84 (225)
T 3c3w_A            8 DDHEVVRRGLVDLLGADPELDVVGEAGSVAEAMARVPAARPDVAVLDVRLPDGNGIELCRDLL---SRMPDLRCLILTSY   84 (225)
T ss_dssp             CSCHHHHHHHHHHHHTCTTEEEEEEESSHHHHHHHHHHHCCSEEEECSEETTEEHHHHHHHHH---HHCTTCEEEEGGGS
T ss_pred             cCCHHHHHHHHHHHhcCCCcEEEEEECCHHHHHHHHhhcCCCEEEEeCCCCCCCHHHHHHHHH---HhCCCCcEEEEECC
Confidence            344444433333333333 663   3344443   4456899999999999999999999999   44678999999988


Q ss_pred             Cchhh
Q 039883           75 NILAR   79 (82)
Q Consensus        75 ~~~~~   79 (82)
                      .+.+.
T Consensus        85 ~~~~~   89 (225)
T 3c3w_A           85 TSDEA   89 (225)
T ss_dssp             SSHHH
T ss_pred             CCHHH
Confidence            76543

>2j48_A Two-component sensor kinase; pseudo-receiver, circadian clock, transferase, response regulator, histidine protein kinase; NMR {Synechococcus elongatus}

Probab=99.06  E-value=7.1e-10  Score=54.45  Aligned_cols=59  Identities=12%  Similarity=0.113  Sum_probs=43.3

Q ss_pred             CceeeecChhH---HhhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCch
Q 039883           18 DGFDLSPTDTE---EVHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENIL   77 (82)
Q Consensus        18 ~~~~~~~~~~~---~~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~~   77 (82)
                      ..+..+.+..+   .+...+||++++|+.+++.+|.++++.++ .....+.+|+|++++..+.
T Consensus        26 ~~v~~~~~~~~~~~~l~~~~~dlii~d~~~~~~~~~~~~~~l~-~~~~~~~~~ii~~~~~~~~   87 (119)
T 2j48_A           26 FKVIWLVDGSTALDQLDLLQPIVILMAWPPPDQSCLLLLQHLR-EHQADPHPPLVLFLGEPPV   87 (119)
T ss_dssp             CEEEEESCHHHHHHHHHHHCCSEEEEECSTTCCTHHHHHHHHH-HTCCCSSCCCEEEESSCCS
T ss_pred             cEEEEecCHHHHHHHHHhcCCCEEEEecCCCCCCHHHHHHHHH-hccccCCCCEEEEeCCCCc
Confidence            33333444443   34556899999999999999999999999 3223478999999987543

>2oqr_A Sensory transduction protein REGX3; response regulator, winged-helix-turn-helix, DNA-binding, 3D swapping, two component system; 2.03A {Mycobacterium tuberculosis H37RV}

Probab=99.05  E-value=2.1e-10  Score=62.75  Aligned_cols=57  Identities=18%  Similarity=0.510  Sum_probs=43.4

Q ss_pred             Cceee--ecChhHH---hhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCchh
Q 039883           18 DGFDL--SPTDTEE---VHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENILA   78 (82)
Q Consensus        18 ~~~~~--~~~~~~~---~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~~~   78 (82)
                      .++++  +.++.++   +...+||++|+|+.+|+++|+++++.++   . .+.+|+|++|+..+..
T Consensus        27 ~g~~v~~~~~~~~al~~~~~~~~dlvllD~~l~~~~g~~~~~~l~---~-~~~~~ii~lt~~~~~~   88 (230)
T 2oqr_A           27 EGFEATVVTDGPAALAEFDRAGADIVLLDLMLPGMSGTDVCKQLR---A-RSSVPVIMVTARDSEI   88 (230)
T ss_dssp             TTCEEEEECSHHHHHHHHHHHCCSEEEEESSCSSSCHHHHHHHHH---H-HCSCSEEEEECCHHHH
T ss_pred             CCCEEEEECCHHHHHHHHhccCCCEEEEECCCCCCCHHHHHHHHH---c-CCCCCEEEEeCCCcHH
Confidence            34444  4444444   4455899999999999999999999999   2 2678999999876654

>3c97_A Signal transduction histidine kinase; structural genomics, signaling, PSI-2, protein structure initiative; 1.70A {Aspergillus oryzae RIB40}

Probab=99.04  E-value=6.5e-10  Score=56.62  Aligned_cols=59  Identities=20%  Similarity=0.339  Sum_probs=42.3

Q ss_pred             CceeeecChhHH---hhccCccEEEEeCCCCCCCHHHHHHHHHhhc--CCCCCccEEEEeeCCc
Q 039883           18 DGFDLSPTDTEE---VHVLAVDLIITDYCMPGMTGCELIKKIKLQS--FTFREIPTVIISSENI   76 (82)
Q Consensus        18 ~~~~~~~~~~~~---~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~--~~~~~~~vi~ls~~~~   76 (82)
                      ..+..+.++.++   +...+||++|+|+.+|+++|+++++.++...  ...+.+|++++++...
T Consensus        35 ~~v~~~~~~~~al~~l~~~~~dlvllD~~lp~~~g~~~~~~l~~~~~~~~~~~~~ii~~s~~~~   98 (140)
T 3c97_A           35 NDITVVTNGLQALQAYQNRQFDVIIMDIQMPVMDGLEAVSEIRNYERTHNTKRASIIAITADTI   98 (140)
T ss_dssp             SEEEEESSHHHHHHHHHHSCCSEEEECTTCCSSCHHHHHHHHHHHHHHHTCCCCCCEEEESSCC
T ss_pred             CceEEECCHHHHHHHHhcCCCCEEEEeCCCCCCcHHHHHHHHHhhhhhcCCCceEEEEEeCccc
Confidence            334445555544   4456899999999999999999999998211  1246789999987644

>3cg0_A Response regulator receiver modulated diguanylate with PAS/PAC sensor; signal receiver domain, diguanylate cyclase; 2.15A {Desulfovibrio desulfuricans subsp}

Probab=99.04  E-value=3.1e-10  Score=57.59  Aligned_cols=58  Identities=19%  Similarity=0.330  Sum_probs=43.8

Q ss_pred             Cceeee---cChhHH---hhccCccEEEEeCCCC-CCCHHHHHHHHHhhcCCCCCccEEEEeeCCchhh
Q 039883           18 DGFDLS---PTDTEE---VHVLAVDLIITDYCMP-GMTGCELIKKIKLQSFTFREIPTVIISSENILAR   79 (82)
Q Consensus        18 ~~~~~~---~~~~~~---~~~~~~d~vi~d~~~~-~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~~~~   79 (82)
                      .+|++.   .+..++   +...+||++|+|+.+| +.+|+++++.++   .. +.+|+|++|+..+...
T Consensus        32 ~g~~v~~~~~~~~~a~~~~~~~~~dlii~d~~~~~~~~g~~~~~~l~---~~-~~~~ii~ls~~~~~~~   96 (140)
T 3cg0_A           32 LGYDVLGVFDNGEEAVRCAPDLRPDIALVDIMLCGALDGVETAARLA---AG-CNLPIIFITSSQDVET   96 (140)
T ss_dssp             HTCEEEEEESSHHHHHHHHHHHCCSEEEEESSCCSSSCHHHHHHHHH---HH-SCCCEEEEECCCCHHH
T ss_pred             CCCeeEEEECCHHHHHHHHHhCCCCEEEEecCCCCCCCHHHHHHHHH---hC-CCCCEEEEecCCCHHH
Confidence            355544   344443   4456899999999998 799999999999   23 7899999998776543

>3eqz_A Response regulator; structural genomics, unknown function, PSI-2, protein struct initiative; 2.15A {Colwellia psychrerythraea} SCOP: c.23.1.0

Probab=99.03  E-value=4.3e-10  Score=56.70  Aligned_cols=55  Identities=22%  Similarity=0.247  Sum_probs=43.0

Q ss_pred             ceeeecChhHHhh---ccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCch
Q 039883           19 GFDLSPTDTEEVH---VLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENIL   77 (82)
Q Consensus        19 ~~~~~~~~~~~~~---~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~~   77 (82)
                      .+..+.+..+++.   .. ||+||+|+.+|+.+|+++++.++   ...+.+|+|++|+..+.
T Consensus        29 ~v~~~~~~~~~~~~~~~~-~dlvi~D~~l~~~~g~~~~~~l~---~~~~~~~ii~~s~~~~~   86 (135)
T 3eqz_A           29 NVEAFQHPRAFLTLSLNK-QDIIILDLMMPDMDGIEVIRHLA---EHKSPASLILISGYDSG   86 (135)
T ss_dssp             CEEEESCHHHHTTSCCCT-TEEEEEECCTTTTHHHHHHHHHH---HTTCCCEEEEEESSCHH
T ss_pred             eeeeecCHHHHHHhhccC-CCEEEEeCCCCCCCHHHHHHHHH---hCCCCCCEEEEEeccch
Confidence            3444555554433   33 99999999999999999999999   45688999999987763

>3luf_A Two-component system response regulator/ggdef domain protein; structural genomics, ASA_2441, PSI-2, protein structure initiative; HET: MSE; 1.76A {Aeromonas salmonicida} PDB: 3mf4_A*

Probab=99.01  E-value=9.5e-11  Score=65.70  Aligned_cols=44  Identities=18%  Similarity=0.308  Sum_probs=36.3

Q ss_pred             hccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCchhh
Q 039883           31 HVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENILAR   79 (82)
Q Consensus        31 ~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~~~~   79 (82)
                      ...+||++|+|+.||+++|++++++++ .    ..+|||++|+..+.+.
T Consensus        45 ~~~~~dlvllD~~mP~~~G~~~~~~lr-~----~~~pvi~lt~~~~~~~   88 (259)
T 3luf_A           45 QGDEYVVALVDLTLPDAPSGEAVKVLL-E----RGLPVVILTADISEDK   88 (259)
T ss_dssp             CTTTEEEEEEESCBTTBTTSHHHHHHH-H----TTCCEEEEECC-CHHH
T ss_pred             hcCCCcEEEEeCCCCCCCHHHHHHHHH-h----CCCCEEEEEccCCHHH
Confidence            344799999999999999999999999 2    2489999999876654

>2gkg_A Response regulator homolog; social motility, receiver domain, signalling, high resolutio signaling protein; 1.00A {Myxococcus xanthus} PDB: 2i6f_A 2nt4_A 2nt3_A

Probab=99.00  E-value=6.8e-10  Score=55.28  Aligned_cols=59  Identities=19%  Similarity=0.221  Sum_probs=42.9

Q ss_pred             CceeeecChhHH---hhccCccEEEEeCCCC-CCCHHHHHHHHHhhcCCCCCccEEEEeeCCchh
Q 039883           18 DGFDLSPTDTEE---VHVLAVDLIITDYCMP-GMTGCELIKKIKLQSFTFREIPTVIISSENILA   78 (82)
Q Consensus        18 ~~~~~~~~~~~~---~~~~~~d~vi~d~~~~-~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~~~   78 (82)
                      ..+..+.+..++   +...+||++|+|+.+| +.+|.++++.++ .....+.+|+|++ +..+.+
T Consensus        30 ~~v~~~~~~~~a~~~~~~~~~dlvi~d~~~~~~~~g~~~~~~l~-~~~~~~~~~ii~~-~~~~~~   92 (127)
T 2gkg_A           30 FTVDETTDGKGSVEQIRRDRPDLVVLAVDLSAGQNGYLICGKLK-KDDDLKNVPIVII-GNPDGF   92 (127)
T ss_dssp             CEEEEECCHHHHHHHHHHHCCSEEEEESBCGGGCBHHHHHHHHH-HSTTTTTSCEEEE-ECGGGH
T ss_pred             ceEEEecCHHHHHHHHHhcCCCEEEEeCCCCCCCCHHHHHHHHh-cCccccCCCEEEE-ecCCch
Confidence            333334444443   4456899999999999 999999999999 3333678999999 665543

>2qvg_A Two component response regulator; NYSGXRC, PSI-2, structural genomics, protein structure initiative; 1.50A {Legionella pneumophila subsp}

Probab=98.99  E-value=6.2e-09  Score=52.94  Aligned_cols=60  Identities=17%  Similarity=0.406  Sum_probs=44.7

Q ss_pred             ceeeecChhHH---hhc------cCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCchhh
Q 039883           19 GFDLSPTDTEE---VHV------LAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENILAR   79 (82)
Q Consensus        19 ~~~~~~~~~~~---~~~------~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~~~~   79 (82)
                      .+..+.+..++   +..      .+||+||+|+.+|+.+|+++++.++ .....+.+|+|++++..+.+.
T Consensus        35 ~v~~~~~~~~a~~~l~~~~~~~~~~~dlii~D~~l~~~~g~~~~~~l~-~~~~~~~~~ii~ls~~~~~~~  103 (143)
T 2qvg_A           35 KIEIAKSGNQALDMLYGRNKENKIHPKLILLDINIPKMNGIEFLKELR-DDSSFTDIEVFVLTAAYTSKD  103 (143)
T ss_dssp             CEEEESSHHHHHHHHHTCTTCCCCCCSEEEEETTCTTSCHHHHHHHHT-TSGGGTTCEEEEEESCCCHHH
T ss_pred             eEEEECCHHHHHHHHHhcccccCCCCCEEEEecCCCCCCHHHHHHHHH-cCccccCCcEEEEeCCCCHHH
Confidence            45555555544   344      6799999999999999999999999 222227899999998766543

>3sy8_A ROCR; TIM barrel phosphodiesterase-A, transcription regulator; HET: EPE; 2.50A {Pseudomonas aeruginosa}

Probab=98.97  E-value=4.8e-10  Score=66.17  Aligned_cols=55  Identities=18%  Similarity=0.267  Sum_probs=40.4

Q ss_pred             eeeecChhHH---hhc-cCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCch
Q 039883           20 FDLSPTDTEE---VHV-LAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENIL   77 (82)
Q Consensus        20 ~~~~~~~~~~---~~~-~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~~   77 (82)
                      +..+.++.++   +.. .+||+||+|+.||+++|+++++.++   ...+.+++|++|+..+.
T Consensus        31 v~~a~~g~eal~~l~~~~~~DlvllDi~mP~~dG~ell~~l~---~~~~~~~ii~~s~~~~~   89 (400)
T 3sy8_A           31 ILEAADGKEAVAILESCGHVDIAICDLQMSGMDGLAFLRHAS---LSGKVHSVILSSEVDPI   89 (400)
T ss_dssp             EEEESSHHHHHHHHHHHSCEEEEEECSSCSSSCHHHHHHHHH---HHTCEEEEEESCCCCGG
T ss_pred             EEEecCHHHHHHHHhhCCCCCEEEEeCCCCCCCHHHHHHHHH---hcCCCceEEEEcCchHH
Confidence            3334455544   445 3799999999999999999999999   34566777777765543

>3t8y_A CHEB, chemotaxis response regulator protein-glutamate methylesterase; CHEA, hydrolase; 1.90A {Thermotoga maritima}

