Psyllid ID: psy3546

---

Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160----
Protein Sequence
MASIDYASNSDPGTGLQKDIADARCTALSYLIETIPANFPGDRLDHYTTQAVKGWKRKLSGIFRTPNVKGFEGSRSRDLITSMLTRAGFRFQEFLLSPTQFGTSLYTEWLRNKKKKRKEKKKKKDKKKKKEEKKKEKRKEEKKKKEEEKKKKKKKKKKKKNALD
Secondary Structure (PSIPRED)
ccccccccccccccccccccccccHHHHHHHHHHccccccccccccHHHHHHHHcccccccEEEEcccccccccHHHHHHHHHHHHccccEEEEEEcccccccccccHHHHHHcccccccccccccHHHHHHccHHHccHHHHHHHHHHHHHHHHHHHHHHccc
Secondary Structure Prediction (SSPRO)
cccEEcccccccccccccccccHHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHHccccEEEEcccccccccHHHHHHHHHHHHccccEEEEEEccccccHHHHHHHHHHHHHHcccccccccccccccccccccccHHHccHHHHHHHHHHHHHHHHHccc
Coil and Loop (DISEMBL)
masidyasnsdpgtglqkDIADARCTALSYLIEtipanfpgdrldhytTQAVKGWKRKLsgifrtpnvkgfegsrsRDLITSMLTRAgfrfqefllsptqfgtSLYTEWLRNKKKKRKEKKKKKDKKKKKEEKKKEKRKEEKKKKEEEKKKKKKKKKKKKNALD
Flexible Loop (DISEMBL)
masidyasnsdpgtglQKDIADARCTALSYLIETipanfpgdrlDHYTTQAVKgwkrklsgifrtpnvkgfegsrsrDLITSMLTRAGFRFqefllsptqfgtslytewlrnkkkkrkekkkkkdkkkkkeekkkekrkeekkkkeeekkkkkkkkkkkknald
Low Complexity Region (SEG)
MASIDYASNSDPGTGLQKDIADARCTALSYLIETIPANFPGDRLDHYTTQAVKGWKRKLSGIFRTPNVKGFEGSRSRDLITSMLTRAGFRFQEFLLSPTQFGTSLYTEWLRNkkkkrkekkkkkdkkkkkeekkkekrkeekkkkeeekkkkkkkkkkkkNALD
Disordered region (IsUnstruct)
******************DIADARCTALSYLIETIPANFPGDRLDHYTTQAVKGWKRKLSGIFRTPNVKGFEGSRSRDLITSMLTRAGFRFQEFLLSPTQFGTSLYTEWL******************************************************
Disordered Region (DISOPRED)
******************DIADARCTALSYLIETIPANFPGDRLDHYTTQAVKGWKRKLSGIFRTPNVKGFEGSRSRDLITSMLTRAGFRFQEFLLSPTQFGTSLYTEWLRNKKKKRK**********************************************
Disordered Region (DISEMBL)
**************GLQKDIADARCTALSYLIETIPANFPGDRLDHYTTQAVKGWKRKLSGIFRTPNVKGFEGSRSRDLITSMLTRAGFRFQEFLLSPTQFGTSLYTEWLR*****************************************************
Disordered Region (DISPRO)
*************TGLQKDIADARCTALSYLIETIPANFPGDRLDHYTTQAVKGWKRKLSGIFRTPNVKGFEGSRSRDLITSMLTRAGFRFQEFLLSPTQFGTSLYTEWLRNKKKKR******************************EKKKKKKKK********
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MASIDYASNSDPGTGLQKDIADARCTALSYLIETIPANFPGDRLDHYTTQAVKGWKRKLSGIFRTPNVKGFEGSRSRDLITSMLTRAGFRFQEFLLSPTQFGTSLYTEWxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxD
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	164	2.2.26 [Sep-21-2011]
Q7YS61	391	tRNA (cytosine-5-)-methyl	yes	N/A	0.439	0.184	0.355	3e-08
O55055	415	tRNA (cytosine(38)-C(5))-	yes	N/A	0.439	0.173	0.355	5e-08
O14717	391	tRNA (cytosine(38)-C(5))-	yes	N/A	0.506	0.212	0.330	2e-07
Q4G073	391	tRNA (cytosine(38)-C(5))-	no	N/A	0.439	0.184	0.344	4e-07

>sp|Q7YS61|TRDMT_BOVIN tRNA (cytosine-5-)-methyltransferase OS=Bos taurus GN=TRDMT1 PE=2 SV=1

 Score = 58.2 bits (139), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 32/90 (35%), Positives = 45/90 (50%), Gaps = 18/90 (20%)

Query: 14  TGLQKDIADARCTALSYLIETIPANFPGDRLDHYTTQAVKGWKRKLSGIFRTPNVKGFEG 73
            GLQ D+ D R  +  ++++ +P      RL            +KL       NVKGFE 
Sbjct: 85  IGLQGDVTDPRTNSFLHILDILP------RL------------QKLPKYILLENVKGFEM 126

Query: 74  SRSRDLITSMLTRAGFRFQEFLLSPTQFGT 103
           S +RDL+   +   GF++QEFLLSPT  G 
Sbjct: 127 SSTRDLLIQTIENCGFQYQEFLLSPTSLGI 156

Specifically methylates cytosine 38 in the anticodon loop of tRNA(Asp).
Bos taurus (taxid: 9913)
EC: 2EC: .EC: 1EC: .EC: 1EC: .EC: 2EC: 0EC: 4

>sp|O55055|TRDMT_MOUSE tRNA (cytosine(38)-C(5))-methyltransferase OS=Mus musculus GN=Trdmt1 PE=2 SV=2

 Score = 57.0 bits (136), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 32/90 (35%), Positives = 45/90 (50%), Gaps = 18/90 (20%)

Query: 14  TGLQKDIADARCTALSYLIETIPANFPGDRLDHYTTQAVKGWKRKLSGIFRTPNVKGFEG 73
            GLQ D+ D R T+  Y+++ +P      RL            +KL       NVKGFE 
Sbjct: 85  IGLQGDMTDPRTTSFLYILDILP------RL------------QKLPKYILLENVKGFEV 126

Query: 74  SRSRDLITSMLTRAGFRFQEFLLSPTQFGT 103
           S +R L+   +   GF++QEFLLSP+  G 
Sbjct: 127 SSTRGLLIQTIEACGFQYQEFLLSPSSLGI 156

Specifically methylates cytosine 38 in the anticodon loop of tRNA(Asp).

Mus musculus (taxid: 10090)

EC: 2

EC: .

EC: 1

EC: .

EC: 1

EC: .

EC: 2

EC: 0

EC: 4

>sp|O14717|TRDMT_HUMAN tRNA (cytosine(38)-C(5))-methyltransferase OS=Homo sapiens GN=TRDMT1 PE=1 SV=1

 Score = 54.7 bits (130), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 35/106 (33%), Positives = 49/106 (46%), Gaps = 23/106 (21%)

Query: 3   SIDYASNSDPG-----TGLQKDIADARCTALSYLIETIPANFPGDRLDHYTTQAVKGWKR 57
           S D    S P       G Q D+ D+R  +  ++++ +P      RL            +
Sbjct: 69  SFDMILMSPPCQPFTRIGRQGDMTDSRTNSFLHILDILP------RL------------Q 110

Query: 58  KLSGIFRTPNVKGFEGSRSRDLITSMLTRAGFRFQEFLLSPTQFGT 103
           KL       NVKGFE S +RDL+   +   GF++QEFLLSPT  G 
Sbjct: 111 KLPKYILLENVKGFEVSSTRDLLIQTIENCGFQYQEFLLSPTSLGI 156

Specifically methylates cytosine 38 in the anticodon loop of tRNA(Asp).

Homo sapiens (taxid: 9606)

EC: 2

EC: .

EC: 1

EC: .

EC: 1

EC: .

EC: 2

EC: 0

EC: 4

>sp|Q4G073|TRDMT_RAT tRNA (cytosine(38)-C(5))-methyltransferase OS=Rattus norvegicus GN=Trdmt1 PE=2 SV=1

 Score = 53.9 bits (128), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 31/90 (34%), Positives = 45/90 (50%), Gaps = 18/90 (20%)

Query: 14  TGLQKDIADARCTALSYLIETIPANFPGDRLDHYTTQAVKGWKRKLSGIFRTPNVKGFEG 73
            GLQ D++D R  +  Y+++ +P      RL            +KL       NVKGFE 
Sbjct: 85  IGLQGDMSDRRTNSFLYILDILP------RL------------QKLPKYILLENVKGFEV 126

Query: 74  SRSRDLITSMLTRAGFRFQEFLLSPTQFGT 103
           S +R L+   +   GF++QEFLLSP+  G 
Sbjct: 127 SSTRGLLIQTMEACGFQYQEFLLSPSSLGI 156

Specifically methylates cytosine 38 in the anticodon loop of tRNA(Asp).

Rattus norvegicus (taxid: 10116)

EC: 2

EC: .

EC: 1

EC: .

EC: 1

EC: .

EC: 2

EC: 0

EC: 4

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	164
73948982	391	PREDICTED: tRNA (cytosine(38)-C(5))-meth	0.756	0.317	0.321	9e-09
301766512	391	PREDICTED: tRNA (cytosine-5-)-methyltran	0.439	0.184	0.388	3e-08
281338132	372	hypothetical protein PANDA_007177 [Ailur	0.439	0.193	0.388	3e-08
410963252	391	PREDICTED: tRNA (cytosine(38)-C(5))-meth	0.756	0.317	0.307	1e-07
345309099	264	PREDICTED: tRNA (cytosine(38)-C(5))-meth	0.439	0.272	0.4	2e-07
431917686	391	tRNA (cytosine-5-)-methyltransferase [Pt	0.506	0.212	0.349	2e-07
395827473	399	PREDICTED: LOW QUALITY PROTEIN: tRNA (cy	0.506	0.208	0.358	2e-07
242253856	408	tRNA (cytosine-5-)-methyltransferase [Su	0.439	0.176	0.366	2e-07
426240827	386	PREDICTED: tRNA (cytosine-5-)-methyltran	0.439	0.186	0.366	2e-07
440909178	391	tRNA (cytosine-5-)-methyltransferase [Bo	0.439	0.184	0.366	3e-07

>gi|73948982|ref|XP_848593.1| PREDICTED: tRNA (cytosine(38)-C(5))-methyltransferase isoform 2 [Canis lupus familiaris]

 Score = 65.1 bits (157), Expect = 9e-09,   Method: Compositional matrix adjust.
 Identities = 46/143 (32%), Positives = 65/143 (45%), Gaps = 19/143 (13%)

Query: 14  TGLQKDIADARCTALSYLIETIPANFPGDRLDHYTTQAVKGWKRKLSGIFRTPNVKGFEG 73
            GLQ D+ D R  +L Y++  +P      RL            +KL       NVKGFE 
Sbjct: 85  IGLQGDVTDPRTNSLLYILNILP------RL------------QKLPKYVLLENVKGFEV 126

Query: 74  SRSRDLITSMLTRAGFRFQEFLLSPTQFGT-SLYTEWLRNKKKKRKEKKKKKDKKKKKEE 132
           S +RDL+   L   GF++QEFLLSPT FG  +    +    K + +    +   +   E 
Sbjct: 127 SSTRDLLIQTLENCGFQYQEFLLSPTSFGIPNSRLRYFLIAKLQSEPLPFQAPGQVLMEF 186

Query: 133 KKKEKRKEEKKKKEEEKKKKKKK 155
            K E    EK   + E K ++KK
Sbjct: 187 PKTESENPEKNTIDAENKIERKK 209

Source: Canis lupus familiaris

Species: Canis lupus

Genus: Canis

Family: Canidae

Order: Carnivora

Class: Mammalia

Phylum: Chordata

Superkingdom: Eukaryota

>gi|301766512|ref|XP_002918675.1| PREDICTED: tRNA (cytosine-5-)-methyltransferase-like [Ailuropoda melanoleuca]

 Score = 63.5 bits (153), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 35/90 (38%), Positives = 46/90 (51%), Gaps = 18/90 (20%)

Query: 14  TGLQKDIADARCTALSYLIETIPANFPGDRLDHYTTQAVKGWKRKLSGIFRTPNVKGFEG 73
            GLQ D+ D R  +L Y+++ +P      RL            +KL       NVKGFE 
Sbjct: 85  IGLQGDVTDPRTNSLLYILDILP------RL------------QKLPKYILLENVKGFEV 126

Query: 74  SRSRDLITSMLTRAGFRFQEFLLSPTQFGT 103
           S +RDL+   L   GF++QEFLLSPT  G 
Sbjct: 127 SSARDLLIQTLENCGFQYQEFLLSPTSLGI 156

Source: Ailuropoda melanoleuca

Species: Ailuropoda melanoleuca

Genus: Ailuropoda

Family: Ursidae

Order: Carnivora

Class: Mammalia

Phylum: Chordata

Superkingdom: Eukaryota

>gi|281338132|gb|EFB13716.1| hypothetical protein PANDA_007177 [Ailuropoda melanoleuca]

 Score = 63.5 bits (153), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 35/90 (38%), Positives = 46/90 (51%), Gaps = 18/90 (20%)

Query: 14  TGLQKDIADARCTALSYLIETIPANFPGDRLDHYTTQAVKGWKRKLSGIFRTPNVKGFEG 73
            GLQ D+ D R  +L Y+++ +P      RL            +KL       NVKGFE 
Sbjct: 66  IGLQGDVTDPRTNSLLYILDILP------RL------------QKLPKYILLENVKGFEV 107

Query: 74  SRSRDLITSMLTRAGFRFQEFLLSPTQFGT 103
           S +RDL+   L   GF++QEFLLSPT  G 
Sbjct: 108 SSARDLLIQTLENCGFQYQEFLLSPTSLGI 137

Source: Ailuropoda melanoleuca

Species: Ailuropoda melanoleuca

Genus: Ailuropoda

Family: Ursidae

Order: Carnivora

Class: Mammalia

Phylum: Chordata

Superkingdom: Eukaryota

>gi|410963252|ref|XP_003988179.1| PREDICTED: tRNA (cytosine(38)-C(5))-methyltransferase [Felis catus]

 Score = 61.2 bits (147), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 44/143 (30%), Positives = 65/143 (45%), Gaps = 19/143 (13%)

Query: 14  TGLQKDIADARCTALSYLIETIPANFPGDRLDHYTTQAVKGWKRKLSGIFRTPNVKGFEG 73
            GLQ D+ D R  +L ++++ +P      RL            +KL       NVKGFE 
Sbjct: 85  IGLQGDVTDPRTNSLLHILDILP------RL------------QKLPKYILLENVKGFEV 126

Query: 74  SRSRDLITSMLTRAGFRFQEFLLSPTQFGT-SLYTEWLRNKKKKRKEKKKKKDKKKKKEE 132
           S +RDL+   +   GF++QEFLLSPT  G  +    +    K + +    +   +  KE 
Sbjct: 127 SSTRDLLIQTIENCGFQYQEFLLSPTSLGIPNSRLRYFLIAKLQSEPLPFQAPGQVLKEF 186

Query: 133 KKKEKRKEEKKKKEEEKKKKKKK 155
            K E    EK     E K ++KK
Sbjct: 187 PKLESEHPEKNTIVAENKIERKK 209

Source: Felis catus

Species: Felis catus

Genus: Felis

Family: Felidae

Order: Carnivora

Class: Mammalia

Phylum: Chordata

Superkingdom: Eukaryota

>gi|345309099|ref|XP_001520279.2| PREDICTED: tRNA (cytosine(38)-C(5))-methyltransferase-like, partial [Ornithorhynchus anatinus]

 Score = 60.8 bits (146), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 36/90 (40%), Positives = 46/90 (51%), Gaps = 18/90 (20%)

Query: 14  TGLQKDIADARCTALSYLIETIPANFPGDRLDHYTTQAVKGWKRKLSGIFRTPNVKGFEG 73
           TGL+ D AD R  +  YL+  +P      RL            RK        NVKGFEG
Sbjct: 27  TGLRGDAADGRTNSFLYLLRILP------RL------------RKPPRYILLENVKGFEG 68

Query: 74  SRSRDLITSMLTRAGFRFQEFLLSPTQFGT 103
           S +RDL+   + + GF++QEFLLSPT  G 
Sbjct: 69  SATRDLLVQTIEKCGFQYQEFLLSPTSLGI 98

Source: Ornithorhynchus anatinus

Species: Ornithorhynchus anatinus

Genus: Ornithorhynchus

Family: Ornithorhynchidae

Order: Monotremata

Class: Mammalia

Phylum: Chordata

Superkingdom: Eukaryota

>gi|431917686|gb|ELK16951.1| tRNA (cytosine-5-)-methyltransferase [Pteropus alecto]

 Score = 60.8 bits (146), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 37/106 (34%), Positives = 49/106 (46%), Gaps = 23/106 (21%)

Query: 3   SIDYASNSDPG-----TGLQKDIADARCTALSYLIETIPANFPGDRLDHYTTQAVKGWKR 57
           S D    S P       GLQ D+ D R  +  Y+++ +P      RL            +
Sbjct: 69  SFDMILMSPPCQPFTRIGLQGDVTDPRTNSFIYILDILP------RL------------Q 110

Query: 58  KLSGIFRTPNVKGFEGSRSRDLITSMLTRAGFRFQEFLLSPTQFGT 103
           KL       NVKGFE S +RDL+   +   GF++QEFLLSPT  G 
Sbjct: 111 KLPKFILLENVKGFEISSTRDLLIQTIESCGFQYQEFLLSPTSLGI 156

Source: Pteropus alecto

Species: Pteropus alecto

Genus: Pteropus

Family: Pteropodidae

Order: Chiroptera

Class: Mammalia

Phylum: Chordata

Superkingdom: Eukaryota

>gi|395827473|ref|XP_003786926.1| PREDICTED: LOW QUALITY PROTEIN: tRNA (cytosine(38)-C(5))-methyltransferase [Otolemur garnettii]

 Score = 60.5 bits (145), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 38/106 (35%), Positives = 48/106 (45%), Gaps = 23/106 (21%)

Query: 3   SIDYASNSDPG-----TGLQKDIADARCTALSYLIETIPANFPGDRLDHYTTQAVKGWKR 57
           S D    S P       GLQ D+ D R  +  Y ++ +P      RL            R
Sbjct: 69  SCDMILMSPPCQPFTRIGLQGDMTDPRTNSFLYFLDILP------RL------------R 110

Query: 58  KLSGIFRTPNVKGFEGSRSRDLITSMLTRAGFRFQEFLLSPTQFGT 103
           KL       NVKGFE S +RDL+   +   GF++QEFLLSPT  G 
Sbjct: 111 KLPKYILLENVKGFEVSSTRDLLIQTMENCGFQYQEFLLSPTSLGI 156

Source: Otolemur garnettii

Species: Otolemur garnettii

Genus: Otolemur

Family: Galagidae

Order: Primates

Class: Mammalia

Phylum: Chordata

Superkingdom: Eukaryota

>gi|242253856|ref|NP_001156357.1| tRNA (cytosine-5-)-methyltransferase [Sus scrofa] gi|226222432|gb|ACO38647.1| DNA methyltransferase 2 [Sus scrofa]

 Score = 60.5 bits (145), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 33/90 (36%), Positives = 45/90 (50%), Gaps = 18/90 (20%)

Query: 14  TGLQKDIADARCTALSYLIETIPANFPGDRLDHYTTQAVKGWKRKLSGIFRTPNVKGFEG 73
            GLQ D+ D R  +  Y+++ +P      RL            +KL       NVKGFE 
Sbjct: 85  IGLQGDVTDPRTNSFLYILDILP------RL------------QKLPKYILLENVKGFEV 126

Query: 74  SRSRDLITSMLTRAGFRFQEFLLSPTQFGT 103
           S +RDL+   +   GF++QEFLLSPT  G 
Sbjct: 127 SSTRDLLIQTIENCGFQYQEFLLSPTSLGI 156

Source: Sus scrofa

Species: Sus scrofa

Genus: Sus

Family: Suidae

Class: Mammalia

Phylum: Chordata

Superkingdom: Eukaryota

>gi|426240827|ref|XP_004014295.1| PREDICTED: tRNA (cytosine-5-)-methyltransferase-like [Ovis aries]

 Score = 60.5 bits (145), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 33/90 (36%), Positives = 45/90 (50%), Gaps = 18/90 (20%)

Query: 14  TGLQKDIADARCTALSYLIETIPANFPGDRLDHYTTQAVKGWKRKLSGIFRTPNVKGFEG 73
            GLQ D+ D R  +  Y+++ +P      RL            +KL       NVKGFE 
Sbjct: 85  IGLQGDVTDPRTNSFLYILDILP------RL------------QKLPKYILVENVKGFEV 126

Query: 74  SRSRDLITSMLTRAGFRFQEFLLSPTQFGT 103
           S +RDL+   +   GF++QEFLLSPT  G 
Sbjct: 127 SSARDLLIQTIENCGFQYQEFLLSPTSLGI 156

Source: Ovis aries

Species: Ovis aries

Genus: Ovis

Family: Bovidae

Class: Mammalia

Phylum: Chordata

Superkingdom: Eukaryota

>gi|440909178|gb|ELR59115.1| tRNA (cytosine-5-)-methyltransferase [Bos grunniens mutus]

 Score = 60.5 bits (145), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 33/90 (36%), Positives = 45/90 (50%), Gaps = 18/90 (20%)

Query: 14  TGLQKDIADARCTALSYLIETIPANFPGDRLDHYTTQAVKGWKRKLSGIFRTPNVKGFEG 73
            GLQ D+ D R  +  Y+++ +P      RL            +KL       NVKGFE 
Sbjct: 85  IGLQGDVTDPRTNSFLYILDILP------RL------------QKLPKYILLENVKGFEM 126

Query: 74  SRSRDLITSMLTRAGFRFQEFLLSPTQFGT 103
           S +RDL+   +   GF++QEFLLSPT  G 
Sbjct: 127 SSTRDLLIQTIENCGFQYQEFLLSPTSLGI 156


  Database: nr
    Posted date:  Mar 3, 2013 10:45 PM
  Number of letters in database: 999,999,864
  Number of sequences in database:  2,912,245
  
  Database: /local_scratch/syshi//blastdatabase/nr.01
    Posted date:  Mar 3, 2013 10:52 PM
  Number of letters in database: 999,999,666
  Number of sequences in database:  2,912,720
  
  Database: /local_scratch/syshi//blastdatabase/nr.02
    Posted date:  Mar 3, 2013 10:58 PM
  Number of letters in database: 999,999,938
  Number of sequences in database:  3,014,250
  
  Database: /local_scratch/syshi//blastdatabase/nr.03
    Posted date:  Mar 3, 2013 11:03 PM
  Number of letters in database: 999,999,780
  Number of sequences in database:  2,805,020
  
  Database: /local_scratch/syshi//blastdatabase/nr.04
    Posted date:  Mar 3, 2013 11:08 PM
  Number of letters in database: 999,999,551
  Number of sequences in database:  2,816,253
  
  Database: /local_scratch/syshi//blastdatabase/nr.05
    Posted date:  Mar 3, 2013 11:13 PM
  Number of letters in database: 999,999,897
  Number of sequences in database:  2,981,387
  
  Database: /local_scratch/syshi//blastdatabase/nr.06
    Posted date:  Mar 3, 2013 11:18 PM
  Number of letters in database: 999,999,649
  Number of sequences in database:  2,911,476
  
  Database: /local_scratch/syshi//blastdatabase/nr.07
    Posted date:  Mar 3, 2013 11:24 PM
  Number of letters in database: 999,999,452
  Number of sequences in database:  2,920,260
  
  Database: /local_scratch/syshi//blastdatabase/nr.08
    Posted date:  Mar 3, 2013 11:25 PM
  Number of letters in database: 64,230,274
  Number of sequences in database:  189,558
  
Lambda     K      H
   0.310    0.128    0.353 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,760,834,461
Number of Sequences: 23463169
Number of extensions: 138544895
Number of successful extensions: 10305908
Number of sequences better than 100.0: 1000
Number of HSP's better than 100.0 without gapping: 60442
Number of HSP's successfully gapped in prelim test: 8431
Number of HSP's that attempted gapping in prelim test: 6414251
Number of HSP's gapped (non-prelim): 2278539
length of query: 164
length of database: 8,064,228,071
effective HSP length: 125
effective length of query: 39
effective length of database: 9,426,299,242
effective search space: 367625670438
effective search space used: 367625670438
T: 11
A: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.7 bits)
S2: 71 (32.0 bits)

Source: Bos grunniens mutus

Species: Bos grunniens

Genus: Bos

Family: Bovidae

Class: Mammalia

Phylum: Chordata

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	164
UNIPROTKB|I3LF34	261	TRDMT1 "Uncharacterized protei	0.280	0.176	0.5	6.1e-10
UNIPROTKB|Q7YS61	391	TRDMT1 "tRNA (cytosine-5-)-met	0.280	0.117	0.5	9.4e-09
ZFIN|ZDB-GENE-041008-138	381	trdmt1 "tRNA aspartic acid met	0.219	0.094	0.527	3.3e-08
UNIPROTKB|O14717	391	TRDMT1 "tRNA (cytosine(38)-C(5	0.280	0.117	0.5	3.9e-08
UNIPROTKB|F1NJ02	398	TRDMT1 "Uncharacterized protei	0.219	0.090	0.555	7.6e-08
UNIPROTKB|E2RM86	391	TRDMT1 "Uncharacterized protei	0.280	0.117	0.543	9.7e-07
FB|FBgn0028707	345	Mt2 "Methyltransferase 2" [Dro	0.213	0.101	0.542	4.3e-05
RGD|1306292	391	Trdmt1 "tRNA aspartic acid met	0.280	0.117	0.456	0.00011
MGI|MGI:1274787	415	Trdmt1 "tRNA aspartic acid met	0.280	0.110	0.456	0.00012

UNIPROTKB|I3LF34 TRDMT1 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 113 (44.8 bits), Expect = 6.1e-10, Sum P(2) = 6.1e-10
 Identities = 23/46 (50%), Positives = 29/46 (63%)

Query:    57 RKLSGIFRTPNVKGFEGSRSRDLITSMLTRAGFRFQEFLLSPTQFG 102
             +KL       NVKGFE S +RDL+   +   GF++QEFLLSPT  G
Sbjct:    55 QKLPKYILLENVKGFEVSSTRDLLIQTIENCGFQYQEFLLSPTSLG 100

GO:0008168 "methyltransferase activity" evidence=IEA

GO:0006306 "DNA methylation" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

UNIPROTKB|Q7YS61 TRDMT1 "tRNA (cytosine-5-)-methyltransferase" [Bos taurus (taxid:9913)]

 Score = 113 (44.8 bits), Expect = 9.4e-09, Sum P(2) = 9.4e-09
 Identities = 23/46 (50%), Positives = 29/46 (63%)

Query:    57 RKLSGIFRTPNVKGFEGSRSRDLITSMLTRAGFRFQEFLLSPTQFG 102
             +KL       NVKGFE S +RDL+   +   GF++QEFLLSPT  G
Sbjct:   110 QKLPKYILLENVKGFEMSSTRDLLIQTIENCGFQYQEFLLSPTSLG 155

GO:0005634 "nucleus" evidence=IEA

GO:0008168 "methyltransferase activity" evidence=IEA

GO:0008033 "tRNA processing" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0006306 "DNA methylation" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

ZFIN|ZDB-GENE-041008-138 trdmt1 "tRNA aspartic acid methyltransferase 1" [Danio rerio (taxid:7955)]

 Score = 100 (40.3 bits), Expect = 3.3e-08, Sum P(2) = 3.3e-08
 Identities = 19/36 (52%), Positives = 23/36 (63%)