Probab=98.96  E-value=4.4e-09  Score=55.01  Aligned_cols=51  Identities=25%  Similarity=0.253  Sum_probs=39.8

Q ss_pred             ecChhHH---hhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCch
Q 039883           23 SPTDTEE---VHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENIL   77 (82)
Q Consensus        23 ~~~~~~~---~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~~   77 (82)
                      +.++.++   +...+||+||+|+.+|+++|+++++.++   ...+ .|+|++++..+.
T Consensus        57 ~~~~~~al~~l~~~~~dlvilD~~l~~~~g~~l~~~lr---~~~~-~~ii~~s~~~~~  110 (164)
T 3t8y_A           57 AKDGLEAVEKAIELKPDVITMDIEMPNLNGIEALKLIM---KKAP-TRVIMVSSLTEE  110 (164)
T ss_dssp             ESSHHHHHHHHHHHCCSEEEECSSCSSSCHHHHHHHHH---HHSC-CEEEEEESSCCT
T ss_pred             cCCHHHHHHHhccCCCCEEEEeCCCCCCCHHHHHHHHH---hcCC-ceEEEEecCCcc
Confidence            3444444   4556899999999999999999999999   3344 799999986553

>1dc7_A NTRC, nitrogen regulation protein; receiver domain, phosphorylation, signal transduction, conformational rearrangement; NMR {Salmonella typhimurium} SCOP: c.23.1.1 PDB: 1j56_A 1krw_A 1krx_A 1ntr_A 1dc8_A*

Probab=98.96  E-value=3.1e-11  Score=60.09  Aligned_cols=58  Identities=28%  Similarity=0.478  Sum_probs=43.2

Q ss_pred             Cceee--ecChhHHh---hccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCchh
Q 039883           18 DGFDL--SPTDTEEV---HVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENILA   78 (82)
Q Consensus        18 ~~~~~--~~~~~~~~---~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~~~   78 (82)
                      .++.+  +.++.+++   ...+||++++|+.+|+.+|+++++.++   ...+.+|+|++|+..+.+
T Consensus        26 ~~~~v~~~~~~~~~~~~~~~~~~dlvi~d~~~~~~~g~~~~~~l~---~~~~~~~ii~~s~~~~~~   88 (124)
T 1dc7_A           26 AGLTCTTFENGNEVLAALASKTPDVLLSDIRMPGMDGLALLKQIK---QRHPMLPVIIMTAHSDLD   88 (124)
T ss_dssp             TTCCCEECCCTTHHHHHSSSCCCSCEEECSCSSHHHHCSTHHHHH---HHCTTSCCCCBCCSTTST
T ss_pred             CCcEEEEeCCHHHHHHHHhcCCCCEEEEeeecCCCCHHHHHHHHH---hhCCCCCEEEEecCCCHH
Confidence            34444  33344443   455799999999999999999999998   346778999999876544

>1p2f_A Response regulator; DRRB, OMPR/PHOB, transcription; HET: MSE; 1.80A {Thermotoga maritima} SCOP: a.4.6.1 c.23.1.1 PDB: 3nns_A*

Probab=98.96  E-value=1.2e-09  Score=59.46  Aligned_cols=75  Identities=16%  Similarity=0.116  Sum_probs=50.7

Q ss_pred             CchhHHHHHHHHhcCCCc-eeeecChhHHhhc-cCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCchhh
Q 039883            2 TTTNGVLLSRLMSDGSDG-FDLSPTDTEEVHV-LAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENILAR   79 (82)
Q Consensus         2 d~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~-~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~~~~   79 (82)
                      |+++.............+ +..+.++.+++.. ..||++|+|+.+|+++|+++++.++   ...+.+|+|++|+..+.+.
T Consensus         9 dd~~~~~~~l~~~L~~~~~v~~~~~~~~al~~~~~~dlvllD~~lp~~~g~~~~~~lr---~~~~~~~ii~lt~~~~~~~   85 (220)
T 1p2f_A            9 DDDKNILKKVSEKLQQLGRVKTFLTGEDFLNDEEAFHVVVLDVMLPDYSGYEICRMIK---ETRPETWVILLTLLSDDES   85 (220)
T ss_dssp             CSCHHHHHHHHHHHTTTEEEEEESSHHHHHHCCSCCSEEEEESBCSSSBHHHHHHHHH---HHCTTSEEEEEESCCSHHH
T ss_pred             eCCHHHHHHHHHHHHhCCCEEEECCHHHHHHhcCCCCEEEEeCCCCCCCHHHHHHHHH---hcCCCCcEEEEEcCCCHHH
Confidence            334444433333333333 3334445555543 4799999999999999999999999   3457899999998876543

>3kyj_B CHEY6 protein, putative histidine protein kinase; protein-protein interaction, histidine kinase, response regulator, phosphorylation; 1.40A {Rhodobacter sphaeroides} PDB: 3kyi_B*

Probab=98.95  E-value=5.5e-10  Score=57.18  Aligned_cols=68  Identities=25%  Similarity=0.290  Sum_probs=45.3

Q ss_pred             CchhHHHHHHHHhcCCC-ceeee---cChhHH---hhcc-CccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEee
Q 039883            2 TTTNGVLLSRLMSDGSD-GFDLS---PTDTEE---VHVL-AVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISS   73 (82)
Q Consensus         2 d~~~~~~~~~~~~~~~~-~~~~~---~~~~~~---~~~~-~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~   73 (82)
                      |++.............. ++.++   .++.++   +... +||+||+|+.||+++|+++++.++   ...+ .|+++++.
T Consensus        20 dd~~~~~~~l~~~L~~~~~~~~v~~~~~~~~al~~l~~~~~~dlvilD~~l~~~~g~~~~~~lr---~~~~-~~iiil~~   95 (145)
T 3kyj_B           20 DDAAMMRLYIASFIKTLPDFKVVAQAANGQEALDKLAAQPNVDLILLDIEMPVMDGMEFLRHAK---LKTR-AKICMLSS   95 (145)
T ss_dssp             CSCHHHHHHHHHHHTTCTTEEEEEEESSHHHHHHHHHHCTTCCEEEECTTSCCCTTCHHHHHHH---HHCC-CEEC-CBS
T ss_pred             cCCHHHHHHHHHHHHhCCCceEEEEECCHHHHHHHHhcCCCCCEEEEeCCCCCCCHHHHHHHHH---hcCC-CCeEEEEE
Confidence            34444444444444444 66643   334443   4455 799999999999999999999999   2233 78888886

>2qv0_A Protein MRKE; structural genomics, transcription, PSI-2, protein structure initiative; 2.40A {Klebsiella pneumoniae}

Probab=98.94  E-value=2.5e-09  Score=54.46  Aligned_cols=44  Identities=23%  Similarity=0.217  Sum_probs=36.8

Q ss_pred             HhhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCC
Q 039883           29 EVHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSEN   75 (82)
Q Consensus        29 ~~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~   75 (82)
                      .+...+||++|+|+.+|+.+|+++++.++   ...+..|+|++|+..
T Consensus        50 ~l~~~~~dlvi~d~~l~~~~g~~~~~~l~---~~~~~~~ii~~s~~~   93 (143)
T 2qv0_A           50 FLQHNKVDAIFLDINIPSLDGVLLAQNIS---QFAHKPFIVFITAWK   93 (143)
T ss_dssp             HHHHCCCSEEEECSSCSSSCHHHHHHHHT---TSTTCCEEEEEESCC
T ss_pred             HHHhCCCCEEEEecCCCCCCHHHHHHHHH---ccCCCceEEEEeCCH
Confidence            34566899999999999999999999999   456677888888763

>1qo0_D AMIR; binding protein, gene regulator, receptor; 2.25A {Pseudomonas aeruginosa} SCOP: c.23.1.3

Probab=98.93  E-value=4.3e-10  Score=60.31  Aligned_cols=57  Identities=12%  Similarity=0.046  Sum_probs=42.0

Q ss_pred             Cceeeec--ChhHHhhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCchhh
Q 039883           18 DGFDLSP--TDTEEVHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENILAR   79 (82)
Q Consensus        18 ~~~~~~~--~~~~~~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~~~~   79 (82)
                      .+|.+..  ++.+++ ...||+||+|+.||+++|. +++.++   ...+.+|+|++|+..+.+.
T Consensus        35 ~g~~v~~~~~~~~al-~~~~dlvl~D~~mp~~~g~-l~~~~~---~~~~~~~ii~lt~~~~~~~   93 (196)
T 1qo0_D           35 IGCSVRQCWPPPEAF-DVPVDVVFTSIFQNRHHDE-IAALLA---AGTPRTTLVALVEYESPAV   93 (196)
T ss_dssp             HTCEEEEECSCCSSC-SSCCSEEEEECCSSTHHHH-HHHHHH---HSCTTCEEEEEECCCSHHH
T ss_pred             cCCeEEEecCchhhC-CCCCCEEEEeCCCCccchH-HHHHHh---ccCCCCCEEEEEcCCChHH
Confidence            4555533  333444 4579999999999999998 888888   2237899999999877654

>1a2o_A CHEB methylesterase; bacterial chemotaxis, adaptation, serine hydrolase; 2.40A {Salmonella typhimurium} SCOP: c.23.1.1 c.40.1.1

Probab=98.93  E-value=4e-09  Score=61.58  Aligned_cols=72  Identities=18%  Similarity=0.218  Sum_probs=49.3

Q ss_pred             CchhHHHHHHHHhcCC-Cceee---ecChhHH---hhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeC
Q 039883            2 TTTNGVLLSRLMSDGS-DGFDL---SPTDTEE---VHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSE   74 (82)
Q Consensus         2 d~~~~~~~~~~~~~~~-~~~~~---~~~~~~~---~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~   74 (82)
                      |++..........+.. .++++   ..++.++   +...+||++++|+.||+++|+++++.++   ...+ +|+|++|+.
T Consensus        10 DD~~~~r~~L~~~L~~~~g~~vv~~a~~~~eAl~~l~~~~pDlVllDi~mp~~dGlell~~l~---~~~p-~pVIvlS~~   85 (349)
T 1a2o_A           10 DDSALMRQIMTEIINSHSDMEMVATAPDPLVARDLIKKFNPDVLTLDVEMPRMDGLDFLEKLM---RLRP-MPVVMVSSL   85 (349)
T ss_dssp             CSCHHHHHHHHHHHHTSTTEEEEEEESSHHHHHHHHHHHCCSEEEEECCCSSSCHHHHHHHHH---HSSC-CCEEEEECC
T ss_pred             ECCHHHHHHHHHHHhcCCCcEEEEEeCCHHHHHHHHhccCCCEEEEECCCCCCCHHHHHHHHH---hcCC-CcEEEEECC
Confidence            4444444443333333 36663   3344443   4456899999999999999999999999   3344 899999987


Q ss_pred             Cch
Q 039883           75 NIL   77 (82)
Q Consensus        75 ~~~   77 (82)
                      .+.
T Consensus        86 ~~~   88 (349)
T 1a2o_A           86 TGK   88 (349)
T ss_dssp             THH
T ss_pred             Ccc
Confidence            653

>2qsj_A DNA-binding response regulator, LUXR family; structural genomics, PSI-2, protein structure initiative; 2.10A {Silicibacter pomeroyi dss-3}

Probab=98.89  E-value=4.8e-10  Score=57.87  Aligned_cols=56  Identities=20%  Similarity=0.182  Sum_probs=34.0

Q ss_pred             eeeecChhH---Hhhc-cCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCchh
Q 039883           20 FDLSPTDTE---EVHV-LAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENILA   78 (82)
Q Consensus        20 ~~~~~~~~~---~~~~-~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~~~   78 (82)
                      +..+.+..+   .+.. .+||++|+|+.+++.+|+++++.++   ...+.+|+|++|+..+.+
T Consensus        32 v~~~~~~~~a~~~l~~~~~~dlvi~d~~l~~~~g~~~~~~l~---~~~~~~~ii~ls~~~~~~   91 (154)
T 2qsj_A           32 VEGAETVSDALAFLEADNTVDLILLDVNLPDAEAIDGLVRLK---RFDPSNAVALISGETDHE   91 (154)
T ss_dssp             EEEESSHHHHHHHHHTTCCCSEEEECC------CHHHHHHHH---HHCTTSEEEEC-----CH
T ss_pred             EEEecCHHHHHHHHhccCCCCEEEEeCCCCCCchHHHHHHHH---HhCCCCeEEEEeCCCCHH
Confidence            344455554   3455 7899999999999999999999999   446789999999876543

>1dcf_A ETR1 protein; beta-alpha five sandwich, transferase; 2.50A {Arabidopsis thaliana} SCOP: c.23.1.2

Probab=98.88  E-value=3.3e-09  Score=53.64  Aligned_cols=61  Identities=18%  Similarity=0.325  Sum_probs=39.7

Q ss_pred             Cceee--ecChhHHhhcc--CccEEEEeCCCCCCCHHHHHHHHHhhcCC--CCCccEEEEeeCCchh
Q 039883           18 DGFDL--SPTDTEEVHVL--AVDLIITDYCMPGMTGCELIKKIKLQSFT--FREIPTVIISSENILA   78 (82)
Q Consensus        18 ~~~~~--~~~~~~~~~~~--~~d~vi~d~~~~~~~~~~~~~~l~~~~~~--~~~~~vi~ls~~~~~~   78 (82)
                      .++++  +.++.+++...  .+|++|+|+.||+++|+++++.+++....  ...+++|++|+..+..
T Consensus        30 ~g~~v~~~~~~~~a~~~~~~~~dlvllD~~lp~~~g~~~~~~l~~~~~~~~~~~~~ii~~s~~~~~~   96 (136)
T 1dcf_A           30 LGCEVTTVSSNEECLRVVSHEHKVVFMDVCMPGVENYQIALRIHEKFTKQRHQRPLLVALSGNTDKS   96 (136)
T ss_dssp             TTCEEEEESSHHHHHHHCCTTCSEEEEECCSSTTTTTHHHHHHHHHHC-CCSCCCEEEEEESCCSHH
T ss_pred             cCCeEEEeCCHHHHHHHHhccCCEEEEeCCCCCCcHHHHHHHHHHhhhhccCCCceEEEEeCCCCHH
Confidence            34444  44444554422  35999999999999999999999721111  1234578888776654

>2vyc_A Biodegradative arginine decarboxylase; pyridoxal phosphate, PLP-dependent E lyase, acid resistance; HET: LLP; 2.4A {Escherichia coli}

Probab=98.71  E-value=4.7e-09  Score=66.39  Aligned_cols=57  Identities=16%  Similarity=0.257  Sum_probs=43.6

Q ss_pred             CCceee--ecChhHH---hhcc-CccEEEEeCCCCC----CCHHHHHHHHHhhcCCCCCccEEEEeeCCc
Q 039883           17 SDGFDL--SPTDTEE---VHVL-AVDLIITDYCMPG----MTGCELIKKIKLQSFTFREIPTVIISSENI   76 (82)
Q Consensus        17 ~~~~~~--~~~~~~~---~~~~-~~d~vi~d~~~~~----~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~   76 (82)
                      ..+|++  ..++.++   +... +||+||+|+.||+    ++|+++++.+|   .....+||+++|+..+
T Consensus        30 ~~g~~v~~a~~g~~al~~~~~~~~~d~vilDi~lp~~~~~~~G~~ll~~iR---~~~~~iPIi~lTa~~~   96 (755)
T 2vyc_A           30 QQNVTVIKSTSFDDGFAILSSNEAIDCLMFSYQMEHPDEHQNVRQLIGKLH---ERQQNVPVFLLGDREK   96 (755)
T ss_dssp             HTTCEEEEESSHHHHHHHHTTTCCCSEEEEECCCCSHHHHHHHHHHHHHHH---HHSTTCCEEEEECHHH
T ss_pred             hCCCEEEEECCHHHHHHHHhcCCCCcEEEEeCCCCcccccccHHHHHHHHH---HhCCCCCEEEEecCCc
Confidence            355555  4455544   3344 4999999999999    99999999999   4456799999998654

>2hqr_A Putative transcriptional regulator; phosporylation-independent response regulator, H. pylori, SY dimer, signaling protein; NMR {Helicobacter pylori}

Probab=98.70  E-value=2.2e-08  Score=54.57  Aligned_cols=71  Identities=11%  Similarity=0.114  Sum_probs=46.0

Q ss_pred             CchhHHHHHHHHhcCCCceee--ecChhHH---hhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCc
Q 039883            2 TTTNGVLLSRLMSDGSDGFDL--SPTDTEE---VHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENI   76 (82)
Q Consensus         2 d~~~~~~~~~~~~~~~~~~~~--~~~~~~~---~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~   76 (82)
                      |+++.............++.+  +.++.++   +...+||++|    ||+++|+++++.++   .....+|+|++|+..+
T Consensus         7 dd~~~~~~~l~~~L~~~g~~v~~~~~~~~al~~l~~~~~dlvi----lp~~~g~~~~~~lr---~~~~~~~ii~lt~~~~   79 (223)
T 2hqr_A            7 EKNSVLGGEIEKGLNVKGFMADVTESLEDGEYLMDIRNYDLVM----VSDKNALSFVSRIK---EKHSSIVVLVSSDNPT   79 (223)
T ss_dssp             CSCHHHHHHHHHHHGGGTCCEEEESSHHHHHHHHTTSCCSEEE----ECCTTHHHHHHHHH---HHCTTSEEEEEESSCC
T ss_pred             cCCHHHHHHHHHHHHHCCcEEEEECCHHHHHHHHhcCCCCEEE----eCCCCHHHHHHHHH---hCCCCCcEEEEECCCC
Confidence            344444433333332344544  4444444   4455899999    89999999999999   3323899999998876


Q ss_pred             hhh
Q 039883           77 LAR   79 (82)
Q Consensus        77 ~~~   79 (82)
                      .+.
T Consensus        80 ~~~   82 (223)
T 2hqr_A           80 SEE   82 (223)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            544

>2pln_A HP1043, response regulator; signaling protein; 1.80A {Helicobacter pylori} PDB: 2hqo_A

Probab=98.63  E-value=4.1e-08  Score=49.62  Aligned_cols=54  Identities=13%  Similarity=0.190  Sum_probs=39.1

Q ss_pred             CceeeecChhHH---hhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCC-CccEEEEeeCCchhh
Q 039883           18 DGFDLSPTDTEE---VHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFR-EIPTVIISSENILAR   79 (82)
Q Consensus        18 ~~~~~~~~~~~~---~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~-~~~vi~ls~~~~~~~   79 (82)
                      ..+..+.+..++   +....||++|    +|+.+|+++++.++   .. + .+|+|++|+..+.+.
T Consensus        43 ~~v~~~~~~~~al~~l~~~~~dlvi----~~~~~g~~~~~~l~---~~-~~~~~ii~ls~~~~~~~  100 (137)
T 2pln_A           43 FMADVTESLEDGEYLMDIRNYDLVM----VSDKNALSFVSRIK---EK-HSSIVVLVSSDNPTSEE  100 (137)
T ss_dssp             CEEEEESCHHHHHHHHHHSCCSEEE----ECSTTHHHHHHHHH---HH-STTSEEEEEESSCCHHH
T ss_pred             cEEEEeCCHHHHHHHHHcCCCCEEE----EcCccHHHHHHHHH---hc-CCCccEEEEeCCCCHHH
Confidence            333334444443   4456899999    89999999999999   33 6 899999998766543

>3cwo_X Beta/alpha-barrel protein based on 1THF and 1TMY; XRAY, CHEY, HISF, half barrel, de novo protein; 3.10A {Thermotoga maritima} PDB: 2lle_A

Probab=98.48  E-value=3.3e-07  Score=50.09  Aligned_cols=45  Identities=27%  Similarity=0.352  Sum_probs=33.4

Q ss_pred             HHhhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCC
Q 039883           28 EEVHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSEN   75 (82)
Q Consensus        28 ~~~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~   75 (82)
                      +.+...+||++|+|+.||+++|+++++.++   ...+..++++++...
T Consensus        19 ~~~~~~~~dlvl~D~~~p~~~g~~~~~~l~---~~~~~~~i~vi~~~~   63 (237)
T 3cwo_X           19 EKYKELKPDIVTMDITMPEMNGIDAIKEIM---KIDPNAKIIVCSAMG   63 (237)
T ss_dssp             HHHHHHCCSCEEEECCSTTSSHHHHHHHHH---HHSSSCCEEEECCSS
T ss_pred             HHHHhcCCCEEEEeCCCCCCCHHHHHHHHH---HhCCCCCEEEEECCC
Confidence            345566899999999999999999999998   233344555555443

>1w25_A Stalked-cell differentiation controlling protein; two-component system, ggdef domain, cyclic dinucleotide, cyclic-digmp; HET: C2E; 2.70A {Caulobacter vibrioides} SCOP: c.23.1.1 c.23.1.1 d.58.29.2 PDB: 2v0n_A* 2wb4_A*

Probab=97.78  E-value=5.4e-05  Score=45.27  Aligned_cols=46  Identities=15%  Similarity=0.253  Sum_probs=38.3

Q ss_pred             ccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCchh
Q 039883           32 VLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENILA   78 (82)
Q Consensus        32 ~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~~~   78 (82)
                      ...||++++|..||+++|+++++.++ ........|++++|+..+..
T Consensus       192 ~~~~dlil~D~~mp~~dG~~~~~~ir-~~~~~~~~pii~lt~~~~~~  237 (459)
T 1w25_A          192 GGPVDLVIVNAAAKNFDGLRFTAALR-SEERTRQLPVLAMVDPDDRG  237 (459)
T ss_dssp             HSSCSEEEEETTCSSSCHHHHHHHHH-TSGGGTTCCEEEEECTTCHH
T ss_pred             cCCCCEEEEecCCCCCcHHHHHHHHH-hCccccCCcEEEEcCCCchH
Confidence            34689999999999999999999999 44456788999999876643

>3n75_A LDC, lysine decarboxylase, inducible; pyridoxal-5'-phosphate dependent decarboxylase, acid stress stringent response; HET: LLP G4P P6G; 2.00A {Escherichia coli} PDB: 3q16_A*

Probab=95.88  E-value=0.0086  Score=38.38  Aligned_cols=57  Identities=12%  Similarity=0.074  Sum_probs=41.4

Q ss_pred             hcCCCceeeecChh--H---Hhhcc-CccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCc
Q 039883           14 SDGSDGFDLSPTDT--E---EVHVL-AVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENI   76 (82)
Q Consensus        14 ~~~~~~~~~~~~~~--~---~~~~~-~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~   76 (82)
                      .+...+|++..+.+  +   .++.. ..++||+|+.++   +.++++.+|   ..+..+||++++....
T Consensus        25 ~Le~~g~~V~~a~s~~Da~~~i~~~~~i~avIld~d~~---~~~ll~~Ir---~~~~~iPVFl~~~~~~   87 (715)
T 3n75_A           25 ALERLNFQIVYPNDRDDLLKLIENNARLCGVIFDWDKY---NLELCEEIS---KMNENLPLYAFANTYS   87 (715)
T ss_dssp             HHHHTTCEEECCSSHHHHHHHHHHCTTEEEEEEEHHHH---HHHHHHHHH---HHCTTCEEEEECCTTC
T ss_pred             HHHHCCcEEEEeCCHHHHHHHHHhCCCceEEEEecccc---HHHHHHHHH---HhCCCCCEEEEecCCc
Confidence            33455777755533  3   33333 588999999986   688999999   5688999999987744

>1g5t_A COB(I)alamin adenosyltransferase; P-loop protein, cobalamin biosynthesis, RECA fold; HET: ATP; 1.80A {Salmonella typhimurium} SCOP: c.37.1.11 PDB: 1g5r_A* 1g64_A*

Probab=86.74  E-value=2.5  Score=22.96  Aligned_cols=42  Identities=17%  Similarity=0.113  Sum_probs=27.4

Q ss_pred             ccCccEEEEeCC-----CCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCch
Q 039883           32 VLAVDLIITDYC-----MPGMTGCELIKKIKLQSFTFREIPTVIISSENIL   77 (82)
Q Consensus        32 ~~~~d~vi~d~~-----~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~~   77 (82)
                      ..++|+||+|-.     +.-.+.-+++..|.   ......- +++|+...+
T Consensus       118 ~~~yDlvILDEi~~al~~g~l~~~ev~~~l~---~Rp~~~~-vIlTGr~ap  164 (196)
T 1g5t_A          118 DPLLDMVVLDELTYMVAYDYLPLEEVISALN---ARPGHQT-VIITGRGCH  164 (196)
T ss_dssp             CTTCSEEEEETHHHHHHTTSSCHHHHHHHHH---TSCTTCE-EEEECSSCC
T ss_pred             cCCCCEEEEeCCCccccCCCCCHHHHHHHHH---hCcCCCE-EEEECCCCc
Confidence            347999999974     34556778888888   4455554 455554443

>3md9_A Hemin-binding periplasmic protein HMUT; transport protein, alpha beta protein, rigid helical backbon substrate-free, heme transport; 1.50A {Yersinia pestis} PDB: 3nu1_A*

Probab=84.66  E-value=1.1  Score=24.67  Aligned_cols=38  Identities=8%  Similarity=0.169  Sum_probs=25.7

Q ss_pred             HHhhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEee
Q 039883           28 EEVHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISS   73 (82)
Q Consensus        28 ~~~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~   73 (82)
                      |.+...+||+||.......   .+....|+     ...+|++++..
T Consensus        53 E~i~~l~PDlIi~~~~~~~---~~~~~~L~-----~~gipvv~~~~   90 (255)
T 3md9_A           53 EGILAMKPTMLLVSELAQP---SLVLTQIA-----SSGVNVVTVPG   90 (255)
T ss_dssp             HHHHTTCCSEEEEETTCSC---HHHHHHHH-----HTTCEEEEECC
T ss_pred             HHHHccCCCEEEEcCCcCc---hhHHHHHH-----HcCCcEEEeCC
Confidence            7788889999998765432   34455665     22368888864

>4h08_A Putative hydrolase; GDSL-like lipase/acylhydrolase family protein, structural GE joint center for structural genomics, JCSG; HET: GOL; 1.80A {Bacteroides thetaiotaomicron}

Probab=84.07  E-value=2.1  Score=22.44  Aligned_cols=41  Identities=20%  Similarity=0.181  Sum_probs=25.7

Q ss_pred             hhccCccEEEEeCCCCCC--CH-------HHHHHHHHhhcCCCCCccEEEEee
Q 039883           30 VHVLAVDLIITDYCMPGM--TG-------CELIKKIKLQSFTFREIPTVIISS   73 (82)
Q Consensus        30 ~~~~~~d~vi~d~~~~~~--~~-------~~~~~~l~~~~~~~~~~~vi~ls~   73 (82)
                      +...+||+|++.+..-+.  +.       .++++.++   ...+.+++|+++.
T Consensus        70 ~~~~~pd~Vvi~~G~ND~~~~~~~~~~~l~~ii~~l~---~~~p~~~ii~~~~  119 (200)
T 4h08_A           70 LKNTKFDVIHFNNGLHGFDYTEEEYDKSFPKLIKIIR---KYAPKAKLIWANT  119 (200)
T ss_dssp             HHHSCCSEEEECCCSSCTTSCHHHHHHHHHHHHHHHH---HHCTTCEEEEECC
T ss_pred             HhcCCCCeEEEEeeeCCCCCCHHHHHHHHHHHHHHHh---hhCCCccEEEecc
Confidence            345589999997666553  22       23445555   4567778887764

>2r7a_A Bacterial heme binding protein; periplasmic binding protein, heme transport, transport protein; HET: HEM; 2.05A {Shigella dysenteriae} PDB: 2rg7_A

Probab=80.26  E-value=2.1  Score=23.57  Aligned_cols=38  Identities=16%  Similarity=0.162  Sum_probs=24.6

Q ss_pred             HHhhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEee
Q 039883           28 EEVHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISS   73 (82)
Q Consensus        28 ~~~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~   73 (82)
                      |.+...+||+||......   ..+....|+     ...+|++++..
T Consensus        53 E~i~~l~PDLIi~~~~~~---~~~~~~~L~-----~~gipvv~~~~   90 (256)
T 2r7a_A           53 EGILSLRPDSVITWQDAG---PQIVLDQLR-----AQKVNVVTLPR   90 (256)
T ss_dssp             HHHHTTCCSEEEEETTCS---CHHHHHHHH-----HTTCEEEEECC
T ss_pred             HHHHccCCCEEEEcCCCC---CHHHHHHHH-----HcCCcEEEecC
Confidence            778888999999865421   134556665     22367887753

---

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	82
d1dz3a_	123	c.23.1.1 (A:) Sporulation response regulator Spo0A	5e-04
d2b4aa1	118	c.23.1.1 (A:2-119) Hypothetical protein BH3024 {Ba	5e-04
d1a04a2	138	c.23.1.1 (A:5-142) Nitrate/nitrite response regula	0.001
d1jbea_	128	c.23.1.1 (A:) CheY protein {Escherichia coli [TaxI	0.003
d1a2oa1	140	c.23.1.1 (A:1-140) Methylesterase CheB, N-terminal	0.004

>d1dz3a_ c.23.1.1 (A:) Sporulation response regulator Spo0A {Bacillus stearothermophilus [TaxId: 1422]} Length = 123

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Sporulation response regulator Spo0A
species: Bacillus stearothermophilus [TaxId: 1422]

 Score = 34.0 bits (78), Expect = 5e-04
 Identities = 10/46 (21%), Positives = 23/46 (50%), Gaps = 3/46 (6%)

Query: 28 EEVHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISS 73
          + +     D+++ D  MP + G  ++++I+     F   P VI+ +
Sbjct: 41 QMLEEKRPDILLLDIIMPHLDGLAVLERIRAG---FEHQPNVIMLT 83