Query:    67 NVKGFEGSRSRDLITSMLTRAGFRFQEFLLSPTQFG 102
             NVKGFE S +RD +   L    + FQEFL+SPT  G
Sbjct:   123 NVKGFESSAARDALLQTLRECDYSFQEFLISPTSLG 158

GO:0006306 "DNA methylation" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0008168 "methyltransferase activity" evidence=IEA

GO:0005575 "cellular_component" evidence=ND

GO:0016740 "transferase activity" evidence=IEA

GO:0032259 "methylation" evidence=IEA

UNIPROTKB|O14717 TRDMT1 "tRNA (cytosine(38)-C(5))-methyltransferase" [Homo sapiens (taxid:9606)]

 Score = 113 (44.8 bits), Expect = 3.9e-08, Sum P(2) = 3.9e-08
 Identities = 23/46 (50%), Positives = 29/46 (63%)

Query:    57 RKLSGIFRTPNVKGFEGSRSRDLITSMLTRAGFRFQEFLLSPTQFG 102
             +KL       NVKGFE S +RDL+   +   GF++QEFLLSPT  G
Sbjct:   110 QKLPKYILLENVKGFEVSSTRDLLIQTIENCGFQYQEFLLSPTSLG 155

GO:0003677 "DNA binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0008033 "tRNA processing" evidence=IEA

GO:0001975 "response to amphetamine" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0003886 "DNA (cytosine-5-)-methyltransferase activity" evidence=TAS

GO:0090116 "C-5 methylation of cytosine" evidence=TAS

UNIPROTKB|F1NJ02 TRDMT1 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 100 (40.3 bits), Expect = 7.6e-08, Sum P(2) = 7.6e-08
 Identities = 20/36 (55%), Positives = 25/36 (69%)

Query:    67 NVKGFEGSRSRDLITSMLTRAGFRFQEFLLSPTQFG 102
             NVKGFE S +R+ +   L   GF++QEFLLSPT  G
Sbjct:   120 NVKGFESSSARNELLRTLETCGFKYQEFLLSPTCLG 155

GO:0003677 "DNA binding" evidence=IEA

GO:0006306 "DNA methylation" evidence=IEA

GO:0008168 "methyltransferase activity" evidence=IEA

UNIPROTKB|E2RM86 TRDMT1 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 120 (47.3 bits), Expect = 9.7e-07, P = 9.7e-07
 Identities = 25/46 (54%), Positives = 30/46 (65%)

Query:    57 RKLSGIFRTPNVKGFEGSRSRDLITSMLTRAGFRFQEFLLSPTQFG 102
             +KL       NVKGFE S +RDL+   L   GF++QEFLLSPT FG
Sbjct:   110 QKLPKYVLLENVKGFEVSSTRDLLIQTLENCGFQYQEFLLSPTSFG 155

GO:0008168 "methyltransferase activity" evidence=IEA

GO:0006306 "DNA methylation" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

FB|FBgn0028707 Mt2 "Methyltransferase 2" [Drosophila melanogaster (taxid:7227)]

 Score = 104 (41.7 bits), Expect = 4.3e-05, P = 4.3e-05
 Identities = 19/35 (54%), Positives = 27/35 (77%)

Query:    67 NVKGFEGSRSRDLITSMLTRAGFRFQEFLLSPTQF 101
             NVKGFE S++R+     L R+GF ++EF+L+PTQF
Sbjct:   118 NVKGFESSQARNQFIESLERSGFHWREFILTPTQF 152

GO:0003886 "DNA (cytosine-5-)-methyltransferase activity" evidence=ISS;IDA;NAS

GO:0008168 "methyltransferase activity" evidence=ISS

GO:0006306 "DNA methylation" evidence=ISS;IDA;NAS

GO:0000790 "nuclear chromatin" evidence=NAS

GO:0043045 "DNA methylation involved in embryo development" evidence=IMP

GO:0005634 "nucleus" evidence=IDA

GO:0003677 "DNA binding" evidence=IEA

GO:0008340 "determination of adult lifespan" evidence=IMP

GO:0030488 "tRNA methylation" evidence=IMP

GO:0016458 "gene silencing" evidence=IMP

GO:0000723 "telomere maintenance" evidence=IMP

GO:0044026 "DNA hypermethylation" evidence=IMP

GO:0006979 "response to oxidative stress" evidence=IMP

GO:0010494 "cytoplasmic stress granule" evidence=IDA

GO:0008175 "tRNA methyltransferase activity" evidence=IMP

GO:0009408 "response to heat" evidence=IMP

RGD|1306292 Trdmt1 "tRNA aspartic acid methyltransferase 1" [Rattus norvegicus (taxid:10116)]

 Score = 101 (40.6 bits), Expect = 0.00011, P = 0.00011
 Identities = 21/46 (45%), Positives = 28/46 (60%)

Query:    57 RKLSGIFRTPNVKGFEGSRSRDLITSMLTRAGFRFQEFLLSPTQFG 102
             +KL       NVKGFE S +R L+   +   GF++QEFLLSP+  G
Sbjct:   110 QKLPKYILLENVKGFEVSSTRGLLIQTMEACGFQYQEFLLSPSSLG 155

GO:0001975 "response to amphetamine" evidence=IEP

GO:0003674 "molecular_function" evidence=ND

GO:0003677 "DNA binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0005575 "cellular_component" evidence=ND

GO:0005634 "nucleus" evidence=IEA

GO:0006306 "DNA methylation" evidence=IEA

GO:0008033 "tRNA processing" evidence=IEA

GO:0008168 "methyltransferase activity" evidence=IEA

MGI|MGI:1274787 Trdmt1 "tRNA aspartic acid methyltransferase 1" [Mus musculus (taxid:10090)]

 Score = 101 (40.6 bits), Expect = 0.00012, P = 0.00012
 Identities = 21/46 (45%), Positives = 28/46 (60%)

Query:    57 RKLSGIFRTPNVKGFEGSRSRDLITSMLTRAGFRFQEFLLSPTQFG 102
             +KL       NVKGFE S +R L+   +   GF++QEFLLSP+  G
Sbjct:   110 QKLPKYILLENVKGFEVSSTRGLLIQTIEACGFQYQEFLLSPSSLG 155


Parameters:
  V=100
  filter=SEG
  E=0.001

  ctxfactor=1.00

  Query                        -----  As Used  -----    -----  Computed  ----
  Frame  MatID Matrix name     Lambda    K       H      Lambda    K       H
   +0      0   BLOSUM62        0.319   0.135   0.405    same    same    same
               Q=9,R=2         0.244   0.0300  0.180     n/a     n/a     n/a

  Query
  Frame  MatID  Length  Eff.Length     E     S W   T  X   E2     S2
   +0      0      164       116   0.00091  102 3  11 22  0.47    30
                                                     29  0.45    32


Statistics:

  Database:  /share/blast/go-seqdb.fasta
   Title:  go_20130330-seqdb.fasta
   Posted:  5:47:42 AM PDT Apr 1, 2013
   Created:  5:47:42 AM PDT Apr 1, 2013
   Format:  XDF-1
   # of letters in database:  169,044,731
   # of sequences in database:  368,745
   # of database sequences satisfying E:  9
  No. of states in DFA:  577 (61 KB)
  Total size of DFA:  124 KB (2079 KB)
  Time to generate neighborhood:  0.00u 0.00s 0.00t   Elapsed:  00:00:05
  No. of threads or processors used:  24
  Search cpu time:  11.86u 0.07s 11.93t   Elapsed:  00:00:24
  Total cpu time:  11.86u 0.07s 11.93t   Elapsed:  00:00:29
  Start:  Thu Aug 15 14:08:40 2013   End:  Thu Aug 15 14:09:09 2013

GO:0003677 "DNA binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0006306 "DNA methylation" evidence=IEA

GO:0008033 "tRNA processing" evidence=IEA

GO:0008168 "methyltransferase activity" evidence=IEA

GO:0016740 "transferase activity" evidence=IEA

GO:0032259 "methylation" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	164
PRK11192	434	PRK11192, PRK11192, ATP-dependent RNA helicase Srm	8e-09
PRK11192	434	PRK11192, PRK11192, ATP-dependent RNA helicase Srm	1e-08
PRK04195	482	PRK04195, PRK04195, replication factor C large sub	8e-07
PRK04195	482	PRK04195, PRK04195, replication factor C large sub	9e-07
PRK11192	434	PRK11192, PRK11192, ATP-dependent RNA helicase Srm	2e-06
pfam12569	516	pfam12569, NARP1, NMDA receptor-regulated protein	1e-05
PRK04195	482	PRK04195, PRK04195, replication factor C large sub	2e-05
pfam12569	516	pfam12569, NARP1, NMDA receptor-regulated protein	3e-05
pfam07946	322	pfam07946, DUF1682, Protein of unknown function (D	3e-05
PRK14552	414	PRK14552, PRK14552, C/D box methylation guide ribo	3e-05
pfam12569	516	pfam12569, NARP1, NMDA receptor-regulated protein	4e-05
pfam07946	322	pfam07946, DUF1682, Protein of unknown function (D	4e-05
pfam08208	193	pfam08208, RNA_polI_A34, DNA-directed RNA polymera	2e-04
pfam08208	193	pfam08208, RNA_polI_A34, DNA-directed RNA polymera	2e-04
PTZ00372	413	PTZ00372, PTZ00372, endonuclease 4-like protein; P	2e-04
PTZ00372	413	PTZ00372, PTZ00372, endonuclease 4-like protein; P	2e-04
pfam08432	182	pfam08432, DUF1742, Fungal protein of unknown func	2e-04
PRK11192	434	PRK11192, PRK11192, ATP-dependent RNA helicase Srm	4e-04
PTZ00372	413	PTZ00372, PTZ00372, endonuclease 4-like protein; P	4e-04
PTZ00372	413	PTZ00372, PTZ00372, endonuclease 4-like protein; P	4e-04
PTZ00372	413	PTZ00372, PTZ00372, endonuclease 4-like protein; P	4e-04
pfam03154	979	pfam03154, Atrophin-1, Atrophin-1 family	5e-04
PTZ00399	651	PTZ00399, PTZ00399, cysteinyl-tRNA-synthetase; Pro	5e-04
PTZ00372	413	PTZ00372, PTZ00372, endonuclease 4-like protein; P	6e-04
pfam00183	529	pfam00183, HSP90, Hsp90 protein	6e-04
TIGR02794	346	TIGR02794, tolA_full, TolA protein	6e-04
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	7e-04
PLN02381	1066	PLN02381, PLN02381, valyl-tRNA synthetase	7e-04
cd00315	275	cd00315, Cyt_C5_DNA_methylase, Cytosine-C5 specifi	7e-04
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	8e-04
PRK00247	429	PRK00247, PRK00247, putative inner membrane protei	8e-04
pfam12569	516	pfam12569, NARP1, NMDA receptor-regulated protein	0.001
PTZ00372	413	PTZ00372, PTZ00372, endonuclease 4-like protein; P	0.001
PTZ00399	651	PTZ00399, PTZ00399, cysteinyl-tRNA-synthetase; Pro	0.001
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	0.001
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	0.001
PLN02381	1066	PLN02381, PLN02381, valyl-tRNA synthetase	0.001
pfam09428	130	pfam09428, DUF2011, Fungal protein of unknown func	0.001
pfam08496	154	pfam08496, Peptidase_S49_N, Peptidase family S49 N	0.001
pfam08229	196	pfam08229, SHR3_chaperone, ER membrane protein SH3	0.001
pfam07946	322	pfam07946, DUF1682, Protein of unknown function (D	0.002
PTZ00372	413	PTZ00372, PTZ00372, endonuclease 4-like protein; P	0.002
PTZ00372	413	PTZ00372, PTZ00372, endonuclease 4-like protein; P	0.002
pfam08432	182	pfam08432, DUF1742, Fungal protein of unknown func	0.002
PTZ00399	651	PTZ00399, PTZ00399, cysteinyl-tRNA-synthetase; Pro	0.002
pfam10243	506	pfam10243, MIP-T3, Microtubule-binding protein MIP	0.002
PRK04950	213	PRK04950, PRK04950, ProP expression regulator; Pro	0.002
pfam09468	287	pfam09468, RNase_H2-Ydr279, Ydr279p protein family	0.002
PTZ00053	470	PTZ00053, PTZ00053, methionine aminopeptidase 2; P	0.002
COG5116	926	COG5116, RPN2, 26S proteasome regulatory complex c	0.002
COG4499	434	COG4499, COG4499, Predicted membrane protein [Func	0.002
pfam07946	322	pfam07946, DUF1682, Protein of unknown function (D	0.003
PRK14552	414	PRK14552, PRK14552, C/D box methylation guide ribo	0.003
pfam00183	529	pfam00183, HSP90, Hsp90 protein	0.003
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	0.003
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	0.003
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	0.003
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	0.003
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	0.003
PRK11642	813	PRK11642, PRK11642, exoribonuclease R; Provisional	0.003
pfam09756	189	pfam09756, DDRGK, DDRGK domain	0.003
pfam03839	217	pfam03839, Sec62, Translocation protein Sec62	0.003
cd09270	211	cd09270, RNase_H2-B, Ribonuclease H2-B is a subuni	0.003
PTZ00372	413	PTZ00372, PTZ00372, endonuclease 4-like protein; P	0.004
PTZ00399	651	PTZ00399, PTZ00399, cysteinyl-tRNA-synthetase; Pro	0.004
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	0.004
pfam09428	130	pfam09428, DUF2011, Fungal protein of unknown func	0.004
pfam08496	154	pfam08496, Peptidase_S49_N, Peptidase family S49 N	0.004
pfam10243	506	pfam10243, MIP-T3, Microtubule-binding protein MIP	0.004
pfam09736	141	pfam09736, Bud13, Pre-mRNA-splicing factor of RES	0.004
PRK07561	859	PRK07561, PRK07561, DNA topoisomerase I subunit om	0.004