>d2b4aa1 c.23.1.1 (A:2-119) Hypothetical protein BH3024 {Bacillus halodurans [TaxId: 86665]} Length = 118

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Hypothetical protein BH3024
species: Bacillus halodurans [TaxId: 86665]

 Score = 33.7 bits (77), Expect = 5e-04
 Identities = 7/38 (18%), Positives = 20/38 (52%), Gaps = 3/38 (7%)

Query: 36 DLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISS 73
          DL+I    +  ++   L+  +K Q+   ++   +I+++
Sbjct: 49 DLLIVSDQLVDLSIFSLLDIVKEQT---KQPSVLILTT 83

>d1a04a2 c.23.1.1 (A:5-142) Nitrate/nitrite response regulator (NarL), receiver domain {Escherichia coli [TaxId: 562]} Length = 138

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Nitrate/nitrite response regulator (NarL), receiver domain
species: Escherichia coli [TaxId: 562]

 Score = 33.3 bits (76), Expect = 0.001
 Identities = 18/64 (28%), Positives = 29/64 (45%), Gaps = 5/64 (7%)

Query: 8  LLSRLMSDGSDGFDLSPTDT-----EEVHVLAVDLIITDYCMPGMTGCELIKKIKLQSFT 62
           + +L+S   D   +          E    L  DLI+ D  MPGM G E + K++ +S +
Sbjct: 17 GVKQLISMAPDITVVGEASNGEQGIELAESLDPDLILLDLNMPGMNGLETLDKLREKSLS 76

Query: 63 FREI 66
           R +
Sbjct: 77 GRIV 80

>d1a2oa1 c.23.1.1 (A:1-140) Methylesterase CheB, N-terminal domain {Salmonella typhimurium [TaxId: 90371]} Length = 140

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Methylesterase CheB, N-terminal domain
species: Salmonella typhimurium [TaxId: 90371]

 Score = 31.5 bits (71), Expect = 0.004
 Identities = 12/38 (31%), Positives = 21/38 (55%), Gaps = 4/38 (10%)

Query: 36 DLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISS 73
          D++  D  MP M G + ++K+       R +P V++SS
Sbjct: 51 DVLTLDVEMPRMDGLDFLEKLM----RLRPMPVVMVSS 84

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	82
d1w25a2	153	Response regulator PleD, receiver domain {Caulobac	99.67
d1peya_	119	Sporulation response regulator Spo0F {Bacillus sub	99.67
d1zesa1	121	PhoB receiver domain {Escherichia coli [TaxId: 562	99.66
d1ys7a2	121	Transcriptional regulatory protein PrrA, N-termina	99.65
d2pl1a1	119	PhoP receiver domain {Escherichia coli [TaxId: 562	99.65
d1dbwa_	123	Transcriptional regulatory protein FixJ, receiver	99.65
d1qkka_	140	Transcriptional regulatory protein DctD, receiver	99.64
d1mb3a_	123	Cell division response regulator DivK {Caulobacter	99.63
d1krwa_	123	NTRC receiver domain {Salmonella typhimurium [TaxI	99.63
d1s8na_	190	Probable two-component system transcriptional regu	99.62
d1ny5a1	137	Transcriptional activator sigm54 (NtrC1), N-termin	99.61
d1kgsa2	122	PhoB receiver domain {Thermotoga maritima [TaxId:	99.61
d1p6qa_	129	CheY protein {Sinorhizobium meliloti, CheY2 [TaxId	99.6
d1mvoa_	121	PhoP receiver domain {Bacillus subtilis [TaxId: 14	99.6
d1jbea_	128	CheY protein {Escherichia coli [TaxId: 562]}	99.6
d1u0sy_	118	CheY protein {Thermotoga maritima [TaxId: 2336]}	99.59
d2a9pa1	117	DNA-binding response regulator MicA, N-terminal do	99.59
d1zh2a1	119	Transcriptional regulatory protein KdpE, N-termina	99.58
d2b4aa1	118	Hypothetical protein BH3024 {Bacillus halodurans [	99.58
d1w25a1	139	Response regulator PleD, receiver domain {Caulobac	99.57
d1xhfa1	121	Aerobic respiration control protein ArcA, N-termin	99.56
d1k66a_	149	Response regulator for cyanobacterial phytochrome	99.54
d2ayxa1	133	Sensor kinase protein RcsC, C-terminal domain {Esc	99.54
d1yioa2	128	Response regulatory protein StyR, N-terminal domai	99.54
d1a04a2	138	Nitrate/nitrite response regulator (NarL), receive	99.53
d1zgza1	120	TorCAD operon transcriptional regulator TorD, N-te	99.53
d1i3ca_	144	Response regulator for cyanobacterial phytochrome	99.53
d1p2fa2	120	Response regulator DrrB {Thermotoga maritima [TaxI	99.52
d1k68a_	140	Response regulator for cyanobacterial phytochrome	99.52
d2r25b1	128	Response regulator Sin1 {Baker's yeast (Saccharomy	99.47
d1dz3a_	123	Sporulation response regulator Spo0A {Bacillus ste	99.46
d1a2oa1	140	Methylesterase CheB, N-terminal domain {Salmonella	99.45
d1dcfa_	134	Receiver domain of the ethylene receptor {Thale cr	99.45
d1qo0d_	189	Positive regulator of the amidase operon AmiR {Pse	99.13
d3bula2	156	Methionine synthase, C-terminal domain {Escherichi	82.67

>d1w25a2 c.23.1.1 (A:141-293) Response regulator PleD, receiver domain {Caulobacter crescentus [TaxId: 155892]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Response regulator PleD, receiver domain
species: Caulobacter crescentus [TaxId: 155892]

Probab=99.67  E-value=2.7e-16  Score=81.26  Aligned_cols=78  Identities=14%  Similarity=0.181  Sum_probs=61.8

Q ss_pred             CchhHHHHHHHHhcCCCceeeecChhHH---hhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCchh
Q 039883            2 TTTNGVLLSRLMSDGSDGFDLSPTDTEE---VHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENILA   78 (82)
Q Consensus         2 d~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~~~   78 (82)
                      |+++..+......+...+|.++.++.++   +...+||+||+|+.||+++|+++++.+| .....+.+|||++|+..+..
T Consensus        20 DD~~~~~~~l~~~L~~~g~~v~~~~~~~~~~~~~~~~DlillD~~mP~~dG~el~~~ir-~~~~~~~iPiI~lt~~~~~~   98 (153)
T d1w25a2          20 DDNERQAQRVAAELGVEHRPVIESDPEKAKISAGGPVDLVIVNAAAKNFDGLRFTAALR-SEERTRQLPVLAMVDPDDRG   98 (153)
T ss_dssp             CSCHHHHHHHHHHHTTTSEEEEECCHHHHHHHHHSSCSEEEEETTCSSSCHHHHHHHHH-TSGGGTTCCEEEEECTTCHH
T ss_pred             eCCHHHHHHHHHHHHHCCCEEEEccHHHHHHHhcCCCCEEEEECccccccchHHHHHHH-hccccccceeEEeecCCCHH
Confidence            5556666666666678889988876643   3466899999999999999999999999 54567789999999987765


Q ss_pred             hh
Q 039883           79 RI   80 (82)
Q Consensus        79 ~~   80 (82)
                      ..
T Consensus        99 ~~  100 (153)
T d1w25a2          99 RM  100 (153)
T ss_dssp             HH
T ss_pred             HH
Confidence            43

>d1peya_ c.23.1.1 (A:) Sporulation response regulator Spo0F {Bacillus subtilis [TaxId: 1423]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Sporulation response regulator Spo0F
species: Bacillus subtilis [TaxId: 1423]

Probab=99.67  E-value=5.3e-17  Score=80.89  Aligned_cols=76  Identities=22%  Similarity=0.343  Sum_probs=56.1

Q ss_pred             CchhHHHHHHHHhcCCCceeee--cChhH---HhhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCc
Q 039883            2 TTTNGVLLSRLMSDGSDGFDLS--PTDTE---EVHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENI   76 (82)
Q Consensus         2 d~~~~~~~~~~~~~~~~~~~~~--~~~~~---~~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~   76 (82)
                      |+++..+..........||++.  .++.+   .+...+||+||+|+.||+++|+++++++|   ...+.+|+|++|+..+
T Consensus         8 DD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~~~~~~~dlillD~~mP~~~G~el~~~lr---~~~~~~pvi~lt~~~~   84 (119)
T d1peya_           8 DDQSGIRILLNEVFNKEGYQTFQAANGLQALDIVTKERPDLVLLDMKIPGMDGIEILKRMK---VIDENIRVIIMTAYGE   84 (119)
T ss_dssp             CSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHHHHHCCSEEEEESCCTTCCHHHHHHHHH---HHCTTCEEEEEESSCC
T ss_pred             eCCHHHHHHHHHHHHHcCCEEEEeCCHHHHHHHHHhCCCCEEEEeccCCCCCHHHHHHHHH---HhCCCCcEEEEecCCC
Confidence            5555666555554445566654  44444   45566899999999999999999999999   4467899999999877


Q ss_pred             hhhh
Q 039883           77 LARI   80 (82)
Q Consensus        77 ~~~~   80 (82)
                      .+..
T Consensus        85 ~~~~   88 (119)
T d1peya_          85 LDMI   88 (119)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            6543

>d1zesa1 c.23.1.1 (A:3-123) PhoB receiver domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: PhoB receiver domain
species: Escherichia coli [TaxId: 562]

Probab=99.66  E-value=1e-16  Score=80.04  Aligned_cols=78  Identities=22%  Similarity=0.316  Sum_probs=57.3

Q ss_pred             CchhHHHHHHHHhcCCCceee--ecChhHHh---hccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCc
Q 039883            2 TTTNGVLLSRLMSDGSDGFDL--SPTDTEEV---HVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENI   76 (82)
Q Consensus         2 d~~~~~~~~~~~~~~~~~~~~--~~~~~~~~---~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~   76 (82)
                      |+++.........+...||++  +.++.+++   ...+||++|+|+.||+++|+++++.+| .....+.+|+|++|+..+
T Consensus         7 DD~~~~~~~l~~~L~~~g~~v~~a~~~~~al~~l~~~~~dlil~D~~mp~~~G~~l~~~lr-~~~~~~~~pvi~lt~~~~   85 (121)
T d1zesa1           7 EDEAPIREMVCFVLEQNGFQPVEAEDYDSAVNQLNEPWPDLILLDWMLPGGSGIQFIKHLK-RESMTRDIPVVMLTARGE   85 (121)
T ss_dssp             CSCHHHHHHHHHHHHHTTCEEEEECSHHHHHHHSSSSCCSEEEECSSCTTSCHHHHHHHHH-HSTTTTTSCEEEEESCCS
T ss_pred             eCCHHHHHHHHHHHHHCCCEEEEECChHHHHHHHHccCCCEEEeecCCCCCCHHHHHHHHH-hCccCCCCeEEEEECCCC
Confidence            455555544444444456665  44555554   455899999999999999999999999 556778899999999877


Q ss_pred             hhhh
Q 039883           77 LARI   80 (82)
Q Consensus        77 ~~~~   80 (82)
                      .+..
T Consensus        86 ~~~~   89 (121)
T d1zesa1          86 EEDR   89 (121)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            6543

>d1ys7a2 c.23.1.1 (A:7-127) Transcriptional regulatory protein PrrA, N-terminal domain {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Transcriptional regulatory protein PrrA, N-terminal domain
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=99.65  E-value=2e-16  Score=79.00  Aligned_cols=75  Identities=19%  Similarity=0.299  Sum_probs=54.9

Q ss_pred             CchhHHHHHHHHhcCCCceee--ecChhH---HhhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCc
Q 039883            2 TTTNGVLLSRLMSDGSDGFDL--SPTDTE---EVHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENI   76 (82)
Q Consensus         2 d~~~~~~~~~~~~~~~~~~~~--~~~~~~---~~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~   76 (82)
                      |++...+......+...||++  +.++.+   .+...+||+||+|+.||+++|+++++.+|   ...+.+|+|++|+..+
T Consensus         8 DD~~~~~~~l~~~L~~~g~~v~~a~~~~eal~~~~~~~~dlvl~D~~mP~~~G~el~~~ir---~~~~~~piI~lt~~~~   84 (121)
T d1ys7a2           8 DDDSDVLASLERGLRLSGFEVATAVDGAEALRSATENRPDAIVLDINMPVLDGVSVVTALR---AMDNDVPVCVLSARSS   84 (121)
T ss_dssp             CSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHHHHSCCSEEEEESSCSSSCHHHHHHHHH---HTTCCCCEEEEECCCT
T ss_pred             ECCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHHhCCCCEEEEEeeccCcccHHHHHHHH---hcCCCCEEEEEEeeCC
Confidence            455555544444444455655  444554   45566899999999999999999999999   4567899999999876


Q ss_pred             hhh
Q 039883           77 LAR   79 (82)
Q Consensus        77 ~~~   79 (82)
                      .+.
T Consensus        85 ~~~   87 (121)
T d1ys7a2          85 VDD   87 (121)
T ss_dssp             TTC
T ss_pred             HHH
Confidence            654

>d2pl1a1 c.23.1.1 (A:1-119) PhoP receiver domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: PhoP receiver domain
species: Escherichia coli [TaxId: 562]

Probab=99.65  E-value=1.7e-16  Score=79.01  Aligned_cols=76  Identities=13%  Similarity=0.188  Sum_probs=56.1

Q ss_pred             CchhHHHHHHHHhcCCCceee--ecChhH---HhhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCc
Q 039883            2 TTTNGVLLSRLMSDGSDGFDL--SPTDTE---EVHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENI   76 (82)
Q Consensus         2 d~~~~~~~~~~~~~~~~~~~~--~~~~~~---~~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~   76 (82)
                      |+++..+......+...||++  +.++.+   .++..+||++|+|+.||+++|++++++++   ...+.+|+|++|+..+
T Consensus         7 DDd~~~~~~l~~~L~~~G~~v~~a~~g~eal~~l~~~~~dliilD~~mP~~~G~e~~~~i~---~~~~~~pvi~lt~~~~   83 (119)
T d2pl1a1           7 EDNALLRHHLKVQIQDAGHQVDDAEDAKEADYYLNEHIPDIAIVDLGLPDEDGLSLIRRWR---SNDVSLPILVLTARES   83 (119)
T ss_dssp             CSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHHHHSCCSEEEECSCCSSSCHHHHHHHHH---HTTCCSCEEEEESCCC
T ss_pred             eCCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHHhcccceeehhccCCCchhHHHHHHHH---hcCcccceEeeeccCC
Confidence            455555544444444556665  445554   45566899999999999999999999999   4567899999999887


Q ss_pred             hhhh
Q 039883           77 LARI   80 (82)
Q Consensus        77 ~~~~   80 (82)
                      .+..
T Consensus        84 ~~~~   87 (119)
T d2pl1a1          84 WQDK   87 (119)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            6543

>d1dbwa_ c.23.1.1 (A:) Transcriptional regulatory protein FixJ, receiver domain {Rhizobium meliloti [TaxId: 382]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Transcriptional regulatory protein FixJ, receiver domain
species: Rhizobium meliloti [TaxId: 382]

Probab=99.65  E-value=1.6e-16  Score=79.50  Aligned_cols=76  Identities=20%  Similarity=0.282  Sum_probs=55.7

Q ss_pred             CchhHHHHHHHHhcCCCceee--ecChhHH---hhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCc
Q 039883            2 TTTNGVLLSRLMSDGSDGFDL--SPTDTEE---VHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENI   76 (82)
Q Consensus         2 d~~~~~~~~~~~~~~~~~~~~--~~~~~~~---~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~   76 (82)
                      |+++..+......+...||++  +.++.++   +...+||++|+|+.||+++|+++++++|   ...+.+|+|++|+..+
T Consensus        10 DDd~~~~~~l~~~L~~~g~~v~~a~~~~~al~~~~~~~~dlvi~D~~mp~~~G~e~~~~lr---~~~~~~~iI~lt~~~~   86 (123)
T d1dbwa_          10 DDEEPVRKSLAFMLTMNGFAVKMHQSAEAFLAFAPDVRNGVLVTDLRMPDMSGVELLRNLG---DLKINIPSIVITGHGD   86 (123)
T ss_dssp             ESSHHHHHHHHHHHHHTTCEEEEESCHHHHHHHGGGCCSEEEEEECCSTTSCHHHHHHHHH---HTTCCCCEEEEECTTC
T ss_pred             ECCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHhhcCCcEEEEeccCccccchHHHHHHH---hcCCCCeEEEEEeeCC
Confidence            455555544444444445554  4455544   4566899999999999999999999999   5678899999999987


Q ss_pred             hhhh
Q 039883           77 LARI   80 (82)
Q Consensus        77 ~~~~   80 (82)
                      .+..
T Consensus        87 ~~~~   90 (123)
T d1dbwa_          87 VPMA   90 (123)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            6544

>d1qkka_ c.23.1.1 (A:) Transcriptional regulatory protein DctD, receiver domain {Sinorhizobium meliloti [TaxId: 382]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Transcriptional regulatory protein DctD, receiver domain
species: Sinorhizobium meliloti [TaxId: 382]

Probab=99.64  E-value=8.3e-17  Score=82.15  Aligned_cols=76  Identities=20%  Similarity=0.312  Sum_probs=55.2

Q ss_pred             CchhHHHHHHHHhcCCCceee--ecChhHHh---hccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCc
Q 039883            2 TTTNGVLLSRLMSDGSDGFDL--SPTDTEEV---HVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENI   76 (82)
Q Consensus         2 d~~~~~~~~~~~~~~~~~~~~--~~~~~~~~---~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~   76 (82)
                      |++..........+...||.+  +.++.+++   ...+||+||+|+.||+++|+++++++|   ...+.+|||++|+..+
T Consensus         7 DDd~~~~~~l~~~L~~~g~~v~~~~~~~~al~~l~~~~~dlil~D~~mP~~~G~el~~~lr---~~~~~~pvI~lT~~~~   83 (140)
T d1qkka_           7 DDDRDLRKAMQQTLELAGFTVSSFASATEALAGLSADFAGIVISDIRMPGMDGLALFRKIL---ALDPDLPMILVTGHGD   83 (140)
T ss_dssp             CSCHHHHHHHHHHHHHTTCEEEEESCHHHHHHTCCTTCCSEEEEESCCSSSCHHHHHHHHH---HHCTTSCEEEEECGGG
T ss_pred             ECCHHHHHHHHHHHHHCCCEEEEeCChHHHHHHHhccCcchHHHhhccCCCCHHHHHHHHH---HhCCCCcEEEEECCCC
Confidence            455555544444333445555  55555544   455899999999999999999999999   4577899999999887


Q ss_pred             hhhh
Q 039883           77 LARI   80 (82)
Q Consensus        77 ~~~~   80 (82)
                      .+..
T Consensus        84 ~~~~   87 (140)
T d1qkka_          84 IPMA   87 (140)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            6654

>d1mb3a_ c.23.1.1 (A:) Cell division response regulator DivK {Caulobacter crescentus [TaxId: 155892]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Cell division response regulator DivK
species: Caulobacter crescentus [TaxId: 155892]

Probab=99.63  E-value=2.1e-16  Score=79.00  Aligned_cols=76  Identities=17%  Similarity=0.189  Sum_probs=52.1

Q ss_pred             CchhHHHHHHHHhcCCCceeeec--ChhH---HhhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCc
Q 039883            2 TTTNGVLLSRLMSDGSDGFDLSP--TDTE---EVHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENI   76 (82)
Q Consensus         2 d~~~~~~~~~~~~~~~~~~~~~~--~~~~---~~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~   76 (82)
                      |++..........+...||++..  ++.+   .+...+||+||+|+.||+++|+++++.+| .......+|+|++|+..+
T Consensus         8 DD~~~~~~~l~~~L~~~g~~v~~a~~~~~al~~~~~~~~dlil~D~~mp~~dG~el~~~ir-~~~~~~~iPii~lt~~~~   86 (123)
T d1mb3a_           8 EDNELNMKLFHDLLEAQGYETLQTREGLSALSIARENKPDLILMDIQLPEISGLEVTKWLK-EDDDLAHIPVVAVTAFAM   86 (123)
T ss_dssp             CSCHHHHHHHHHHHHHTTCEEEEESCHHHHHHHHHHHCCSEEEEESBCSSSBHHHHHHHHH-HSTTTTTSCEEEEC----
T ss_pred             ECCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHHhCCCCEEEEEeccCCCcHHHHHHHHH-hCCCcCCCCeEEEEEecC
Confidence            44555554444444456666644  4444   45566899999999999999999999999 556678899999998765


Q ss_pred             hh
Q 039883           77 LA   78 (82)
Q Consensus        77 ~~   78 (82)
                      ..
T Consensus        87 ~~   88 (123)
T d1mb3a_          87 KG   88 (123)
T ss_dssp             --
T ss_pred             HH
Confidence            44

>d1krwa_ c.23.1.1 (A:) NTRC receiver domain {Salmonella typhimurium [TaxId: 90371]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: NTRC receiver domain
species: Salmonella typhimurium [TaxId: 90371]

Probab=99.63  E-value=1.2e-16  Score=80.01  Aligned_cols=76  Identities=21%  Similarity=0.350  Sum_probs=56.4

Q ss_pred             CchhHHHHHHHHhcCCCceeee--cChhH---HhhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCc
Q 039883            2 TTTNGVLLSRLMSDGSDGFDLS--PTDTE---EVHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENI   76 (82)
Q Consensus         2 d~~~~~~~~~~~~~~~~~~~~~--~~~~~---~~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~   76 (82)
                      |+++..+......+...||++.  .++.+   .+...+||+||+|+.||+++|++++++++   ...+.+|+|++|+..+
T Consensus        10 DDd~~~~~~l~~~L~~~g~~v~~a~~~~~a~~~l~~~~~dlii~D~~mp~~~G~el~~~l~---~~~~~~piI~~t~~~~   86 (123)
T d1krwa_          10 DDDSSIRWVLERALAGAGLTCTTFENGNEVLAALASKTPDVLLSDIRMPGMDGLALLKQIK---QRHPMLPVIIMTAHSD   86 (123)
T ss_dssp             SSSHHHHHHHHHHHHHTTCEEEEESSSHHHHHHHTTCCCSEEEECCSSSSSTTHHHHHHHH---HHSSSCCEEESCCCSC
T ss_pred             ECCHHHHHHHHHHHHHCCCEEEEeCCHHHHHHHHHhCCCCEEEehhhcCCchHHHHHHHHH---HhCCCCeEEEEecCCC
Confidence            4555555555444445566554  44554   45566899999999999999999999998   4577899999999887


Q ss_pred             hhhh
Q 039883           77 LARI   80 (82)
Q Consensus        77 ~~~~   80 (82)
                      .+..
T Consensus        87 ~~~~   90 (123)
T d1krwa_          87 LDAA   90 (123)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            6643

>d1s8na_ c.23.1.1 (A:) Probable two-component system transcriptional regulator Rv1626 {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Probable two-component system transcriptional regulator Rv1626
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=99.62  E-value=4.6e-16  Score=82.70  Aligned_cols=76  Identities=17%  Similarity=0.224  Sum_probs=57.9

Q ss_pred             CchhHHHHHHHHhcCCCceeee---cChhH---HhhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCC
Q 039883            2 TTTNGVLLSRLMSDGSDGFDLS---PTDTE---EVHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSEN   75 (82)
Q Consensus         2 d~~~~~~~~~~~~~~~~~~~~~---~~~~~---~~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~   75 (82)
                      ||++..+......+...+|+++   .++.+   .+...+||+||+|++||+++|+++++.++   . .+.+|||++|+..
T Consensus        10 DD~~~~r~~l~~~L~~~g~~vv~~a~~g~eal~~~~~~~pDlvllDi~mP~~dG~e~~~~ir---~-~~~~pIi~lTa~~   85 (190)
T d1s8na_          10 EDEALIRMDLAEMLREEGYEIVGEAGDGQEAVELAELHKPDLVIMDVKMPRRDGIDAASEIA---S-KRIAPIVVLTAFS   85 (190)
T ss_dssp             CSSHHHHHHHHHHHHHTTCEEEEEESSHHHHHHHHHHHCCSEEEEESSCSSSCHHHHHHHHH---H-TTCSCEEEEEEGG
T ss_pred             eCCHHHHHHHHHHHHHCCCEEEEEECCHHHHHHHHhcCCCCEEEEeccccCcchHHHHHHHH---h-cCCCCEEEEeCCC
Confidence            5666666666665556778764   33444   45567999999999999999999999999   2 2458999999998


Q ss_pred             chhhhh
Q 039883           76 ILARID   81 (82)
Q Consensus        76 ~~~~~~   81 (82)
                      +.+.+.
T Consensus        86 ~~~~~~   91 (190)
T d1s8na_          86 QRDLVE   91 (190)
T ss_dssp             GHHHHH
T ss_pred             CHHHHH
Confidence            876653

>d1ny5a1 c.23.1.1 (A:1-137) Transcriptional activator sigm54 (NtrC1), N-terminal domain {Aquifex aeolicus [TaxId: 63363]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Transcriptional activator sigm54 (NtrC1), N-terminal domain
species: Aquifex aeolicus [TaxId: 63363]

Probab=99.61  E-value=2.4e-16  Score=80.14  Aligned_cols=76  Identities=14%  Similarity=0.179  Sum_probs=55.7

Q ss_pred             CchhHHHHHHHHhcCCCceee--ecChhHH---hhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCc
Q 039883            2 TTTNGVLLSRLMSDGSDGFDL--SPTDTEE---VHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENI   76 (82)
Q Consensus         2 d~~~~~~~~~~~~~~~~~~~~--~~~~~~~---~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~   76 (82)
                      |+++.........+...||++  +.++.++   +...+||+||+|+.||+++|+++++.+|   ...+.+|||++|+..+
T Consensus         7 DDd~~~~~~l~~~L~~~g~~v~~a~~~~eAl~~l~~~~~dlvilD~~mp~~~G~e~~~~lr---~~~~~~piI~lT~~~~   83 (137)
T d1ny5a1           7 EDDKVFRGLLEEYLSMKGIKVESAERGKEAYKLLSEKHFNVVLLDLLLPDVNGLEILKWIK---ERSPETEVIVITGHGT   83 (137)
T ss_dssp             CCCHHHHHHHHHHHHHHTCEEEEESSHHHHHHHHHHSCCSEEEEESBCSSSBHHHHHHHHH---HHCTTSEEEEEEETTC
T ss_pred             ecCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHhhccccccchHHHhhhhhhHHHHHHHHH---HhCCCCCEEEEECCCC
Confidence            455555544444444445555  4455544   4566899999999999999999999999   4578899999999887


Q ss_pred             hhhh
Q 039883           77 LARI   80 (82)
Q Consensus        77 ~~~~   80 (82)
                      .+..
T Consensus        84 ~~~~   87 (137)
T d1ny5a1          84 IKTA   87 (137)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            6543

>d1kgsa2 c.23.1.1 (A:2-123) PhoB receiver domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: PhoB receiver domain
species: Thermotoga maritima [TaxId: 2336]

Probab=99.61  E-value=6.5e-16  Score=77.14  Aligned_cols=76  Identities=13%  Similarity=0.132  Sum_probs=55.1

Q ss_pred             CchhHHHHHHHHhcCCCceee--ecChhH---HhhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCc
Q 039883            2 TTTNGVLLSRLMSDGSDGFDL--SPTDTE---EVHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENI   76 (82)
Q Consensus         2 d~~~~~~~~~~~~~~~~~~~~--~~~~~~---~~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~   76 (82)
                      |++..........+...||++  +.++.+   .+...+||+||+|+.||+++|+++++++|   ...+..|+|++|+..+
T Consensus         8 dDd~~~~~~l~~~L~~~g~~v~~a~~~~~al~~l~~~~~dlillD~~mp~~~g~~~~~~lr---~~~~~~piI~lt~~~~   84 (122)
T d1kgsa2           8 EDERDLADLITEALKKEMFTVDVCYDGEEGMYMALNEPFDVVILDIMLPVHDGWEILKSMR---ESGVNTPVLMLTALSD   84 (122)
T ss_dssp             CSSHHHHHHHHHHHHHTTCEEEEESSHHHHHHHHHHSCCSEEEEESCCSSSCHHHHHHHHH---HTTCCCCEEEEESSCH
T ss_pred             eCCHHHHHHHHHHHHHCCCEEEEEcchHHHHHHHHhhCccccccccccccchhHHHHHHHH---hcCCCCcEEEEcCCCC
Confidence            445555544444444455555  444554   45566899999999999999999999999   4567889999999887


Q ss_pred             hhhh
Q 039883           77 LARI   80 (82)
Q Consensus        77 ~~~~   80 (82)
                      .+..
T Consensus        85 ~~~~   88 (122)
T d1kgsa2          85 VEYR   88 (122)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            6543

>d1p6qa_ c.23.1.1 (A:) CheY protein {Sinorhizobium meliloti, CheY2 [TaxId: 382]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: CheY protein
species: Sinorhizobium meliloti, CheY2 [TaxId: 382]

Probab=99.60  E-value=1.6e-15  Score=76.40  Aligned_cols=78  Identities=17%  Similarity=0.218  Sum_probs=56.5