>gnl|CDD|236877 PRK11192, PRK11192, ATP-dependent RNA helicase SrmB; Provisional

 Score = 53.0 bits (128), Expect = 8e-09
 Identities = 17/51 (33%), Positives = 29/51 (56%)

Query: 110 LRNKKKKRKEKKKKKDKKKKKEEKKKEKRKEEKKKKEEEKKKKKKKKKKKK 160
           LR K K   EKK  K  KK   ++ ++K KE++K K +++ +  K   K++
Sbjct: 376 LRPKTKAPSEKKTGKPSKKVLAKRAEKKEKEKEKPKVKKRHRDTKNIGKRR 426

Length = 434

>gnl|CDD|236877 PRK11192, PRK11192, ATP-dependent RNA helicase SrmB; Provisional

 Score = 52.3 bits (126), Expect = 1e-08
 Identities = 16/52 (30%), Positives = 25/52 (48%)

Query: 111 RNKKKKRKEKKKKKDKKKKKEEKKKEKRKEEKKKKEEEKKKKKKKKKKKKNA 162
           + K    K+  K   K   K  +KKEK KE+ K K+  +  K   K++K + 
Sbjct: 379 KTKAPSEKKTGKPSKKVLAKRAEKKEKEKEKPKVKKRHRDTKNIGKRRKPSG 430

Length = 434

>gnl|CDD|235250 PRK04195, PRK04195, replication factor C large subunit; Provisional

 Score = 47.2 bits (113), Expect = 8e-07
 Identities = 19/69 (27%), Positives = 46/69 (66%)

Query: 93  EFLLSPTQFGTSLYTEWLRNKKKKRKEKKKKKDKKKKKEEKKKEKRKEEKKKKEEEKKKK 152
           EFL    +    +     + +KK+ +EKK+KK K    ++K++E+ +E++KK+EE+++++
Sbjct: 400 EFLTGSKKATKKIKKIVEKAEKKREEEKKEKKKKAFAGKKKEEEEEEEKEKKEEEKEEEE 459

Query: 153 KKKKKKKKN 161
           ++ +++K+ 
Sbjct: 460 EEAEEEKEE 468

Length = 482

>gnl|CDD|235250 PRK04195, PRK04195, replication factor C large subunit; Provisional

 Score = 46.8 bits (112), Expect = 9e-07
 Identities = 21/54 (38%), Positives = 44/54 (81%)

Query: 111 RNKKKKRKEKKKKKDKKKKKEEKKKEKRKEEKKKKEEEKKKKKKKKKKKKNALD 164
           + +KKK+    KKK++++++E++KKE+ KEE++++ EE+K+++++KKKK+  L 
Sbjct: 427 KKEKKKKAFAGKKKEEEEEEEKEKKEEEKEEEEEEAEEEKEEEEEKKKKQATLF 480

Length = 482

>gnl|CDD|236877 PRK11192, PRK11192, ATP-dependent RNA helicase SrmB; Provisional

 Score = 46.1 bits (110), Expect = 2e-06
 Identities = 16/51 (31%), Positives = 29/51 (56%)

Query: 112 NKKKKRKEKKKKKDKKKKKEEKKKEKRKEEKKKKEEEKKKKKKKKKKKKNA 162
           ++KK  K  KK   K+ +K+EK+KEK K +K+ ++ +   K++K       
Sbjct: 384 SEKKTGKPSKKVLAKRAEKKEKEKEKPKVKKRHRDTKNIGKRRKPSGTSEE 434

Length = 434

>gnl|CDD|221641 pfam12569, NARP1, NMDA receptor-regulated protein 1

 Score = 43.8 bits (104), Expect = 1e-05
 Identities = 12/43 (27%), Positives = 27/43 (62%)

Query: 119 EKKKKKDKKKKKEEKKKEKRKEEKKKKEEEKKKKKKKKKKKKN 161
             ++KK +KK+++ +KK +++E +K   ++K +   KK K  +
Sbjct: 408 PAERKKLRKKQRKAEKKAEKEEAEKAAAKKKAEAAAKKAKGPD 450

This domain family is found in eukaryotes, and is approximately 40 amino acids in length. The family is found in association with pfam07719, pfam00515. There is a single completely conserved residue L that may be functionally important. NARP1 is the mammalian homologue of a yeast N-terminal acetyltransferase that regulates entry into the G(0) phase of the cell cycle. Length = 516

>gnl|CDD|235250 PRK04195, PRK04195, replication factor C large subunit; Provisional

 Score = 43.0 bits (102), Expect = 2e-05
 Identities = 16/57 (28%), Positives = 37/57 (64%), Gaps = 1/57 (1%)

Query: 108 EWLRNKKKKRKEKKKKKDKKKKKEEKKKEKRKEEKKKKEEEKKKKKKKKKKKKNALD 164
           E+L   KK   +K KK  +K +K+ ++++K K++K    ++K+++++++K+KK    
Sbjct: 400 EFLTGSKKA-TKKIKKIVEKAEKKREEEKKEKKKKAFAGKKKEEEEEEEKEKKEEEK 455

Length = 482

>gnl|CDD|221641 pfam12569, NARP1, NMDA receptor-regulated protein 1

 Score = 43.0 bits (102), Expect = 3e-05
 Identities = 15/43 (34%), Positives = 24/43 (55%)

Query: 118 KEKKKKKDKKKKKEEKKKEKRKEEKKKKEEEKKKKKKKKKKKK 160
             ++KK  KK++K EKK EK + EK   +++ +   KK K   
Sbjct: 408 PAERKKLRKKQRKAEKKAEKEEAEKAAAKKKAEAAAKKAKGPD 450

This domain family is found in eukaryotes, and is approximately 40 amino acids in length. The family is found in association with pfam07719, pfam00515. There is a single completely conserved residue L that may be functionally important. NARP1 is the mammalian homologue of a yeast N-terminal acetyltransferase that regulates entry into the G(0) phase of the cell cycle. Length = 516

>gnl|CDD|219655 pfam07946, DUF1682, Protein of unknown function (DUF1682)

 Score = 42.2 bits (100), Expect = 3e-05
 Identities = 18/52 (34%), Positives = 39/52 (75%), Gaps = 2/52 (3%)

Query: 108 EWLRNKKKKRKEKKKKKDKKKKKEEKKKEKRK--EEKKKKEEEKKKKKKKKK 157
           + L+  +++R+E+ ++K ++KKKEE++ +  K   E+++K EEK++KK+ +K
Sbjct: 271 KILKAAEEERQEEAQEKKEEKKKEEREAKLAKLSPEEQRKLEEKERKKQARK 322

The members of this family are all hypothetical eukaryotic proteins of unknown function. One member is described as being an adipocyte-specific protein, but no evidence of this was found. Length = 322

>gnl|CDD|237753 PRK14552, PRK14552, C/D box methylation guide ribonucleoprotein complex aNOP56 subunit; Provisional

 Score = 42.3 bits (100), Expect = 3e-05
 Identities = 26/51 (50%), Positives = 39/51 (76%), Gaps = 3/51 (5%)

Query: 110 LRNKKKKR-KEKKKK--KDKKKKKEEKKKEKRKEEKKKKEEEKKKKKKKKK 157
           L+ +  KR +E K+K  K  KKK+EEKK +KRK++KK+K++ KK+KKK +K
Sbjct: 364 LKEELNKRIEEIKEKYPKPPKKKREEKKPQKRKKKKKRKKKGKKRKKKGRK 414

Length = 414

>gnl|CDD|221641 pfam12569, NARP1, NMDA receptor-regulated protein 1

 Score = 42.2 bits (100), Expect = 4e-05
 Identities = 16/53 (30%), Positives = 30/53 (56%)

Query: 112 NKKKKRKEKKKKKDKKKKKEEKKKEKRKEEKKKKEEEKKKKKKKKKKKKNALD 164
           +  +++K +KK++  +KK E+++ EK   +KK +   KK K    + KK   D
Sbjct: 407 SPAERKKLRKKQRKAEKKAEKEEAEKAAAKKKAEAAAKKAKGPDGETKKVDPD 459

This domain family is found in eukaryotes, and is approximately 40 amino acids in length. The family is found in association with pfam07719, pfam00515. There is a single completely conserved residue L that may be functionally important. NARP1 is the mammalian homologue of a yeast N-terminal acetyltransferase that regulates entry into the G(0) phase of the cell cycle. Length = 516

>gnl|CDD|219655 pfam07946, DUF1682, Protein of unknown function (DUF1682)

 Score = 42.2 bits (100), Expect = 4e-05
 Identities = 19/50 (38%), Positives = 37/50 (74%)

Query: 113 KKKKRKEKKKKKDKKKKKEEKKKEKRKEEKKKKEEEKKKKKKKKKKKKNA 162
           K  K  E++++++ ++KKEEKKKE+R+ +  K   E+++K ++K++KK A
Sbjct: 271 KILKAAEEERQEEAQEKKEEKKKEEREAKLAKLSPEEQRKLEEKERKKQA 320

The members of this family are all hypothetical eukaryotic proteins of unknown function. One member is described as being an adipocyte-specific protein, but no evidence of this was found. Length = 322

>gnl|CDD|219746 pfam08208, RNA_polI_A34, DNA-directed RNA polymerase I subunit RPA34

 Score = 40.1 bits (94), Expect = 2e-04
 Identities = 25/50 (50%), Positives = 37/50 (74%)

Query: 110 LRNKKKKRKEKKKKKDKKKKKEEKKKEKRKEEKKKKEEEKKKKKKKKKKK 159
            +  + + +EKK+KK KK+ K+EKK++K K+EK  + +  KKKKKKKKKK
Sbjct: 144 EKEAEVEEEEKKEKKKKKEVKKEKKEKKDKKEKMVEPKGSKKKKKKKKKK 193

5. This is a family of proteins conserved from yeasts to human. Subunit A34.5 of RNA polymerase I is a non-essential subunit which is thought to help Pol I overcome topological constraints imposed on ribosomal DNA during the process of transcription. Length = 193

>gnl|CDD|219746 pfam08208, RNA_polI_A34, DNA-directed RNA polymerase I subunit RPA34

 Score = 40.1 bits (94), Expect = 2e-04
 Identities = 27/48 (56%), Positives = 38/48 (79%)

Query: 113 KKKKRKEKKKKKDKKKKKEEKKKEKRKEEKKKKEEEKKKKKKKKKKKK 160
           +K+   E+++KK+KKKKKE KK++K K++KK+K  E K  KKKKKKKK
Sbjct: 144 EKEAEVEEEEKKEKKKKKEVKKEKKEKKDKKEKMVEPKGSKKKKKKKK 191

5. This is a family of proteins conserved from yeasts to human. Subunit A34.5 of RNA polymerase I is a non-essential subunit which is thought to help Pol I overcome topological constraints imposed on ribosomal DNA during the process of transcription. Length = 193

>gnl|CDD|240388 PTZ00372, PTZ00372, endonuclease 4-like protein; Provisional

 Score = 40.5 bits (95), Expect = 2e-04
 Identities = 19/49 (38%), Positives = 31/49 (63%)

Query: 112 NKKKKRKEKKKKKDKKKKKEEKKKEKRKEEKKKKEEEKKKKKKKKKKKK 160
            KK K+++K  +  KK +K++KKK+++KE K + E +   K  KK KK 
Sbjct: 54  TKKDKKEDKNNESKKKSEKKKKKKKEKKEPKSEGETKLGFKTPKKSKKT 102

Length = 413

>gnl|CDD|240388 PTZ00372, PTZ00372, endonuclease 4-like protein; Provisional

 Score = 40.1 bits (94), Expect = 2e-04
 Identities = 23/53 (43%), Positives = 31/53 (58%)

Query: 112 NKKKKRKEKKKKKDKKKKKEEKKKEKRKEEKKKKEEEKKKKKKKKKKKKNALD 164
            K+ K  E KKK +KKKKK+++KKE + E + K   +  KK KK KKK     
Sbjct: 58  KKEDKNNESKKKSEKKKKKKKEKKEPKSEGETKLGFKTPKKSKKTKKKPPKPK 110

Length = 413

>gnl|CDD|219838 pfam08432, DUF1742, Fungal protein of unknown function (DUF1742)

 Score = 39.7 bits (93), Expect = 2e-04
 Identities = 20/56 (35%), Positives = 33/56 (58%)

Query: 106 YTEWLRNKKKKRKEKKKKKDKKKKKEEKKKEKRKEEKKKKEEEKKKKKKKKKKKKN 161
           Y E  + K KK+K KKKK   K KK++KK +K +++ +K+ E+K +   K   +  
Sbjct: 78  YEEKQKWKWKKKKSKKKKDKDKDKKDDKKDDKSEKKDEKEAEDKLEDLTKSYSETL 133

This is a family of fungal proteins of unknown function. Length = 182

>gnl|CDD|236877 PRK11192, PRK11192, ATP-dependent RNA helicase SrmB; Provisional

 Score = 39.2 bits (92), Expect = 4e-04
 Identities = 14/37 (37%), Positives = 22/37 (59%)

Query: 111 RNKKKKRKEKKKKKDKKKKKEEKKKEKRKEEKKKKEE 147
           +  +KK KEK+K K KK+ ++ K   KR++     EE
Sbjct: 398 KRAEKKEKEKEKPKVKKRHRDTKNIGKRRKPSGTSEE 434

Length = 434

>gnl|CDD|240388 PTZ00372, PTZ00372, endonuclease 4-like protein; Provisional

 Score = 39.3 bits (92), Expect = 4e-04
 Identities = 23/50 (46%), Positives = 31/50 (62%)

Query: 112 NKKKKRKEKKKKKDKKKKKEEKKKEKRKEEKKKKEEEKKKKKKKKKKKKN 161
           N + K+K +KKKK KK+KKE K + + K   K  ++ KK KKK  K K N
Sbjct: 63  NNESKKKSEKKKKKKKEKKEPKSEGETKLGFKTPKKSKKTKKKPPKPKPN 112