Q ss_pred             CchhHHHHHHHHhcCCCcee-e--ecChhH---HhhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCC
Q 039883            2 TTTNGVLLSRLMSDGSDGFD-L--SPTDTE---EVHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSEN   75 (82)
Q Consensus         2 d~~~~~~~~~~~~~~~~~~~-~--~~~~~~---~~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~   75 (82)
                      |++...+......+...||. +  +.++.+   .+...+||+||+|+.||+++|+++++.+| .....+.+|+|++|+..
T Consensus        13 DD~~~~~~~l~~~L~~~g~~~v~~a~~~~~al~~l~~~~~dlii~D~~mP~~~G~el~~~lr-~~~~~~~~pii~lt~~~   91 (129)
T d1p6qa_          13 DDQVTSRLLLGDALQQLGFKQITAAGDGEQGMKIMAQNPHHLVISDFNMPKMDGLGLLQAVR-ANPATKKAAFIILTAQG   91 (129)
T ss_dssp             CSSHHHHHHHHHHHHTTTCSCEECCSSHHHHHHHHHTSCCSEEEECSSSCSSCHHHHHHHHT-TCTTSTTCEEEECCSCC
T ss_pred             ECCHHHHHHHHHHHHHCCCeEEEEECCHHHHHHHHHhCCCCeEEeeeecCCCChHHHHHHHH-hCcccCCCeEEEEEecC
Confidence            45555555554445556664 3  334444   45566899999999999999999999999 54567889999999887


Q ss_pred             chhhh
Q 039883           76 ILARI   80 (82)
Q Consensus        76 ~~~~~   80 (82)
                      +.+..
T Consensus        92 ~~~~~   96 (129)
T d1p6qa_          92 DRALV   96 (129)
T ss_dssp             CHHHH
T ss_pred             CHHHH
Confidence            76543

>d1mvoa_ c.23.1.1 (A:) PhoP receiver domain {Bacillus subtilis [TaxId: 1423]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: PhoP receiver domain
species: Bacillus subtilis [TaxId: 1423]

Probab=99.60  E-value=7.8e-16  Score=76.74  Aligned_cols=75  Identities=16%  Similarity=0.301  Sum_probs=55.0

Q ss_pred             CchhHHHHHHHHhcCCCceee--ecChhH---HhhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCc
Q 039883            2 TTTNGVLLSRLMSDGSDGFDL--SPTDTE---EVHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENI   76 (82)
Q Consensus         2 d~~~~~~~~~~~~~~~~~~~~--~~~~~~---~~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~   76 (82)
                      |+++..+......+...||++  +.++.+   .+...+||+||+|+.||+++|++++++++   ...+..|+|++|+..+
T Consensus         9 DDd~~~~~~l~~~L~~~g~~v~~a~~~~~al~~l~~~~~dlillD~~mp~~~G~~~~~~~r---~~~~~~~ii~lt~~~~   85 (121)
T d1mvoa_           9 DDEESIVTLLQYNLERSGYDVITASDGEEALKKAETEKPDLIVLDVMLPKLDGIEVCKQLR---QQKLMFPILMLTAKDE   85 (121)
T ss_dssp             CSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHHHHHCCSEEEEESSCSSSCHHHHHHHHH---HTTCCCCEEEEECTTC
T ss_pred             ECCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHhcccccEEEecccccCCCCchhhhhhh---ccCCCCEEEEEEeeCC
Confidence            455555555444444556655  445554   45566899999999999999999999999   4567789999998876


Q ss_pred             hhh
Q 039883           77 LAR   79 (82)
Q Consensus        77 ~~~   79 (82)
                      .+.
T Consensus        86 ~~~   88 (121)
T d1mvoa_          86 EFD   88 (121)
T ss_dssp             CCC
T ss_pred             HHH
Confidence            543

>d1u0sy_ c.23.1.1 (Y:) CheY protein {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: CheY protein
species: Thermotoga maritima [TaxId: 2336]

Probab=99.59  E-value=5.5e-16  Score=77.05  Aligned_cols=76  Identities=18%  Similarity=0.209  Sum_probs=56.4

Q ss_pred             CchhHHHHHHHHhcCCCceeee---cChhH---HhhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCC
Q 039883            2 TTTNGVLLSRLMSDGSDGFDLS---PTDTE---EVHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSEN   75 (82)
Q Consensus         2 d~~~~~~~~~~~~~~~~~~~~~---~~~~~---~~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~   75 (82)
                      |+++..+..........+|++.   .++.+   .+...+||+||+|+.||+++|+++++++|   ...+.+|+|++|+..
T Consensus         8 DD~~~~~~~l~~~L~~~g~~v~~~a~~~~~al~~~~~~~~dliilD~~mp~~~G~e~~~~ir---~~~~~~pvi~ls~~~   84 (118)
T d1u0sy_           8 DDAAFMRMMLKDIITKAGYEVAGEATNGREAVEKYKELKPDIVTMDITMPEMNGIDAIKEIM---KIDPNAKIIVCSAMG   84 (118)
T ss_dssp             CSCHHHHHHHHHHHHHTTCEEEEEESSHHHHHHHHHHHCCSEEEEECSCGGGCHHHHHHHHH---HHCTTCCEEEEECTT
T ss_pred             eCCHHHHHHHHHHHHHcCCceEEEECCHHHHHHHHHhccCCEEEEecCCCCCCHHHHHHHHH---HhCCCCcEEEEEccC
Confidence            4555555555554555677653   34444   45566899999999999999999999999   456789999999887


Q ss_pred             chhhh
Q 039883           76 ILARI   80 (82)
Q Consensus        76 ~~~~~   80 (82)
                      +.+..
T Consensus        85 ~~~~~   89 (118)
T d1u0sy_          85 QQAMV   89 (118)
T ss_dssp             CHHHH
T ss_pred             CHHHH
Confidence            76543

>d2a9pa1 c.23.1.1 (A:2-118) DNA-binding response regulator MicA, N-terminal domain {Streptococcus pneumoniae [TaxId: 1313]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: DNA-binding response regulator MicA, N-terminal domain
species: Streptococcus pneumoniae [TaxId: 1313]

Probab=99.59  E-value=2e-15  Score=74.87  Aligned_cols=74  Identities=18%  Similarity=0.303  Sum_probs=53.2

Q ss_pred             CchhHHHHHHHHhcCCCceee--ecChhH---HhhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCc
Q 039883            2 TTTNGVLLSRLMSDGSDGFDL--SPTDTE---EVHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENI   76 (82)
Q Consensus         2 d~~~~~~~~~~~~~~~~~~~~--~~~~~~---~~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~   76 (82)
                      |+++.........+...||++  +.++.+   .+...+||+||+|+.||+++|+++++.++   . .+.+|+|++|+..+
T Consensus         7 dDd~~~~~~l~~~L~~~g~~v~~a~~~~eal~~~~~~~~dlillD~~mp~~~G~~~~~~i~---~-~~~~pvI~lt~~~~   82 (117)
T d2a9pa1           7 DDEKPISDIIKFNMTKEGYEVVTAFNGREALEQFEAEQPDIIILDLMLPEIDGLEVAKTIR---K-TSSVPILMLSAKDS   82 (117)
T ss_dssp             CSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHHHHHCCSEEEECSSCSSSCHHHHHHHHH---T-TCCCCEEEEESCCS
T ss_pred             ECCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHHhcCCCEEEeccccCCCCccHHHHHHH---h-CCCCCEEEEecCCC
Confidence            445555544444444455555  444554   45566899999999999999999999999   3 45789999999877


Q ss_pred             hhh
Q 039883           77 LAR   79 (82)
Q Consensus        77 ~~~   79 (82)
                      .+.
T Consensus        83 ~~~   85 (117)
T d2a9pa1          83 EFD   85 (117)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            654

>d1zh2a1 c.23.1.1 (A:2-120) Transcriptional regulatory protein KdpE, N-terminal domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Transcriptional regulatory protein KdpE, N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=99.58  E-value=1.3e-15  Score=75.81  Aligned_cols=74  Identities=20%  Similarity=0.301  Sum_probs=54.7

Q ss_pred             CchhHHHHHHHHhcCCCceeeec--ChhH---HhhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCc
Q 039883            2 TTTNGVLLSRLMSDGSDGFDLSP--TDTE---EVHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENI   76 (82)
Q Consensus         2 d~~~~~~~~~~~~~~~~~~~~~~--~~~~---~~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~   76 (82)
                      |+++..+......+...||++..  ++.+   .+...+||+||+|+.||+++|+++++.+|   . .+..|+|++|+..+
T Consensus         7 DDd~~~~~~l~~~L~~~g~~v~~a~~~~eal~~l~~~~~dliilD~~mP~~~G~e~~~~ir---~-~~~~piI~lt~~~~   82 (119)
T d1zh2a1           7 EDEQAIRRFLRTALEGDGMRVFEAETLQRGLLEAATRKPDLIILDLGLPDGDGIEFIRDLR---Q-WSAVPVIVLSARSE   82 (119)
T ss_dssp             CSCHHHHHHHHHHHHTTTCEEEEESSHHHHHHHHHHHCCSEEEEESEETTEEHHHHHHHHH---T-TCCCCEEEEESCCS
T ss_pred             ECCHHHHHHHHHHHHHCCCEEEEeCCHHHHHHHHHhcCCCEEEeccccCCCCCchHHHHHH---h-ccCCcEEEEeccCC
Confidence            45555555555555556666644  4444   45566899999999999999999999999   3 45679999999877


Q ss_pred             hhh
Q 039883           77 LAR   79 (82)
Q Consensus        77 ~~~   79 (82)
                      .+.
T Consensus        83 ~~~   85 (119)
T d1zh2a1          83 ESD   85 (119)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            654

>d2b4aa1 c.23.1.1 (A:2-119) Hypothetical protein BH3024 {Bacillus halodurans [TaxId: 86665]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Hypothetical protein BH3024
species: Bacillus halodurans [TaxId: 86665]

Probab=99.58  E-value=3.4e-15  Score=74.14  Aligned_cols=72  Identities=10%  Similarity=0.085  Sum_probs=52.1

Q ss_pred             CchhHHHHHHHHhcCCCceeeec--ChhHHhh----ccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCC
Q 039883            2 TTTNGVLLSRLMSDGSDGFDLSP--TDTEEVH----VLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSEN   75 (82)
Q Consensus         2 d~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~----~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~   75 (82)
                      |+++.........+...||++..  ++.+++.    ..+||+||+|+.||+++|+++++++|   ...+.+|+|++|+..
T Consensus         9 dDd~~~~~~l~~~L~~~g~~v~~~~~~~~al~~l~~~~~~dliilD~~lp~~~G~el~~~ir---~~~~~~pii~lt~~~   85 (118)
T d2b4aa1           9 EDEPSHATLIQYHLNQLGAEVTVHPSGSAFFQHRSQLSTCDLLIVSDQLVDLSIFSLLDIVK---EQTKQPSVLILTTGR   85 (118)
T ss_dssp             CSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHTGGGGGSCSEEEEETTCTTSCHHHHHHHHT---TSSSCCEEEEEESCC
T ss_pred             ECCHHHHHHHHHHHHhcCCCeEEECCHHHHHHHHHhcCCCCEEEEeCCCCCCCHHHHHHHHH---hcCCCCcEEEEECCc
Confidence            45555555555544556666644  4444433    33699999999999999999999999   556789999999865


Q ss_pred             c
Q 039883           76 I   76 (82)
Q Consensus        76 ~   76 (82)
                      +
T Consensus        86 ~   86 (118)
T d2b4aa1          86 H   86 (118)
T ss_dssp             -
T ss_pred             c
Confidence            4

>d1w25a1 c.23.1.1 (A:2-140) Response regulator PleD, receiver domain {Caulobacter crescentus [TaxId: 155892]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Response regulator PleD, receiver domain
species: Caulobacter crescentus [TaxId: 155892]

Probab=99.57  E-value=3.1e-15  Score=76.14  Aligned_cols=78  Identities=21%  Similarity=0.252  Sum_probs=56.2

Q ss_pred             CchhHHHHHHHHhcCCCceee--ecChhHH---hhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCc
Q 039883            2 TTTNGVLLSRLMSDGSDGFDL--SPTDTEE---VHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENI   76 (82)
Q Consensus         2 d~~~~~~~~~~~~~~~~~~~~--~~~~~~~---~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~   76 (82)
                      |+++.........+...||++  +.++.++   +....||+|++|+.||+++|.++++.+| .....+.+|||++|+..+
T Consensus         8 DD~~~~~~~l~~~L~~~g~~v~~a~~~~eal~~~~~~~~dlil~D~~~p~~~G~~~~~~ir-~~~~~~~~piI~lt~~~~   86 (139)
T d1w25a1           8 DDIEANVRLLEAKLTAEYYEVSTAMDGPTALAMAARDLPDIILLDVMMPGMDGFTVCRKLK-DDPTTRHIPVVLITALDG   86 (139)
T ss_dssp             CSSTTHHHHHHHHHHHTTCEEEEESSHHHHHHHHHHHCCSEEEEESCCSSSCHHHHHHHHH-HSTTTTTSCEEEEECSSC
T ss_pred             ECCHHHHHHHHHHHHHCCCEEEEEccchhhhhhhhcccceeeeeeccccCCCchHHHHHhh-hcccccCCCEEEEEcCCC
Confidence            344444444444433455555  4455544   4466899999999999999999999999 555678899999999887


Q ss_pred             hhhh
Q 039883           77 LARI   80 (82)
Q Consensus        77 ~~~~   80 (82)
                      .+..
T Consensus        87 ~~~~   90 (139)
T d1w25a1          87 RGDR   90 (139)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            6643

>d1xhfa1 c.23.1.1 (A:2-122) Aerobic respiration control protein ArcA, N-terminal domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Aerobic respiration control protein ArcA, N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=99.56  E-value=4.2e-15  Score=74.07  Aligned_cols=74  Identities=12%  Similarity=0.227  Sum_probs=56.0

Q ss_pred             CchhHHHHHHHHhcCCCceeeecC--hh---HHhhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCc
Q 039883            2 TTTNGVLLSRLMSDGSDGFDLSPT--DT---EEVHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENI   76 (82)
Q Consensus         2 d~~~~~~~~~~~~~~~~~~~~~~~--~~---~~~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~   76 (82)
                      |+++.........+...||++..+  +.   +.+...+||+||+|+.||+++|+++++.++ .   .+.+|+|++|+..+
T Consensus         9 DDd~~~~~~l~~~L~~~g~~v~~a~~~~~al~~l~~~~~dlii~D~~mp~~~G~~~~~~~r-~---~~~~pii~lt~~~~   84 (121)
T d1xhfa1           9 EDELVTRNTLKSIFEAEGYDVFEATDGAEMHQILSEYDINLVIMDINLPGKNGLLLARELR-E---QANVALMFLTGRDN   84 (121)
T ss_dssp             CSCHHHHHHHHHHHHTTTCEEEEESSHHHHHHHHHHSCCSEEEECSSCSSSCHHHHHHHHH-H---HCCCEEEEEESCCS
T ss_pred             ECCHHHHHHHHHHHHHCCCEEEEECChHHHHHHHHhcCCCEEEeecccCCccCcHHHHHHH-h---cCCCcEEEEECCCC
Confidence            555666655555555677777554  44   345566899999999999999999999998 2   35789999999877


Q ss_pred             hhh
Q 039883           77 LAR   79 (82)
Q Consensus        77 ~~~   79 (82)
                      .+.
T Consensus        85 ~~~   87 (121)
T d1xhfa1          85 EVD   87 (121)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            654

>d1k66a_ c.23.1.1 (A:) Response regulator for cyanobacterial phytochrome {Calothrix sp. pcc 7601, RcpB [TaxId: 1188]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Response regulator for cyanobacterial phytochrome
species: Calothrix sp. pcc 7601, RcpB [TaxId: 1188]

Probab=99.54  E-value=9.6e-15  Score=75.05  Aligned_cols=78  Identities=21%  Similarity=0.306  Sum_probs=55.0

Q ss_pred             CchhHHHHHHHHhcCCCce--e--eecChhHHhhc-------------cCccEEEEeCCCCCCCHHHHHHHHHhhcCCCC
Q 039883            2 TTTNGVLLSRLMSDGSDGF--D--LSPTDTEEVHV-------------LAVDLIITDYCMPGMTGCELIKKIKLQSFTFR   64 (82)
Q Consensus         2 d~~~~~~~~~~~~~~~~~~--~--~~~~~~~~~~~-------------~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~   64 (82)
                      |+++..+......+...++  +  .+.++.++++.             ..||+||+|+.||+++|+++++++| .....+
T Consensus        13 DD~~~~~~~l~~~L~~~g~~~~v~~a~~g~eAl~~l~~~~~~~~~~~~~~pdlillD~~mP~~~G~el~~~ir-~~~~~~   91 (149)
T d1k66a_          13 EDSDEDFSTFQRLLQREGVVNPIYRCITGDQALDFLYQTGSYCNPDIAPRPAVILLDLNLPGTDGREVLQEIK-QDEVLK   91 (149)
T ss_dssp             CCCHHHHHHHHHHHHHTTBCSCEEEECSHHHHHHHHHTCCSSSCGGGCCCCSEEEECSCCSSSCHHHHHHHHT-TSTTGG
T ss_pred             ECCHHHHHHHHHHHHHcCCceEEEEECChHHHHHHHHhhccccccccccCCCeEEccccccCCCcHHHHHHHH-hccccC
Confidence            4445555444444433443  3  45566655532             2599999999999999999999999 555677


Q ss_pred             CccEEEEeeCCchhhh
Q 039883           65 EIPTVIISSENILARI   80 (82)
Q Consensus        65 ~~~vi~ls~~~~~~~~   80 (82)
                      .+|||++|+..+.+..
T Consensus        92 ~ipiI~lT~~~~~~~~  107 (149)
T d1k66a_          92 KIPVVIMTTSSNPKDI  107 (149)
T ss_dssp             GSCEEEEESCCCHHHH
T ss_pred             CCeEEEEeCCCCHHHH
Confidence            8999999998776554

>d2ayxa1 c.23.1.1 (A:817-949) Sensor kinase protein RcsC, C-terminal domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Sensor kinase protein RcsC, C-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=99.54  E-value=9.8e-16  Score=77.51  Aligned_cols=76  Identities=16%  Similarity=0.226  Sum_probs=53.1

Q ss_pred             CchhHHHHHHHHhcCCCce--eeecChhHH---hhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCc
Q 039883            2 TTTNGVLLSRLMSDGSDGF--DLSPTDTEE---VHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENI   76 (82)
Q Consensus         2 d~~~~~~~~~~~~~~~~~~--~~~~~~~~~---~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~   76 (82)
                      |+++..+..........||  ..+.++.++   +...+||+||+|+.||+++|+++++++|   ...+.+||+++|+..+
T Consensus        15 DD~~~~~~~l~~~L~~~g~~v~~a~~g~ea~~~~~~~~~dlillD~~mP~~dG~el~~~ir---~~~~~~pii~lt~~~~   91 (133)
T d2ayxa1          15 DDHPINRRLLADQLGSLGYQCKTANDGVDALNVLSKNHIDIVLSDVNMPNMDGYRLTQRIR---QLGLTLPVIGVTANAL   91 (133)
T ss_dssp             ESSHHHHHHHHHHHHHHTSEEEEECCSHHHHHHHHHSCCSEEEEEESSCSSCCHHHHHHHH---HHHCCSCEEEEESSTT
T ss_pred             ECCHHHHHHHHHHHHHcCCEEEEECcHHHHHHHHhccCceEEEEeccCCCCCHHHHHHHHH---HhCCCCCEEEEeccCC
Confidence            3444444333333333444  445555544   4566899999999999999999999999   3456789999999877


Q ss_pred             hhhh
Q 039883           77 LARI   80 (82)
Q Consensus        77 ~~~~   80 (82)
                      .+..
T Consensus        92 ~~~~   95 (133)
T d2ayxa1          92 AEEK   95 (133)
T ss_dssp             SHHH
T ss_pred             HHHH
Confidence            6543

>d1yioa2 c.23.1.1 (A:3-130) Response regulatory protein StyR, N-terminal domain {Pseudomonas fluorescens [TaxId: 294]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Response regulatory protein StyR, N-terminal domain
species: Pseudomonas fluorescens [TaxId: 294]

Probab=99.54  E-value=6.5e-15  Score=73.98  Aligned_cols=74  Identities=22%  Similarity=0.245  Sum_probs=54.6

Q ss_pred             CchhHHHHHHHHhcCCCceee--ecChhHHh---hccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCc
Q 039883            2 TTTNGVLLSRLMSDGSDGFDL--SPTDTEEV---HVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENI   76 (82)
Q Consensus         2 d~~~~~~~~~~~~~~~~~~~~--~~~~~~~~---~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~   76 (82)
                      |++..........+...||++  +.++.+++   ...+||+||+|+.||+++|+++++.++   ...+..|++++|+..+
T Consensus         9 DDd~~~~~~l~~~L~~~g~~v~~a~~~~~al~~~~~~~~dliilD~~mp~~~G~~~~~~i~---~~~~~~~ii~lt~~~~   85 (128)
T d1yioa2           9 DDDMSVREGLRNLLRSAGFEVETFDCASTFLEHRRPEQHGCLVLDMRMPGMSGIELQEQLT---AISDGIPIVFITAHGD   85 (128)
T ss_dssp             CSCHHHHHHHHHHHHTTTCEEEEESSHHHHHHHCCTTSCEEEEEESCCSSSCHHHHHHHHH---HTTCCCCEEEEESCTT
T ss_pred             ECCHHHHHHHHHHHHHcCCCccccccHHHHHHHHHhcCCCEeehhhhcccchhHHHHHHHH---hhCCCCeEEEEEEECC
Confidence            455555555555555556655  44455554   455799999999999999999999999   5677889999998766


Q ss_pred             hh
Q 039883           77 LA   78 (82)
Q Consensus        77 ~~   78 (82)
                      .+
T Consensus        86 ~~   87 (128)
T d1yioa2          86 IP   87 (128)
T ss_dssp             SC
T ss_pred             HH
Confidence            54

>d1a04a2 c.23.1.1 (A:5-142) Nitrate/nitrite response regulator (NarL), receiver domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Nitrate/nitrite response regulator (NarL), receiver domain
species: Escherichia coli [TaxId: 562]

Probab=99.53  E-value=2e-14  Score=72.95  Aligned_cols=76  Identities=20%  Similarity=0.171  Sum_probs=54.2

Q ss_pred             CchhHHHHHHHHhcCCC-c-eee--ecChhHH---hhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeC
Q 039883            2 TTTNGVLLSRLMSDGSD-G-FDL--SPTDTEE---VHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSE   74 (82)
Q Consensus         2 d~~~~~~~~~~~~~~~~-~-~~~--~~~~~~~---~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~   74 (82)
                      |+++..+.......... . +.+  ..++.++   +...+||++|+|+.||+++|+++++.+|   ...+..|+|++|+.
T Consensus         9 DD~~~~r~~l~~~L~~~~~~~~v~~a~~~~~al~~~~~~~~DlvllD~~mP~~~G~el~~~ir---~~~~~~~vivlt~~   85 (138)
T d1a04a2           9 DDHPMLRTGVKQLISMAPDITVVGEASNGEQGIELAESLDPDLILLDLNMPGMNGLETLDKLR---EKSLSGRIVVFSVS   85 (138)
T ss_dssp             CSCHHHHHHHHHHHTTCTTEEEEEEESSHHHHHHHHHHHCCSEEEEETTSTTSCHHHHHHHHH---HSCCCSEEEEEECC
T ss_pred             CCCHHHHHHHHHHHHhCCCcEEEEEECCHHHHHHHHHhcCCCEEEEecCCCCCCHHHHHHHHH---hhCCCCCEEEEEEE
Confidence            55555554444433322 2 333  3445544   4566899999999999999999999999   56788999999998


Q ss_pred             Cchhhh
Q 039883           75 NILARI   80 (82)
Q Consensus        75 ~~~~~~   80 (82)
                      .+.+..
T Consensus        86 ~~~~~~   91 (138)
T d1a04a2          86 NHEEDV   91 (138)
T ss_dssp             CCHHHH
T ss_pred             CCHHHH
Confidence            776654

>d1zgza1 c.23.1.1 (A:2-121) TorCAD operon transcriptional regulator TorD, N-terminal domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: TorCAD operon transcriptional regulator TorD, N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=99.53  E-value=1.7e-14  Score=71.72  Aligned_cols=74  Identities=15%  Similarity=0.216  Sum_probs=53.9

Q ss_pred             CchhHHHHHHHHhcCCCceeee--cChh---HHhhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCc
Q 039883            2 TTTNGVLLSRLMSDGSDGFDLS--PTDT---EEVHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENI   76 (82)
Q Consensus         2 d~~~~~~~~~~~~~~~~~~~~~--~~~~---~~~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~   76 (82)
                      |+++.........+...||++.  .++.   +.+...+||+|++|+.||+++|+++++.++    ..+..|+|++|+..+
T Consensus         8 DDd~~~~~~l~~~L~~~g~~v~~a~~~~~a~~~~~~~~~dliilD~~mp~~~g~~~~~~~~----~~~~~piI~lt~~~~   83 (120)
T d1zgza1           8 EDEPVTQARLQSYFTQEGYTVSVTASGAGLREIMQNQSVDLILLDINLPDENGLMLTRALR----ERSTVGIILVTGRSD   83 (120)
T ss_dssp             CSSHHHHHHHHHHHHHTTCEEEEESSHHHHHHHHHHSCCSEEEEESCCSSSCHHHHHHHHH----TTCCCEEEEEESSCC
T ss_pred             eCCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHHhcCCCEEeeehhhccchhHHHHHHHh----ccCCCeEEEEEccCC
Confidence            4555555444444445556554  4444   455677899999999999999999999988    356789999999877


Q ss_pred             hhh
Q 039883           77 LAR   79 (82)
Q Consensus        77 ~~~   79 (82)
                      .+.
T Consensus        84 ~~~   86 (120)
T d1zgza1          84 RID   86 (120)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            654

>d1i3ca_ c.23.1.1 (A:) Response regulator for cyanobacterial phytochrome {Synechocystis sp. PCC 6803, RCP1 [TaxId: 1148]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Response regulator for cyanobacterial phytochrome
species: Synechocystis sp. PCC 6803, RCP1 [TaxId: 1148]

Probab=99.53  E-value=4.8e-14  Score=72.05  Aligned_cols=78  Identities=17%  Similarity=0.257  Sum_probs=54.6

Q ss_pred             CchhHHHHHHH--HhcCCCceee--ecChhHHhhc----------cCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCcc
Q 039883            2 TTTNGVLLSRL--MSDGSDGFDL--SPTDTEEVHV----------LAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIP   67 (82)
Q Consensus         2 d~~~~~~~~~~--~~~~~~~~~~--~~~~~~~~~~----------~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~   67 (82)
                      |++........  +...+.++++  +.++.+++..          .+||+||+|+.||+++|+++++++| .......+|
T Consensus        10 dD~~~~~~~l~~~L~~~g~~~~v~~a~~g~~Al~~l~~~~~~~~~~~pdlIllD~~mP~~~G~el~~~ir-~~~~~~~iP   88 (144)
T d1i3ca_          10 EDSKADSRLVQEVLKTSTIDHELIILRDGLAAMAFLQQQGEYENSPRPNLILLDLNLPKKDGREVLAEIK-QNPDLKRIP   88 (144)
T ss_dssp             CCCHHHHHHHHHHHHSCCSCEEEEEECSHHHHHHHHTTCGGGTTCCCCSEEEECSCCSSSCHHHHHHHHH-HCTTTTTSC
T ss_pred             ECCHHHHHHHHHHHHHcCCCeEEEEECCHHHHHHHHHhchhhhccCCCCEEEEECccccccchHHHHHHH-hCcccCCCe
Confidence            34444443333  3344555555  4455555432          2599999999999999999999999 555678899


Q ss_pred             EEEEeeCCchhhh
Q 039883           68 TVIISSENILARI   80 (82)
Q Consensus        68 vi~ls~~~~~~~~   80 (82)
                      ||++|+..+.+..
T Consensus        89 vi~lT~~~~~~~~  101 (144)
T d1i3ca_          89 VVVLTTSHNEDDV  101 (144)
T ss_dssp             EEEEESCCCHHHH
T ss_pred             EEEEECCCCHHHH
Confidence            9999998776544

>d1p2fa2 c.23.1.1 (A:1-120) Response regulator DrrB {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Response regulator DrrB
species: Thermotoga maritima [TaxId: 2336]

Probab=99.52  E-value=2.6e-14  Score=71.09  Aligned_cols=76  Identities=16%  Similarity=0.114  Sum_probs=55.4

Q ss_pred             CchhHHHHHHHHhcCCCce-eeecChhHHhhcc-CccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCchhh
Q 039883            2 TTTNGVLLSRLMSDGSDGF-DLSPTDTEEVHVL-AVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENILAR   79 (82)
Q Consensus         2 d~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~-~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~~~~   79 (82)
                      |+++.........+...++ ..+.++.+++... +||+||+|+.||+++|+++++.+|   ...+.+|+|++|+..+.+.
T Consensus         9 DDd~~~~~~l~~~L~~~g~v~~~~~~~~al~~~~~~dlillD~~mP~~~G~~~~~~lr---~~~~~~~ii~it~~~~~~~   85 (120)
T d1p2fa2           9 DDDKNILKKVSEKLQQLGRVKTFLTGEDFLNDEEAFHVVVLDVMLPDYSGYEICRMIK---ETRPETWVILLTLLSDDES   85 (120)
T ss_dssp             CSCHHHHHHHHHHHTTTEEEEEESSHHHHHHCCSCCSEEEEESBCSSSBHHHHHHHHH---HHCTTSEEEEEESCCSHHH
T ss_pred             ECCHHHHHHHHHHHHhCCEEEEECCHHHHHhcCCCCCEEEEeCcccccchhHHHHHHh---hcCCCCcEEEEecCCCHHH
Confidence            4555555444444444454 3344555777544 699999999999999999999999   4567899999999887654


Q ss_pred             h
Q 039883           80 I   80 (82)
Q Consensus        80 ~   80 (82)
                      .
T Consensus        86 ~   86 (120)
T d1p2fa2          86 V   86 (120)
T ss_dssp             H
T ss_pred             H
Confidence            3