Length = 413

>gnl|CDD|240388 PTZ00372, PTZ00372, endonuclease 4-like protein; Provisional

 Score = 39.3 bits (92), Expect = 4e-04
 Identities = 19/50 (38%), Positives = 29/50 (58%)

Query: 112 NKKKKRKEKKKKKDKKKKKEEKKKEKRKEEKKKKEEEKKKKKKKKKKKKN 161
           NK      KK KK+ K  + +KK EK+K++KK+K+E K + + K   K  
Sbjct: 47  NKVATTSTKKDKKEDKNNESKKKSEKKKKKKKEKKEPKSEGETKLGFKTP 96

Length = 413

>gnl|CDD|240388 PTZ00372, PTZ00372, endonuclease 4-like protein; Provisional

 Score = 39.3 bits (92), Expect = 4e-04
 Identities = 17/49 (34%), Positives = 27/49 (55%)

Query: 112 NKKKKRKEKKKKKDKKKKKEEKKKEKRKEEKKKKEEEKKKKKKKKKKKK 160
             K      KK K + K  E KKK ++K++KKK+++E K + + K   K
Sbjct: 46  ENKVATTSTKKDKKEDKNNESKKKSEKKKKKKKEKKEPKSEGETKLGFK 94

Length = 413

>gnl|CDD|217393 pfam03154, Atrophin-1, Atrophin-1 family

 Score = 39.3 bits (91), Expect = 5e-04
 Identities = 17/56 (30%), Positives = 39/56 (69%)

Query: 101 FGTSLYTEWLRNKKKKRKEKKKKKDKKKKKEEKKKEKRKEEKKKKEEEKKKKKKKK 156
           + T L +  L  K+++  EK K++ ++K +EE+++EK KE+++++E E++ ++  K
Sbjct: 568 YFTPLASSKLAKKREEAVEKAKREAEQKAREEREREKEKEKEREREREREAERAAK 623

Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteristic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity. Length = 979

>gnl|CDD|240402 PTZ00399, PTZ00399, cysteinyl-tRNA-synthetase; Provisional

 Score = 39.2 bits (92), Expect = 5e-04
 Identities = 19/43 (44%), Positives = 33/43 (76%), Gaps = 1/43 (2%)

Query: 112 NKKKKRKEKKKKKDKKKKKEEKKKEKRKEEKKKKEEEKKKKKK 154
           +K++ ++EK++K+  K++K  +K +K +EEKKKKE EK +K K
Sbjct: 549 DKEELQREKEEKEALKEQKRLRKLKK-QEEKKKKELEKLEKAK 590

Length = 651

>gnl|CDD|240388 PTZ00372, PTZ00372, endonuclease 4-like protein; Provisional

 Score = 38.9 bits (91), Expect = 6e-04
 Identities = 19/47 (40%), Positives = 29/47 (61%)

Query: 115 KKRKEKKKKKDKKKKKEEKKKEKRKEEKKKKEEEKKKKKKKKKKKKN 161
               E++ K      K++KK++K  E KKK E++KKKKK+KK+ K  
Sbjct: 40  STFSEEENKVATTSTKKDKKEDKNNESKKKSEKKKKKKKEKKEPKSE 86

Length = 413

>gnl|CDD|215774 pfam00183, HSP90, Hsp90 protein

 Score = 39.0 bits (91), Expect = 6e-04
 Identities = 21/60 (35%), Positives = 41/60 (68%)

Query: 101 FGTSLYTEWLRNKKKKRKEKKKKKDKKKKKEEKKKEKRKEEKKKKEEEKKKKKKKKKKKK 160
           +   L+ E    K+   +E++++K++KK++EEK  +K +E  +++E+E+KKKK KK K+ 
Sbjct: 21  YPIYLWVEKEVEKEVPDEEEEEEKEEKKEEEEKTTDKEEEVDEEEEKEEKKKKTKKVKET 80

Length = 529

>gnl|CDD|234017 TIGR02794, tolA_full, TolA protein

 Score = 38.7 bits (90), Expect = 6e-04
 Identities = 21/49 (42%), Positives = 28/49 (57%)

Query: 113 KKKKRKEKKKKKDKKKKKEEKKKEKRKEEKKKKEEEKKKKKKKKKKKKN 161
           K +   EKK K++ KK+ EE+ K K   E KKK  E KKK + + K K 
Sbjct: 135 KAEAEAEKKAKEEAKKQAEEEAKAKAAAEAKKKAAEAKKKAEAEAKAKA 183

TolA couples the inner membrane complex of itself with TolQ and TolR to the outer membrane complex of TolB and OprL (also called Pal). Most of the length of the protein consists of low-complexity sequence that may differ in both length and composition from one species to another, complicating efforts to discriminate TolA (the most divergent gene in the tol-pal system) from paralogs such as TonB. Selection of members of the seed alignment and criteria for setting scoring cutoffs are based largely conserved operon struction. //The Tol-Pal complex is required for maintaining outer membrane integrity. Also involved in transport (uptake) of colicins and filamentous DNA, and implicated in pathogenesis. Transport is energized by the proton motive force. TolA is an inner membrane protein that interacts with periplasmic TolB and with outer membrane porins ompC, phoE and lamB [Transport and binding proteins, Other, Cellular processes, Pathogenesis]. Length = 346

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 39.0 bits (90), Expect = 7e-04
 Identities = 17/49 (34%), Positives = 28/49 (57%)

Query: 114  KKKRKEKKKKKDKKKKKEEKKKEKRKEEKKKKEEEKKKKKKKKKKKKNA 162
            KKK +E KK  +  K + E   ++ +  ++K E  +KKK++ KKK   A
Sbjct: 1335 KKKAEEAKKAAEAAKAEAEAAADEAEAAEEKAEAAEKKKEEAKKKADAA 1383

Length = 2084

>gnl|CDD|215214 PLN02381, PLN02381, valyl-tRNA synthetase

 Score = 38.7 bits (90), Expect = 7e-04
 Identities = 17/55 (30%), Positives = 31/55 (56%)

Query: 108 EWLRNKKKKRKEKKKKKDKKKKKEEKKKEKRKEEKKKKEEEKKKKKKKKKKKKNA 162
           E L  KKKK ++ K+K+ KK K  +K+ + + + ++  +     KK +KK +K  
Sbjct: 16  EELERKKKKEEKAKEKELKKLKAAQKEAKAKLQAQQASDGTNVPKKSEKKSRKRD 70

Length = 1066

>gnl|CDD|238192 cd00315, Cyt_C5_DNA_methylase, Cytosine-C5 specific DNA methylases; Methyl transfer reactions play an important role in many aspects of biology

 Score = 38.4 bits (90), Expect = 7e-04
 Identities = 18/93 (19%), Positives = 28/93 (30%), Gaps = 23/93 (24%)

Query: 15  GLQKDIADARCTALSYLIETIPANFPGDRLDHYTTQAVKGWKRKLSGIFRTPNVKGFEG- 73
           G +K   D R T    +I  +    P                      F   NVKG    
Sbjct: 79  GKRKGFEDTRGTLFFEIIRILKEKKPK--------------------YFLLENVKGLLTH 118

Query: 74  --SRSRDLITSMLTRAGFRFQEFLLSPTQFGTS 104
               +  +I + L   G+     LL+ + +G  
Sbjct: 119 DNGNTLKVILNTLEELGYNVYWKLLNASDYGVP 151

Cytosine-specific DNA methylases are found both in prokaryotes and eukaryotes. DNA methylation, or the covalent addition of a methyl group to cytosine within the context of the CpG dinucleotide, has profound effects on the mammalian genome. These effects include transcriptional repression via inhibition of transcription factor binding or the recruitment of methyl-binding proteins and their associated chromatin remodeling factors, X chromosome inactivation, imprinting and the suppression of parasitic DNA sequences. DNA methylation is also essential for proper embryonic development and is an important player in both DNA repair and genome stability. Length = 275

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 38.6 bits (89), Expect = 8e-04
 Identities = 17/46 (36%), Positives = 24/46 (52%)

Query: 113  KKKKRKEKKKKKDKKKKKEEKKKEKRKEEKKKKEEEKKKKKKKKKK 158
             KK  +  K + +    + E  +EK +  +KKKEE KKK    KKK
Sbjct: 1341 AKKAAEAAKAEAEAAADEAEAAEEKAEAAEKKKEEAKKKADAAKKK 1386

Length = 2084

>gnl|CDD|178945 PRK00247, PRK00247, putative inner membrane protein translocase component YidC; Validated

 Score = 38.3 bits (89), Expect = 8e-04
 Identities = 17/77 (22%), Positives = 34/77 (44%), Gaps = 8/77 (10%)

Query: 95  LLSPTQFGTSLYTEWLRNKKKKRKEKKKKKDKKKKKEEKKKEKRKE-------EKKKKEE 147
           +++P +    L+ E    KK +  EK + K +KK+  +K++   +E       E+     
Sbjct: 316 IITPWRAPE-LHAENAEIKKTRTAEKNEAKARKKEIAQKRRAAEREINREARQERAAAMA 374

Query: 148 EKKKKKKKKKKKKNALD 164
             + ++   K KK  L 
Sbjct: 375 RARARRAAVKAKKKGLI 391

Length = 429

>gnl|CDD|221641 pfam12569, NARP1, NMDA receptor-regulated protein 1

 Score = 38.0 bits (89), Expect = 0.001
 Identities = 16/44 (36%), Positives = 26/44 (59%), Gaps = 1/44 (2%)

Query: 110 LRNKKKKRKEKKKKKDKKKKKEEKKKEKRKEEKKKKEEEKKKKK 153
           LR K++K  EKK +K++ +K   KKK +   +K K  + + KK 
Sbjct: 414 LRKKQRK-AEKKAEKEEAEKAAAKKKAEAAAKKAKGPDGETKKV 456

This domain family is found in eukaryotes, and is approximately 40 amino acids in length. The family is found in association with pfam07719, pfam00515. There is a single completely conserved residue L that may be functionally important. NARP1 is the mammalian homologue of a yeast N-terminal acetyltransferase that regulates entry into the G(0) phase of the cell cycle. Length = 516

>gnl|CDD|240388 PTZ00372, PTZ00372, endonuclease 4-like protein; Provisional

 Score = 37.8 bits (88), Expect = 0.001
 Identities = 18/48 (37%), Positives = 31/48 (64%)

Query: 113 KKKKRKEKKKKKDKKKKKEEKKKEKRKEEKKKKEEEKKKKKKKKKKKK 160
               +K+KK+ K+ + KK+ +KK+K+K+EKK+ + E + K   K  KK
Sbjct: 51  TTSTKKDKKEDKNNESKKKSEKKKKKKKEKKEPKSEGETKLGFKTPKK 98

Length = 413

>gnl|CDD|240402 PTZ00399, PTZ00399, cysteinyl-tRNA-synthetase; Provisional

 Score = 37.7 bits (88), Expect = 0.001
 Identities = 18/45 (40%), Positives = 33/45 (73%)

Query: 116 KRKEKKKKKDKKKKKEEKKKEKRKEEKKKKEEEKKKKKKKKKKKK 160
           K  +K++ + +K++KE  K++KR  + KK+EE+KKK+ +K +K K
Sbjct: 546 KLDDKEELQREKEEKEALKEQKRLRKLKKQEEKKKKELEKLEKAK 590

Length = 651

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 38.2 bits (88), Expect = 0.001
 Identities = 17/49 (34%), Positives = 27/49 (55%)

Query: 115  KKRKEKKKKKDKKKKKEEKKKEKRKEEKKKKEEEKKKKKKKKKKKKNAL 163
            KK+ E+ KK  +  K E +      E  ++K E  +KKK++ KKK +A 
Sbjct: 1335 KKKAEEAKKAAEAAKAEAEAAADEAEAAEEKAEAAEKKKEEAKKKADAA 1383

Length = 2084

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 38.2 bits (88), Expect = 0.001
 Identities = 22/50 (44%), Positives = 30/50 (60%)

Query: 115  KKRKEKKKKKDKKKKKEEKKKEKRKEEKKKKEEEKKKKKKKKKKKKNALD 164
            KK+ E+ KK D+ KKK E+ K+K    KKK EE KK  +  K + + A D
Sbjct: 1308 KKKAEEAKKADEAKKKAEEAKKKADAAKKKAEEAKKAAEAAKAEAEAAAD 1357

Length = 2084

>gnl|CDD|215214 PLN02381, PLN02381, valyl-tRNA synthetase

 Score = 38.3 bits (89), Expect = 0.001
 Identities = 17/54 (31%), Positives = 30/54 (55%)

Query: 111 RNKKKKRKEKKKKKDKKKKKEEKKKEKRKEEKKKKEEEKKKKKKKKKKKKNALD 164
           R KKK+ K K+K+  K K  +++ K K + ++        KK +KK +K++  D
Sbjct: 20  RKKKKEEKAKEKELKKLKAAQKEAKAKLQAQQASDGTNVPKKSEKKSRKRDVED 73

Length = 1066

>gnl|CDD|220237 pfam09428, DUF2011, Fungal protein of unknown function (DUF2011)

 Score = 36.9 bits (86), Expect = 0.001
 Identities = 15/51 (29%), Positives = 35/51 (68%)

Query: 111 RNKKKKRKEKKKKKDKKKKKEEKKKEKRKEEKKKKEEEKKKKKKKKKKKKN 161
             KKK+++  KK++   + + E+ KE+ ++EK+ ++  +KK K+++K+K+ 
Sbjct: 80  EKKKKRKRPGKKRRIALRLRRERTKERAEKEKRTRKNREKKFKRRQKEKEK 130

This is a family of fungal proteins whose function is unknown. Length = 130

>gnl|CDD|219868 pfam08496, Peptidase_S49_N, Peptidase family S49 N-terminal

 Score = 36.7 bits (86), Expect = 0.001
 Identities = 15/34 (44%), Positives = 23/34 (67%)

Query: 118 KEKKKKKDKKKKKEEKKKEKRKEEKKKKEEEKKK 151
           K++ K  +K +KK EK K K +++K KKEE K +
Sbjct: 65  KKELKAWEKAEKKAEKAKAKAEKKKAKKEEPKPR 98

This domain is found to the N-terminus of bacterial signal peptidases of the S49 family (pfam01343). Length = 154

>gnl|CDD|149343 pfam08229, SHR3_chaperone, ER membrane protein SH3

 Score = 37.3 bits (87), Expect = 0.001
 Identities = 17/55 (30%), Positives = 23/55 (41%), Gaps = 14/55 (25%)

Query: 106 YTEWLRNKKKKRKEKKKKKDKKKKKEEKKKEKRKEEKKKKEEEKKKKKKKKKKKK 160
           Y EW              KD K  +E   +E       K+EE  + +KK+ KKKK
Sbjct: 156 YAEW--------------KDAKLLEEFAAEEAEAAAAAKEEESAEGEKKESKKKK 196

This family of proteins are membrane localised chaperones that are required for correct plasma membrane localisation of amino acid permeases (AAPs). SH3 prevents AAPs proteins from aggregating and assists in their correct folding. In the absence of SH3, AAPs are retained in the ER. Length = 196

>gnl|CDD|219655 pfam07946, DUF1682, Protein of unknown function (DUF1682)

 Score = 37.2 bits (87), Expect = 0.002
 Identities = 18/47 (38%), Positives = 33/47 (70%), Gaps = 1/47 (2%)

Query: 117 RKEKKKKKDKKKKKEEKKKEKRKEEKKKKEEEKKKKKKKKKKKKNAL 163
             E  +K DK +++EE+K  K  EE+++ EE ++KK++KKK+++ A 
Sbjct: 254 SPEVLRKVDKTREEEEEKILKAAEEERQ-EEAQEKKEEKKKEEREAK 299

The members of this family are all hypothetical eukaryotic proteins of unknown function. One member is described as being an adipocyte-specific protein, but no evidence of this was found. Length = 322

>gnl|CDD|240388 PTZ00372, PTZ00372, endonuclease 4-like protein; Provisional

 Score = 37.4 bits (87), Expect = 0.002
 Identities = 20/49 (40%), Positives = 30/49 (61%)

Query: 112 NKKKKRKEKKKKKDKKKKKEEKKKEKRKEEKKKKEEEKKKKKKKKKKKK 160
              KK K++ K  + KKK E+KKK+K+++++ K E E K   K  KK K
Sbjct: 52  TSTKKDKKEDKNNESKKKSEKKKKKKKEKKEPKSEGETKLGFKTPKKSK 100

Length = 413

>gnl|CDD|240388 PTZ00372, PTZ00372, endonuclease 4-like protein; Provisional

 Score = 37.4 bits (87), Expect = 0.002
 Identities = 22/59 (37%), Positives = 31/59 (52%)

Query: 103 TSLYTEWLRNKKKKRKEKKKKKDKKKKKEEKKKEKRKEEKKKKEEEKKKKKKKKKKKKN 161
                E   N+ KK+ EKKKKK K+KK+ + + E +   K  K+ +K KKK  K K   
Sbjct: 55  KKDKKEDKNNESKKKSEKKKKKKKEKKEPKSEGETKLGFKTPKKSKKTKKKPPKPKPNE 113

Length = 413

>gnl|CDD|219838 pfam08432, DUF1742, Fungal protein of unknown function (DUF1742)

 Score = 36.6 bits (85), Expect = 0.002
 Identities = 21/48 (43%), Positives = 34/48 (70%)

Query: 112 NKKKKRKEKKKKKDKKKKKEEKKKEKRKEEKKKKEEEKKKKKKKKKKK 159
            K KK  E+K+K   KKKK +KKK+K K++K  K+++K +KK +K+ +
Sbjct: 72  EKVKKEYEEKQKWKWKKKKSKKKKDKDKDKKDDKKDDKSEKKDEKEAE 119

This is a family of fungal proteins of unknown function. Length = 182

>gnl|CDD|240402 PTZ00399, PTZ00399, cysteinyl-tRNA-synthetase; Provisional

 Score = 36.9 bits (86), Expect = 0.002
 Identities = 13/41 (31%), Positives = 30/41 (73%)

Query: 123 KKDKKKKKEEKKKEKRKEEKKKKEEEKKKKKKKKKKKKNAL 163
           K++ +++KEEK+  K ++  +K +++++KKKK+ +K + A 
Sbjct: 550 KEELQREKEEKEALKEQKRLRKLKKQEEKKKKELEKLEKAK 590

Length = 651

>gnl|CDD|220648 pfam10243, MIP-T3, Microtubule-binding protein MIP-T3

 Score = 37.6 bits (87), Expect = 0.002
 Identities = 24/53 (45%), Positives = 37/53 (69%)

Query: 112 NKKKKRKEKKKKKDKKKKKEEKKKEKRKEEKKKKEEEKKKKKKKKKKKKNALD 164
            K+K++ +++KKK K+K KEE K  K KEE K+K   K+K+K+K+KK +   D
Sbjct: 107 EKEKEQVKEEKKKKKEKPKEEPKDRKPKEEAKEKRPPKEKEKEKEKKVEEPRD 159

This protein, which interacts with both microtubules and TRAF3 (tumour necrosis factor receptor-associated factor 3), is conserved from worms to humans. The N-terminal region is the microtubule binding domain and is well-conserved; the C-terminal 100 residues, also well-conserved, constitute the coiled-coil region which binds to TRAF3. The central region of the protein is rich in lysine and glutamic acid and carries KKE motifs which may also be necessary for tubulin-binding, but this region is the least well-conserved. Length = 506

>gnl|CDD|235322 PRK04950, PRK04950, ProP expression regulator; Provisional

 Score = 37.2 bits (87), Expect = 0.002
 Identities = 12/47 (25%), Positives = 28/47 (59%)

Query: 114 KKKRKEKKKKKDKKKKKEEKKKEKRKEEKKKKEEEKKKKKKKKKKKK 160
           K K + ++ ++  KK++   +KEK    ++K + +  +KK+K + +K
Sbjct: 107 KAKVQAQRAEQQAKKREAAGEKEKAPRRERKPKPKAPRKKRKPRAQK 153

Length = 213

>gnl|CDD|220252 pfam09468, RNase_H2-Ydr279, Ydr279p protein family (RNase H2 complex component)

 Score = 37.3 bits (87), Expect = 0.002
 Identities = 19/57 (33%), Positives = 31/57 (54%)

Query: 105 LYTEWLRNKKKKRKEKKKKKDKKKKKEEKKKEKRKEEKKKKEEEKKKKKKKKKKKKN 161
           L      +KKKKR+ ++  +  + + E+K+K K + +KKK +E K  K  KK   K 
Sbjct: 223 LDKYLKESKKKKRETEEDVEAAESRAEKKRKSKEEIKKKKPKESKGVKALKKVVAKG 279

RNases H are enzymes that specifically hydrolyse RNA when annealed to a complementary DNA and are present in all living organisms. In yeast RNase H2 is composed of a complex of three proteins (Rnh2Ap, Ydr279p and Ylr154p), this family represents the homologues of Ydr279p. It is not known whether non yeast proteins in this family fulfil the same function. Length = 287

>gnl|CDD|240246 PTZ00053, PTZ00053, methionine aminopeptidase 2; Provisional

 Score = 37.4 bits (87), Expect = 0.002
 Identities = 23/59 (38%), Positives = 35/59 (59%), Gaps = 8/59 (13%)

Query: 112 NKKKKRKEKKKKKDKKKKKEEKK--------KEKRKEEKKKKEEEKKKKKKKKKKKKNA 162
            K++ +++  KKK+KK KK+             + +E + K+  +KKKKKKKKKKKKN 
Sbjct: 13  QKQQNKQKGTKKKNKKSKKDVDDDDAFLAELISENQEAENKQNNKKKKKKKKKKKKKNL 71

Length = 470

>gnl|CDD|227446 COG5116, RPN2, 26S proteasome regulatory complex component [Posttranslational modification, protein turnover, chaperones]

 Score = 37.2 bits (86), Expect = 0.002
 Identities = 18/61 (29%), Positives = 24/61 (39%), Gaps = 10/61 (16%)

Query: 114 KKKRKEKKKKK-----DKKKKKEEKKKEKRKEEKKKKEEEKKKK-----KKKKKKKKNAL 163
           K   + K+K K     DK+ K E    E   E    K+ E+K          KKKK   +
Sbjct: 792 KAAARAKQKPKEKGPNDKEIKIESPSVETEGERCTIKQREEKGIDAPAILNVKKKKPYKV 851

Query: 164 D 164
           D
Sbjct: 852 D 852

Length = 926

>gnl|CDD|226894 COG4499, COG4499, Predicted membrane protein [Function unknown]

 Score = 37.1 bits (86), Expect = 0.002
 Identities = 13/50 (26%), Positives = 34/50 (68%)

Query: 111 RNKKKKRKEKKKKKDKKKKKEEKKKEKRKEEKKKKEEEKKKKKKKKKKKK 160
             + K   +  ++ + K K+E+ K+E+ ++++K++ +E K+K++K ++KK
Sbjct: 385 LGEVKDETDASEEAEAKAKEEKLKQEENEKKQKEQADEDKEKRQKDERKK 434

Length = 434

>gnl|CDD|219655 pfam07946, DUF1682, Protein of unknown function (DUF1682)

 Score = 36.5 bits (85), Expect = 0.003
 Identities = 13/50 (26%), Positives = 36/50 (72%)

Query: 110 LRNKKKKRKEKKKKKDKKKKKEEKKKEKRKEEKKKKEEEKKKKKKKKKKK 159
           L  +  ++ +K ++++++K  +  ++E+++E ++KKEE+KK++++ K  K
Sbjct: 253 LSPEVLRKVDKTREEEEEKILKAAEEERQEEAQEKKEEKKKEEREAKLAK 302

The members of this family are all hypothetical eukaryotic proteins of unknown function. One member is described as being an adipocyte-specific protein, but no evidence of this was found. Length = 322

>gnl|CDD|237753 PRK14552, PRK14552, C/D box methylation guide ribonucleoprotein complex aNOP56 subunit; Provisional

 Score = 36.9 bits (86), Expect = 0.003
 Identities = 20/44 (45%), Positives = 31/44 (70%)

Query: 118 KEKKKKKDKKKKKEEKKKEKRKEEKKKKEEEKKKKKKKKKKKKN 161
           KE+  K+ ++ K++  K  K+K E+KK ++ KKKKK+KKK KK 
Sbjct: 365 KEELNKRIEEIKEKYPKPPKKKREEKKPQKRKKKKKRKKKGKKR 408

Length = 414

>gnl|CDD|215774 pfam00183, HSP90, Hsp90 protein

 Score = 36.7 bits (85), Expect = 0.003
 Identities = 17/46 (36%), Positives = 35/46 (76%)

Query: 119 EKKKKKDKKKKKEEKKKEKRKEEKKKKEEEKKKKKKKKKKKKNALD 164
           E+++++ ++KK+EE+K   ++EE  ++EE+++KKKK KK K+   +
Sbjct: 38  EEEEEEKEEKKEEEEKTTDKEEEVDEEEEKEEKKKKTKKVKETTTE 83

Length = 529

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 37.0 bits (85), Expect = 0.003
 Identities = 21/54 (38%), Positives = 28/54 (51%), Gaps = 5/54 (9%)

Query: 114  KKKRKEKKKKKDKKKKKEEKKKE-----KRKEEKKKKEEEKKKKKKKKKKKKNA 162
            KKK +E KK  + KKK EE KK+     K+ EE KK  E  K + +    +  A
Sbjct: 1308 KKKAEEAKKADEAKKKAEEAKKKADAAKKKAEEAKKAAEAAKAEAEAAADEAEA 1361

Length = 2084

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 37.0 bits (85), Expect = 0.003
 Identities = 23/54 (42%), Positives = 35/54 (64%), Gaps = 3/54 (5%)

Query: 113  KKKKRKEKKKKKDKKKKKEEKKKE---KRKEEKKKKEEEKKKKKKKKKKKKNAL 163
             + +  E+K +  +KKK+E KKK    K+K E+KKK +E KKK ++ KKK + L
Sbjct: 1357 DEAEAAEEKAEAAEKKKEEAKKKADAAKKKAEEKKKADEAKKKAEEDKKKADEL 1410

Length = 2084

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 37.0 bits (85), Expect = 0.003
 Identities = 19/49 (38%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 114  KKKRKEKKKKKDKKKKKEEKKKEKRKEEKKKKEEEKKKKKKKKKKKKNA 162
            KKK +E KKK D  KKK E+ K K  E  K + E    + +  ++K  A
Sbjct: 1321 KKKAEEAKKKADAAKKKAEEAK-KAAEAAKAEAEAAADEAEAAEEKAEA 1368

Length = 2084

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 36.7 bits (84), Expect = 0.003
 Identities = 17/49 (34%), Positives = 27/49 (55%)

Query: 114  KKKRKEKKKKKDKKKKKEEKKKEKRKEEKKKKEEEKKKKKKKKKKKKNA 162
             K   E    + +  +++ +  EK+KEE KKK +  KKK ++KKK   A
Sbjct: 1348 AKAEAEAAADEAEAAEEKAEAAEKKKEEAKKKADAAKKKAEEKKKADEA 1396

Length = 2084

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 36.7 bits (84), Expect = 0.003
 Identities = 25/52 (48%), Positives = 32/52 (61%), Gaps = 3/52 (5%)

Query: 114  KKKRKEKKKKKDKKKKKEEKKKE---KRKEEKKKKEEEKKKKKKKKKKKKNA 162
            KK    KKK  + KKK EEKKK    K+K E+ KK +E KKK ++ KK + A
Sbjct: 1411 KKAAAAKKKADEAKKKAEEKKKADEAKKKAEEAKKADEAKKKAEEAKKAEEA 1462

Length = 2084

>gnl|CDD|236944 PRK11642, PRK11642, exoribonuclease R; Provisional

 Score = 37.0 bits (86), Expect = 0.003
 Identities = 16/45 (35%), Positives = 19/45 (42%), Gaps = 1/45 (2%)