>d1k68a_ c.23.1.1 (A:) Response regulator for cyanobacterial phytochrome {Calothrix sp. pcc 7601, RcpA [TaxId: 1188]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Response regulator for cyanobacterial phytochrome
species: Calothrix sp. pcc 7601, RcpA [TaxId: 1188]

Probab=99.52  E-value=3.3e-14  Score=72.34  Aligned_cols=78  Identities=21%  Similarity=0.295  Sum_probs=54.3

Q ss_pred             CchhHHHHHHH--HhcCCCceee--ecChhHHhh----------ccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCcc
Q 039883            2 TTTNGVLLSRL--MSDGSDGFDL--SPTDTEEVH----------VLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIP   67 (82)
Q Consensus         2 d~~~~~~~~~~--~~~~~~~~~~--~~~~~~~~~----------~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~   67 (82)
                      |+++.......  +...+.++++  +.++.+++.          ..+||+||+|+.||+++|+++++++| .....+.+|
T Consensus         9 DD~~~~~~~l~~~L~~~g~~~~v~~a~~g~eAl~~l~~~~~~~~~~~pdlillD~~mP~~dG~el~~~ir-~~~~~~~iP   87 (140)
T d1k68a_           9 EDNKADIRLIQEALANSTVPHEVVTVRDGMEAMAYLRQEGEYANASRPDLILLDLNLPKKDGREVLAEIK-SDPTLKRIP   87 (140)
T ss_dssp             CCCHHHHHHHHHHHHTCSSCCEEEEECSHHHHHHHHTTCGGGGSCCCCSEEEECSSCSSSCHHHHHHHHH-HSTTGGGSC
T ss_pred             ECCHHHHHHHHHHHHHcCCCeEEEEECCHHHHHHHHHHhHHhhccCCCCEEEEeeccccccChHHHHHHH-hCcccCCCc
Confidence            34444443333  3334444554  445555543          23599999999999999999999999 556677899


Q ss_pred             EEEEeeCCchhhh
Q 039883           68 TVIISSENILARI   80 (82)
Q Consensus        68 vi~ls~~~~~~~~   80 (82)
                      ||++|+..+.+..
T Consensus        88 vI~ls~~~~~~~~  100 (140)
T d1k68a_          88 VVVLSTSINEDDI  100 (140)
T ss_dssp             EEEEESCCCHHHH
T ss_pred             EEEEeCCCCHHHH
Confidence            9999988776543

>d2r25b1 c.23.1.1 (B:1087-1214) Response regulator Sin1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Response regulator Sin1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.47  E-value=3.6e-13  Score=67.56  Aligned_cols=77  Identities=16%  Similarity=0.071  Sum_probs=52.4

Q ss_pred             CchhHHHHHHH--HhcCCC-ceeeecChhHHhh--------ccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEE
Q 039883            2 TTTNGVLLSRL--MSDGSD-GFDLSPTDTEEVH--------VLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVI   70 (82)
Q Consensus         2 d~~~~~~~~~~--~~~~~~-~~~~~~~~~~~~~--------~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~   70 (82)
                      |+++..+....  +...+. .++.+.++.++++        ..+||+||+|+.||+++|+++++++| .. .....|+|+
T Consensus         8 DD~~~~~~~l~~~L~~~g~~~v~~a~~g~eAl~~l~~~~~~~~~~dlillD~~mP~~dG~el~~~ir-~~-~~~~~piI~   85 (128)
T d2r25b1           8 EDNHVNQEVIKRMLNLEGIENIELACDGQEAFDKVKELTSKGENYNMIFMDVQMPKVDGLLSTKMIR-RD-LGYTSPIVA   85 (128)
T ss_dssp             CSCHHHHHHHHHHHHHTTCCCEEEESSHHHHHHHHHHHHHHTCCCSEEEECSCCSSSCHHHHHHHHH-HH-SCCCSCEEE
T ss_pred             eCCHHHHHHHHHHHHHcCCeEEEEEcChHHHHHHHHhhhhccCCCCEEEEEeCCCCCCHHHHHHHHH-Hc-cCCCCeEEE
Confidence            44444443333  333332 3455666665543        24799999999999999999999998 33 245689999


Q ss_pred             EeeCCchhhh
Q 039883           71 ISSENILARI   80 (82)
Q Consensus        71 ls~~~~~~~~   80 (82)
                      +|+..+.+..
T Consensus        86 lT~~~~~~~~   95 (128)
T d2r25b1          86 LTAFADDSNI   95 (128)
T ss_dssp             EESCCSHHHH
T ss_pred             EECCCCHHHH
Confidence            9998776543

>d1dz3a_ c.23.1.1 (A:) Sporulation response regulator Spo0A {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Sporulation response regulator Spo0A
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=99.46  E-value=1.7e-13  Score=68.27  Aligned_cols=77  Identities=9%  Similarity=0.127  Sum_probs=50.6

Q ss_pred             CchhHHHHHHHHhcCC-Cceee---ecChhHH---hhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeC
Q 039883            2 TTTNGVLLSRLMSDGS-DGFDL---SPTDTEE---VHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSE   74 (82)
Q Consensus         2 d~~~~~~~~~~~~~~~-~~~~~---~~~~~~~---~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~   74 (82)
                      |++...+......... .++++   +.++.++   ++..+||++|+|+.||+++|+++++++| .. ....+|+|++|+.
T Consensus         8 DD~~~~~~~l~~~L~~~~~~~~v~~a~~g~~al~~~~~~~~dlillD~~mP~~dG~e~~~~ir-~~-~~~~~~ii~~t~~   85 (123)
T d1dz3a_           8 DDNRELVSLLDEYISSQPDMEVIGTAYNGQDCLQMLEEKRPDILLLDIIMPHLDGLAVLERIR-AG-FEHQPNVIMLTAF   85 (123)
T ss_dssp             CSCHHHHHHHHHHHHTSTTEEEEEEESSHHHHHHHHHHHCCSEEEEESCCSSSCHHHHHHHHH-HH-CSSCCEEEEEEET
T ss_pred             eCCHHHHHHHHHHHHhCCCcEEEEEECCHHHHHHHHHhcCCCEEEEcCCCCCCCHHHHHHHHH-hc-CCCCCeEEEEECc
Confidence            4444444333333322 23443   3445544   4566899999999999999999999999 32 2234579999988


Q ss_pred             Cchhhh
Q 039883           75 NILARI   80 (82)
Q Consensus        75 ~~~~~~   80 (82)
                      .+.+..
T Consensus        86 ~~~~~~   91 (123)
T d1dz3a_          86 GQEDVT   91 (123)
T ss_dssp             TCHHHH
T ss_pred             CCHHHH
Confidence            776543

>d1a2oa1 c.23.1.1 (A:1-140) Methylesterase CheB, N-terminal domain {Salmonella typhimurium [TaxId: 90371]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Methylesterase CheB, N-terminal domain
species: Salmonella typhimurium [TaxId: 90371]

Probab=99.45  E-value=1.3e-13  Score=70.12  Aligned_cols=71  Identities=14%  Similarity=0.069  Sum_probs=48.0

Q ss_pred             CchhHHHHHHHHhcCCCc--eee--ecChhH---HhhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeC
Q 039883            2 TTTNGVLLSRLMSDGSDG--FDL--SPTDTE---EVHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSE   74 (82)
Q Consensus         2 d~~~~~~~~~~~~~~~~~--~~~--~~~~~~---~~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~   74 (82)
                      ||+...+......+...+  +.+  ..++.+   .+...+||+||+|+.||+++|+++++.++   ...+..++++++..
T Consensus        10 DD~~~~r~~l~~~L~~~g~~~~v~~a~~g~~al~~~~~~~pDlvllDi~MP~~dG~e~~~~ir---~~~~~~~i~i~~~~   86 (140)
T d1a2oa1          10 DDSALMRQIMTEIINSHSDMEMVATAPDPLVARDLIKKFNPDVLTLDVEMPRMDGLDFLEKLM---RLRPMPVVMVSSLT   86 (140)
T ss_dssp             CSCHHHHHHHHHHHHTSTTEEEEEEESSHHHHHHHHHHHCCSEEEEECCCSSSCHHHHHHHHH---HSSCCCEEEEECCT
T ss_pred             eCCHHHHHHHHHHHHhCCCeEEEEEECCHHHHHHHHHhcCCCEEEEcCCCCCCCHHHHHHHHH---HhCCCCcEEEEEec
Confidence            555566555444444444  434  334444   45567899999999999999999999999   45566666666654


Q ss_pred             C
Q 039883           75 N   75 (82)
Q Consensus        75 ~   75 (82)
                      .
T Consensus        87 ~   87 (140)
T d1a2oa1          87 G   87 (140)
T ss_dssp             H
T ss_pred             C
Confidence            3

>d1dcfa_ c.23.1.2 (A:) Receiver domain of the ethylene receptor {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: Receiver domain of the ethylene receptor
domain: Receiver domain of the ethylene receptor
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=99.45  E-value=3.8e-13  Score=67.90  Aligned_cols=78  Identities=13%  Similarity=0.172  Sum_probs=53.7

Q ss_pred             CchhHHHHHH--HHhcCCCceeeecChhHHhh--ccCccEEEEeCCCCCCCHHHHHHHHHhh--cCCCCCccEEEEeeCC
Q 039883            2 TTTNGVLLSR--LMSDGSDGFDLSPTDTEEVH--VLAVDLIITDYCMPGMTGCELIKKIKLQ--SFTFREIPTVIISSEN   75 (82)
Q Consensus         2 d~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~--~~~~d~vi~d~~~~~~~~~~~~~~l~~~--~~~~~~~~vi~ls~~~   75 (82)
                      |+++..+...  .+...+..+..+.++.++++  ..+||+||+|+.||+++|+++++.+|+.  ....+.+|||++|+..
T Consensus        14 DD~~~~~~~l~~~L~~~G~~v~~a~~g~eal~~l~~~~dlillD~~mP~~dG~el~~~ir~~~~~~~~~~~~ii~lT~~~   93 (134)
T d1dcfa_          14 DENGVSRMVTKGLLVHLGCEVTTVSSNEECLRVVSHEHKVVFMDVCMPGVENYQIALRIHEKFTKQRHQRPLLVALSGNT   93 (134)
T ss_dssp             CSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHCCTTCSEEEEECCSSTTTTTHHHHHHHHHHC-CCSCCCEEEEEESCC
T ss_pred             eCCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHhhcCCCeEEEEeccCCCchHHHHHHHHHhcccccCCCCeEEEEeCCC
Confidence            3444444333  33444455555666777766  4479999999999999999999999832  2345668899999876


Q ss_pred             chhh
Q 039883           76 ILAR   79 (82)
Q Consensus        76 ~~~~   79 (82)
                      +.+.
T Consensus        94 ~~~~   97 (134)
T d1dcfa_          94 DKST   97 (134)
T ss_dssp             SHHH
T ss_pred             CHHH
Confidence            6554

>d1qo0d_ c.23.1.3 (D:) Positive regulator of the amidase operon AmiR {Pseudomonas aeruginosa [TaxId: 287]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: Positive regulator of the amidase operon AmiR
domain: Positive regulator of the amidase operon AmiR
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=99.13  E-value=5e-11  Score=62.73  Aligned_cols=74  Identities=9%  Similarity=-0.088  Sum_probs=48.9

Q ss_pred             CchhHHHH--HHHHhcCCCceeeecChhHHhhccCccEEEEeCCCCCCCHHHHHHHHHhhcCCCCCccEEEEeeCCchhh
Q 039883            2 TTTNGVLL--SRLMSDGSDGFDLSPTDTEEVHVLAVDLIITDYCMPGMTGCELIKKIKLQSFTFREIPTVIISSENILAR   79 (82)
Q Consensus         2 d~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~d~vi~d~~~~~~~~~~~~~~l~~~~~~~~~~~vi~ls~~~~~~~   79 (82)
                      |++.....  ...+...++.+..++++.+++. ..||+||+|+.||+++|..+.+..+    ..+.+|||++|+..+.+.
T Consensus        18 dd~~~~~~~l~~~L~~~G~~v~~~~~~~~al~-~~~Dlvl~D~~mp~~~~~~~~~~~~----~~p~~pvI~lta~~~~~~   92 (189)
T d1qo0d_          18 NPPGEVSDALVLQLIRIGCSVRQCWPPPEAFD-VPVDVVFTSIFQNRHHDEIAALLAA----GTPRTTLVALVEYESPAV   92 (189)
T ss_dssp             SCTTHHHHHHHHHHHHHTCEEEEECSCCSSCS-SCCSEEEEECCSSTHHHHHHHHHHH----SCTTCEEEEEECCCSHHH
T ss_pred             eCCHHHHHHHHHHHHHcCCcceecCCHHHhcc-CCCCEEEEcCCCCCcHHHHHHHHHH----cCCCCCEEEEeccchHHH
Confidence            33444443  3333443444444555556663 5899999999999887766655444    578899999999988765


Q ss_pred             h
Q 039883           80 I   80 (82)
Q Consensus        80 ~   80 (82)
                      +
T Consensus        93 ~   93 (189)
T d1qo0d_          93 L   93 (189)
T ss_dssp             H
T ss_pred             H
Confidence            4

>d3bula2 c.23.6.1 (A:741-896) Methionine synthase, C-terminal domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: Cobalamin (vitamin B12)-binding domain
family: Cobalamin (vitamin B12)-binding domain
domain: Methionine synthase, C-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=82.67  E-value=1.7  Score=21.41  Aligned_cols=58  Identities=12%  Similarity=0.085  Sum_probs=36.5

Q ss_pred             hcCCCceeeecChh--------HHhhccCccEEEEeCCCCCC-C-HHHHHHHHHhhcCCCCCccEEEEeeC
Q 039883           14 SDGSDGFDLSPTDT--------EEVHVLAVDLIITDYCMPGM-T-GCELIKKIKLQSFTFREIPTVIISSE   74 (82)
Q Consensus        14 ~~~~~~~~~~~~~~--------~~~~~~~~d~vi~d~~~~~~-~-~~~~~~~l~~~~~~~~~~~vi~ls~~   74 (82)
                      .+...||++..-+.        +++....||+|.+...|... . -.++.+.++   ....+.|+++--+.
T Consensus        29 ~l~~~G~~Vi~LG~~~p~e~~~~~~~~~~~d~i~lS~l~~~~~~~~~~~~~~l~---~~g~~~~vivGG~~   96 (156)
T d3bula2          29 VLQCNNYEIVDLGVMVPAEKILRTAKEVNADLIGLSGLITPSLDEMVNVAKEME---RQGFTIPLLIGGAT   96 (156)
T ss_dssp             HHHTTTCEEEECCSSBCHHHHHHHHHHHTCSEEEEECCSTHHHHHHHHHHHHHH---HTTCCSCEEEESTT
T ss_pred             HHHHCCCEEEECCCCCCHHHHHHHHHhhCCCEEEEecccccchHHHHHHHHHHH---hccccceEEEeccc
Confidence            34567788766433        56667799999999998752 2 233455556   34556676655433