Query: 117 RKEKKKKKDKKKKKEEKKKEKRKEEKKKKEEEKKKKKKKKKKKKN 161
           R EKK K    KK   K K K   + +K     K K+  KKK   
Sbjct: 770 RGEKKAKPKAAKKDARKAK-KPSAKTQKIAAATKAKRAAKKKVAE 813

Length = 813

>gnl|CDD|220383 pfam09756, DDRGK, DDRGK domain

 Score = 36.2 bits (84), Expect = 0.003
 Identities = 15/44 (34%), Positives = 37/44 (84%)

Query: 116 KRKEKKKKKDKKKKKEEKKKEKRKEEKKKKEEEKKKKKKKKKKK 159
           +R+E+KK ++K++ + ++++E  +E +KKKEEE++K+++++ +K
Sbjct: 27  EREERKKLEEKREGERKEEEELEEEREKKKEEEERKEREEQARK 70

This is a family of proteins of approximately 300 residues, found in plants and vertebrates. They contain a highly conserved DDRGK motif. Length = 189

>gnl|CDD|217756 pfam03839, Sec62, Translocation protein Sec62

 Score = 36.3 bits (84), Expect = 0.003
 Identities = 19/54 (35%), Positives = 27/54 (50%)

Query: 111 RNKKKKRKEKKKKKDKKKKKEEKKKEKRKEEKKKKEEEKKKKKKKKKKKKNALD 164
            N +   K   + K  +K K   K +  +  KK   +EKK++KKK KKKK  L 
Sbjct: 28  GNPEIYNKINSQDKAIEKFKLLIKAQMAERVKKLHSQEKKEEKKKPKKKKVPLQ 81

Length = 217

>gnl|CDD|187751 cd09270, RNase_H2-B, Ribonuclease H2-B is a subunit of the eukaryotic RNase H complex which cleaves RNA-DNA hybrids

 Score = 36.1 bits (84), Expect = 0.003
 Identities = 22/56 (39%), Positives = 33/56 (58%), Gaps = 1/56 (1%)

Query: 107 TEWLRNKKKKRKEKKKKKDKKKKKEEKKKEKRKEEKKKKEEEKKKKKKKKKKKKNA 162
             WL  KK +R +KK+   K+ +    KK+    E++KK+++KK  KKKK KK  A
Sbjct: 146 LAWLL-KKVERLKKKELDIKEAEAARDKKKSNNAEEEKKKKKKKSAKKKKLKKVAA 200

Ribonuclease H2B is one of the three proteins of eukaryotic RNase H2 complex that is required for nucleic acid binding and hydrolysis. RNase H is classified into two families, type I (prokaryotic RNase HI, eukaryotic RNase H1 and viral RNase H) and type II (prokaryotic RNase HII and HIII, and eukaryotic RNase H2/HII). RNase H endonucleolytically hydrolyzes an RNA strand when it is annealed to a complementary DNA strand in the presence of divalent cations, in DNA replication and repair. The enzyme can be found in bacteria, archaea, and eukaryotes. Most prokaryotic and eukaryotic genomes contain multiple RNase H genes. Despite a lack of evidence for homology from sequence comparisons, type I and type II RNase H share a common fold and similar steric configurations of the four acidic active-site residues, suggesting identical or very similar catalytic mechanisms. Eukaryotic RNase HII is active during replication and is believed to play a role in removal of Okazaki fragment primers and single ribonucleotides in DNA-DNA duplexes. Eukaryotic RNase HII is functional when it forms a complex with RNase H2B and RNase H2C proteins. It is speculated that the two accessory subunits are required for correct folding of the catalytic subunit of RNase HII. Mutations in the three subunits of human RNase HII cause neurological disorder. Length = 211

>gnl|CDD|240388 PTZ00372, PTZ00372, endonuclease 4-like protein; Provisional

 Score = 36.2 bits (84), Expect = 0.004
 Identities = 17/53 (32%), Positives = 31/53 (58%)

Query: 107 TEWLRNKKKKRKEKKKKKDKKKKKEEKKKEKRKEEKKKKEEEKKKKKKKKKKK 159
            E L    ++  +      KK KKE+K  E +K+ +KKK+++K+KK+ K + +
Sbjct: 36  KEILSTFSEEENKVATTSTKKDKKEDKNNESKKKSEKKKKKKKEKKEPKSEGE 88

Length = 413

>gnl|CDD|240402 PTZ00399, PTZ00399, cysteinyl-tRNA-synthetase; Provisional

 Score = 36.5 bits (85), Expect = 0.004
 Identities = 15/37 (40%), Positives = 26/37 (70%)

Query: 108 EWLRNKKKKRKEKKKKKDKKKKKEEKKKEKRKEEKKK 144
           E  R K++K   K++K+ +K KK+E+KK+K  E+ +K
Sbjct: 552 ELQREKEEKEALKEQKRLRKLKKQEEKKKKELEKLEK 588

Length = 651

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 36.7 bits (84), Expect = 0.004
 Identities = 26/55 (47%), Positives = 32/55 (58%), Gaps = 4/55 (7%)

Query: 112  NKKKKRKEKKKKKDKKKKKEEKKK----EKRKEEKKKKEEEKKKKKKKKKKKKNA 162
              KKK +E KK  + KKK EE KK    +K+ EE KKK +E KK  + KKK   A
Sbjct: 1461 EAKKKAEEAKKADEAKKKAEEAKKADEAKKKAEEAKKKADEAKKAAEAKKKADEA 1515

Length = 2084

>gnl|CDD|220237 pfam09428, DUF2011, Fungal protein of unknown function (DUF2011)

 Score = 34.9 bits (81), Expect = 0.004
 Identities = 15/50 (30%), Positives = 33/50 (66%)

Query: 111 RNKKKKRKEKKKKKDKKKKKEEKKKEKRKEEKKKKEEEKKKKKKKKKKKK 160
           +   +++++KKK+K   KK+    + +R+  K++ E+EK+ +K ++KK K
Sbjct: 73  KELLREKEKKKKRKRPGKKRRIALRLRRERTKERAEKEKRTRKNREKKFK 122

This is a family of fungal proteins whose function is unknown. Length = 130

>gnl|CDD|219868 pfam08496, Peptidase_S49_N, Peptidase family S49 N-terminal

 Score = 35.6 bits (83), Expect = 0.004
 Identities = 14/28 (50%), Positives = 18/28 (64%)

Query: 134 KKEKRKEEKKKKEEEKKKKKKKKKKKKN 161
           KKE +  EK +K+ EK K K +KKK K 
Sbjct: 65  KKELKAWEKAEKKAEKAKAKAEKKKAKK 92

This domain is found to the N-terminus of bacterial signal peptidases of the S49 family (pfam01343). Length = 154

>gnl|CDD|220648 pfam10243, MIP-T3, Microtubule-binding protein MIP-T3

 Score = 36.4 bits (84), Expect = 0.004
 Identities = 20/50 (40%), Positives = 37/50 (74%)

Query: 111 RNKKKKRKEKKKKKDKKKKKEEKKKEKRKEEKKKKEEEKKKKKKKKKKKK 160
           + + K+ K+KKK+K K++ K+ K KE+ KE++  KE+EK+K+KK ++ + 
Sbjct: 110 KEQVKEEKKKKKEKPKEEPKDRKPKEEAKEKRPPKEKEKEKEKKVEEPRD 159

This protein, which interacts with both microtubules and TRAF3 (tumour necrosis factor receptor-associated factor 3), is conserved from worms to humans. The N-terminal region is the microtubule binding domain and is well-conserved; the C-terminal 100 residues, also well-conserved, constitute the coiled-coil region which binds to TRAF3. The central region of the protein is rich in lysine and glutamic acid and carries KKE motifs which may also be necessary for tubulin-binding, but this region is the least well-conserved. Length = 506

>gnl|CDD|220371 pfam09736, Bud13, Pre-mRNA-splicing factor of RES complex

 Score = 35.4 bits (82), Expect = 0.004
 Identities = 20/50 (40%), Positives = 38/50 (76%)

Query: 111 RNKKKKRKEKKKKKDKKKKKEEKKKEKRKEEKKKKEEEKKKKKKKKKKKK 160
            + ++KR+EK+++K++K++KEEK+KE  K   +K+E EK+ ++ +K K K
Sbjct: 12  IDIEEKREEKEREKEEKERKEEKEKEWGKGLVQKEEREKRLEELEKAKNK 61

This entry is characterized by proteins with alternating conserved and low-complexity regions. Bud13 together with Snu17p and a newly identified factor, Pml1p/Ylr016c, form a novel trimeric complex. called The RES complex, pre-mRNA retention and splicing complex. Subunits of this complex are not essential for viability of yeasts but they are required for efficient splicing in vitro and in vivo. Furthermore, inactivation of this complex causes pre-mRNA leakage from the nucleus. Bud13 contains a unique, phylogenetically conserved C-terminal region of unknown function. Length = 141

>gnl|CDD|236048 PRK07561, PRK07561, DNA topoisomerase I subunit omega; Validated

 Score = 36.3 bits (85), Expect = 0.004
 Identities = 12/50 (24%), Positives = 20/50 (40%)

Query: 108 EWLRNKKKKRKEKKKKKDKKKKKEEKKKEKRKEEKKKKEEEKKKKKKKKK 157
           E L    +K ++ +   D   K    KK   K  +K K++    +K  K 
Sbjct: 809 EALELLAEKPEKLRYLADAPAKDPAGKKAAVKFSRKTKQQYVASEKDGKA 858

Length = 859

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	164
PF00145	335	DNA_methylase: C-5 cytosine-specific DNA methylase	99.95
COG0270	328	Dcm Site-specific DNA methylase [DNA replication,	99.94
cd00315	275	Cyt_C5_DNA_methylase Cytosine-C5 specific DNA meth	99.92
TIGR00675	315	dcm DNA-methyltransferase (dcm). All proteins in t	99.91
KOG0919|consensus	338		99.9
PRK10458	467	DNA cytosine methylase; Provisional	99.87
PRK13562	84	acetolactate synthase 1 regulatory subunit; Provis	91.38
PRK06737	76	acetolactate synthase 1 regulatory subunit; Valida	84.38
PRK08178	96	acetolactate synthase 1 regulatory subunit; Review	82.59
COG4747	142	ACT domain-containing protein [General function pr	80.87

>PF00145 DNA_methylase: C-5 cytosine-specific DNA methylase; InterPro: IPR001525 C-5 cytosine-specific DNA methylases (2

Probab=99.95  E-value=1.7e-29  Score=202.14  Aligned_cols=96  Identities=17%  Similarity=0.123  Sum_probs=80.9

Q ss_pred             CCcCCCCCcccccCcCCCCCCccchHHHHHHHhccccCCCCCCCchhhhhhhccccccceEEEeecCcCCCCc---hHHH
Q psy3546           2 ASIDYASNSDPGTGLQKDIADARCTALSYLIETIPANFPGDRLDHYTTQAVKGWKRKLSGIFRTPNVKGFEGS---RSRD   78 (164)
Q Consensus         2 ~~~~fPCQ~FS~aG~rkd~~D~R~~L~~~~iriI~~~~p~~~P~~~~~~~~~~~~~~~~~iFl~ENVkGf~~s---~~~d   78 (164)
                      ..-|||||+||.+|.+++.+|+|+.||.+++++|.+++    |+                +|+||||+||..+   ..++
T Consensus        65 l~ggpPCQ~fS~ag~~~~~~d~r~~L~~~~~~~v~~~~----Pk----------------~~~~ENV~~l~~~~~~~~~~  124 (335)
T PF00145_consen   65 LIGGPPCQGFSIAGKRKGFDDPRNSLFFEFLRIVKELK----PK----------------YFLLENVPGLLSSKNGEVFK  124 (335)
T ss_dssp             EEEE---TTTSTTSTHHCCCCHTTSHHHHHHHHHHHHS-----S----------------EEEEEEEGGGGTGGGHHHHH
T ss_pred             EEeccCCceEeccccccccccccchhhHHHHHHHhhcc----ce----------------EEEecccceeeccccccccc
Confidence            34689999999999999999999999999999999998    68                5599999999876   5699


Q ss_pred             HHHHHHHhCCCeEEEEEeCCCCCCCCCcceEEEecccch
Q psy3546          79 LITSMLTRAGFRFQEFLLSPTQFGTSLYTEWLRNKKKKR  117 (164)
Q Consensus        79 ~I~s~L~~~GY~v~~~lLnatdfGVPQ~Rr~~i~~rkk~  117 (164)
                      .|++.|+++||.+++.+|||.+|||||.|+|+++.+.++
T Consensus       125 ~i~~~l~~lGY~v~~~vlna~~yGvPQ~R~R~fivg~r~  163 (335)
T PF00145_consen  125 EILEELEELGYNVQWRVLNAADYGVPQNRERVFIVGIRK  163 (335)
T ss_dssp             HHHHHHHHTTEEEEEEEEEGGGGTSSBE-EEEEEEEEEG
T ss_pred             cccccccccceeehhccccHhhCCCCCceeeEEEEEECC
Confidence            999999999999999999999999999995555555444

1.1.37 from EC) (C5 Mtase) are enzymes that specifically methylate the C-5 carbon of cytosines in DNA to produce C5-methylcytosine [, , ]. In mammalian cells, cytosine-specific methyltransferases methylate certain CpG sequences, which are believed to modulate gene expression and cell differentiation. In bacteria, these enzymes are a component of restriction-modification systems and serve as valuable tools for the manipulation of DNA [, ]. The structure of HhaI methyltransferase (M.HhaI) has been resolved to 2.5 A []: the molecule folds into 2 domains - a larger catalytic domain containing catalytic and cofactor binding sites, and a smaller DNA recognition domain.; GO: 0003677 DNA binding, 0006306 DNA methylation; PDB: 4DA4_A 3PT6_B 3AV6_A 3AV5_A 3AV4_A 3PT9_A 1DCT_A 3LX6_A 3ME5_A 2QRV_A ....

>COG0270 Dcm Site-specific DNA methylase [DNA replication, recombination, and repair]

Probab=99.94  E-value=9.6e-28  Score=204.09  Aligned_cols=94  Identities=20%  Similarity=0.186  Sum_probs=85.1

Q ss_pred             cCCCCCcccccCcCCCCCCccchHHHHHHHhccccCCCCCCCchhhhhhhccccccceEEEeecCcCCCCc--hHHHHHH
Q psy3546           4 IDYASNSDPGTGLQKDIADARCTALSYLIETIPANFPGDRLDHYTTQAVKGWKRKLSGIFRTPNVKGFEGS--RSRDLIT   81 (164)
Q Consensus         4 ~~fPCQ~FS~aG~rkd~~D~R~~L~~~~iriI~~~~p~~~P~~~~~~~~~~~~~~~~~iFl~ENVkGf~~s--~~~d~I~   81 (164)
                      =|||||+||.+|.+++.+|+|++||++++++|..++    |+                +|+||||+||..+  ..++.|+
T Consensus        73 gGpPCQ~FS~aG~r~~~~D~R~~L~~~~~r~I~~~~----P~----------------~fv~ENV~gl~~~~~~~~~~i~  132 (328)
T COG0270          73 GGPPCQDFSIAGKRRGYDDPRGSLFLEFIRLIEQLR----PK----------------FFVLENVKGLLSSKGQTFDEIK  132 (328)
T ss_pred             eCCCCcchhhcCcccCCcCccceeeHHHHHHHHhhC----CC----------------EEEEecCchHHhcCchHHHHHH
Confidence            389999999999999999999999999999999999    57                6699999999875  6899999


Q ss_pred             HHHHhCCCeEEEEEeCCCCCCCCCcceEEEecccch
Q psy3546          82 SMLTRAGFRFQEFLLSPTQFGTSLYTEWLRNKKKKR  117 (164)
Q Consensus        82 s~L~~~GY~v~~~lLnatdfGVPQ~Rr~~i~~rkk~  117 (164)
                      +.|+++||.+.+.||||.||||||+|+++++.+.++
T Consensus       133 ~~L~~~GY~~~~~ilna~dyGvPQ~ReRvfiig~~~  168 (328)
T COG0270         133 KELEELGYGVEFNILNAADYGVPQSRERVFIVGFRR  168 (328)
T ss_pred             HHHHHcCCcchHheeeHHhcCCCCCccEEEEEEecC
Confidence            999999999999999999999999996655555443

>cd00315 Cyt_C5_DNA_methylase Cytosine-C5 specific DNA methylases; Methyl transfer reactions play an important role in many aspects of biology

Probab=99.92  E-value=2.1e-25  Score=185.76  Aligned_cols=94  Identities=18%  Similarity=0.209  Sum_probs=84.3

Q ss_pred             CCcCCCCCcccccCcCCCCCCccchHHHHHHHhccccCCCCCCCchhhhhhhccccccceEEEeecCcCCCC---chHHH
Q psy3546           2 ASIDYASNSDPGTGLQKDIADARCTALSYLIETIPANFPGDRLDHYTTQAVKGWKRKLSGIFRTPNVKGFEG---SRSRD   78 (164)
Q Consensus         2 ~~~~fPCQ~FS~aG~rkd~~D~R~~L~~~~iriI~~~~p~~~P~~~~~~~~~~~~~~~~~iFl~ENVkGf~~---s~~~d   78 (164)
                      ...|+|||+||.+|.+++.+|+|+.|+.+++++|..++    |+                +|+||||+||..   +..++
T Consensus        66 l~~gpPCq~fS~ag~~~~~~d~r~~L~~~~~~~i~~~~----P~----------------~~v~ENV~g~~~~~~~~~~~  125 (275)
T cd00315          66 LTGGFPCQPFSIAGKRKGFEDTRGTLFFEIIRILKEKK----PK----------------YFLLENVKGLLTHDNGNTLK  125 (275)
T ss_pred             EEeCCCChhhhHHhhcCCCCCchHHHHHHHHHHHHhcC----CC----------------EEEEEcCcchhccCchHHHH
Confidence            35689999999999999999999999999999999998    68                559999999986   67899


Q ss_pred             HHHHHHHhCCCeEEEEEeCCCCCCCCCcc-eEEEeccc
Q psy3546          79 LITSMLTRAGFRFQEFLLSPTQFGTSLYT-EWLRNKKK  115 (164)
Q Consensus        79 ~I~s~L~~~GY~v~~~lLnatdfGVPQ~R-r~~i~~rk  115 (164)
                      .|++.|+++||.+.+.+|||.+|||||.| |+|+++-.
T Consensus       126 ~i~~~l~~~GY~~~~~~l~a~~~GvPQ~R~R~~~ia~~  163 (275)
T cd00315         126 VILNTLEELGYNVYWKLLNASDYGVPQNRERVFIIGIR  163 (275)
T ss_pred             HHHHHHHhCCcEEEEEEEEHHHcCCCCCCcEEEEEEEe
Confidence            99999999999999999999999999999 55555443

Cytosine-specific DNA methylases are found both in prokaryotes and eukaryotes. DNA methylation, or the covalent addition of a methyl group to cytosine within the context of the CpG dinucleotide, has profound effects on the mammalian genome. These effects include transcriptional repression via inhibition of transcription factor binding or the recruitment of methyl-binding proteins and their associated chromatin remodeling factors, X chromosome inactivation, imprinting and the suppression of parasitic DNA sequences. DNA methylation is also essential for proper embryonic development and is an important player in both DNA repair and genome stability.

>TIGR00675 dcm DNA-methyltransferase (dcm)

Probab=99.91  E-value=1.1e-24  Score=184.90  Aligned_cols=94  Identities=19%  Similarity=0.239  Sum_probs=83.1

Q ss_pred             CcCCCCCcccccCcCCCCCCccchHHHHHHHhccccCCCCCCCchhhhhhhccccccceEEEeecCcCCCCc---hHHHH
Q psy3546           3 SIDYASNSDPGTGLQKDIADARCTALSYLIETIPANFPGDRLDHYTTQAVKGWKRKLSGIFRTPNVKGFEGS---RSRDL   79 (164)
Q Consensus         3 ~~~fPCQ~FS~aG~rkd~~D~R~~L~~~~iriI~~~~p~~~P~~~~~~~~~~~~~~~~~iFl~ENVkGf~~s---~~~d~   79 (164)
                      .-|+|||+||.+|.+++.+|+|+.||.+++++|.+++    |+                +|+||||+||..+   ..++.
T Consensus        64 ~gg~PCq~fS~ag~~~~~~d~r~~L~~~~~r~i~~~~----P~----------------~~v~ENV~~l~~~~~~~~~~~  123 (315)
T TIGR00675        64 LGGFPCQPFSIAGKRKGFEDTRGTLFFEIVRILKEKK----PK----------------FFLLENVKGLVSHDKGRTFKV  123 (315)
T ss_pred             EecCCCcccchhcccCCCCCchhhHHHHHHHHHhhcC----CC----------------EEEeeccHHHHhcccchHHHH
Confidence            4689999999999999999999999999999999998    68                5599999999753   57899


Q ss_pred             HHHHHHhCCCeEEEEEeCCCCCCCCCcceEEEecccc
Q psy3546          80 ITSMLTRAGFRFQEFLLSPTQFGTSLYTEWLRNKKKK  116 (164)
Q Consensus        80 I~s~L~~~GY~v~~~lLnatdfGVPQ~Rr~~i~~rkk  116 (164)
                      |+++|..+||.+.+.+||+.||||||.|+|+++.+.+
T Consensus       124 i~~~l~~~GY~v~~~~l~a~dyGvPQ~R~R~f~ia~r  160 (315)
T TIGR00675       124 IIETLEELGYKVYYKVLNAKDFGVPQNRERIYIVGFR  160 (315)
T ss_pred             HHHHHHhCCCEEEEEEEcHHHCCCCCCccEEEEEEEe
Confidence            9999999999999999999999999999555444444

All proteins in this family for which functions are known are DNA-cytosine methyltransferases. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).

>KOG0919|consensus

Probab=99.90  E-value=4.6e-25  Score=191.87  Aligned_cols=97  Identities=30%  Similarity=0.431  Sum_probs=92.4

Q ss_pred             CCCcCCCCCcccccCcCCCCCCccchHHHHHHHhccccCCCCCCCchhhhhhhccccccceEEEeecCcCCCCchHHHHH
Q psy3546           1 MASIDYASNSDPGTGLQKDIADARCTALSYLIETIPANFPGDRLDHYTTQAVKGWKRKLSGIFRTPNVKGFEGSRSRDLI   80 (164)
Q Consensus         1 ~~~~~fPCQ~FS~aG~rkd~~D~R~~L~~~~iriI~~~~p~~~P~~~~~~~~~~~~~~~~~iFl~ENVkGf~~s~~~d~I   80 (164)
                      |.....|||||++.|+|+|+.|+|+++|.+++.+|++++.  .|.               || +||||+||+.|..++.+
T Consensus        72 m~lMSPpCQPfTRiG~q~D~~D~Rs~aflhil~~lP~~q~--LPe---------------YI-L~ENVkGFE~S~ar~~~  133 (338)
T KOG0919|consen   72 MLLMSPPCQPFTRIGLQRDTEDKRSDAFLHILGLLPECQE--LPE---------------YI-LMENVKGFESSQARNQF  133 (338)
T ss_pred             eEeeCCCCCchhhhcccccccCchhHHHHHHHhhhhhhhh--hhH---------------HH-HHhhcccchhhhHHHHH
Confidence            5567899999999999999999999999999999999985  788               89 99999999999999999


Q ss_pred             HHHHHhCCCeEEEEEeCCCCCCCCCcc-eEEEeccc
Q psy3546          81 TSMLTRAGFRFQEFLLSPTQFGTSLYT-EWLRNKKK  115 (164)
Q Consensus        81 ~s~L~~~GY~v~~~lLnatdfGVPQ~R-r~~i~~rk  115 (164)
                      ++.|+++||++++|+|+|++||||++| |||+++|.
T Consensus       134 i~~lencGf~~~EfiLsPtqfniPNsR~Ryy~iArl  169 (338)
T KOG0919|consen  134 IESLENCGFHWREFILSPTQFNIPNSRYRYYCIARL  169 (338)
T ss_pred             HHHHHhcCchhhheeccccccCCCCcchheeehhhh
Confidence            999999999999999999999999999 99998874

>PRK10458 DNA cytosine methylase; Provisional

Probab=99.87  E-value=2e-22  Score=182.26  Aligned_cols=94  Identities=17%  Similarity=0.212  Sum_probs=79.7

Q ss_pred             CcCCCCCcccccCcCCC--------C-CCccchHHHHHHHhccccCCCCCCCchhhhhhhccccccceEEEeecCcCCCC
Q psy3546           3 SIDYASNSDPGTGLQKD--------I-ADARCTALSYLIETIPANFPGDRLDHYTTQAVKGWKRKLSGIFRTPNVKGFEG   73 (164)
Q Consensus         3 ~~~fPCQ~FS~aG~rkd--------~-~D~R~~L~~~~iriI~~~~p~~~P~~~~~~~~~~~~~~~~~iFl~ENVkGf~~   73 (164)
                      .-||||||||.+|.++.        . +|+|++||.+++++|.+.+    |+                +|+||||+||.+
T Consensus       174 ~gGpPCQ~FS~AG~~k~~~~gr~~g~~~d~rg~Lf~~~~rii~~~k----Pk----------------~fvlENV~gl~s  233 (467)
T PRK10458        174 LAGFPCQPFSLAGVSKKNSLGRAHGFECETQGTLFFDVARIIDAKR----PA----------------IFVLENVKNLKS  233 (467)
T ss_pred             EEcCCCCccchhcccccccccccccccCCccccHHHHHHHHHHHhC----CC----------------EEEEeCcHhhhc
Confidence            45999999999997542        2 3889999999999999998    68                569999999976


Q ss_pred             c---hHHHHHHHHHHhCCCeEE---------EEEeCCCCCCCCCcceEEEecccch
Q psy3546          74 S---RSRDLITSMLTRAGFRFQ---------EFLLSPTQFGTSLYTEWLRNKKKKR  117 (164)
Q Consensus        74 s---~~~d~I~s~L~~~GY~v~---------~~lLnatdfGVPQ~Rr~~i~~rkk~  117 (164)
                      +   ..++.|++.|.++||.+.         +.||||.+| |||.|+|+++.+.++
T Consensus       234 ~~~g~~f~~i~~~L~~lGY~v~~~~~~g~~~~~vlna~~f-VPQ~R~RvfiVg~r~  288 (467)
T PRK10458        234 HDKGKTFRIIMQTLDELGYDVADAEDNGPDDPKIIDGKHF-LPQHRERIVLVGFRR  288 (467)
T ss_pred             ccccHHHHHHHHHHHHcCCeEEeccccCcccceEeehhhC-CCccCcEEEEEEEeC
Confidence            4   589999999999999996         589999999 999996666555553

>PRK13562 acetolactate synthase 1 regulatory subunit; Provisional

Probab=91.38  E-value=0.67  Score=34.48  Aligned_cols=48  Identities=13%  Similarity=0.105  Sum_probs=36.3

Q ss_pred             cccceEEEeecCcCCCCchHHHHHHHHHHhCCCeEEEEEeCCCCCCCCCcceEEEec
Q psy3546          57 RKLSGIFRTPNVKGFEGSRSRDLITSMLTRAGFRFQEFLLSPTQFGTSLYTEWLRNK  113 (164)
Q Consensus        57 ~~~~~iFl~ENVkGf~~s~~~d~I~s~L~~~GY~v~~~lLnatdfGVPQ~Rr~~i~~  113 (164)
                      +-||.  ++||.+|.     ...|...|++.||++...-+.++.  .|...|+-|+.
T Consensus         3 ~~isv--lVeN~~GV-----L~Rit~lFsRRg~NI~SLtvg~Te--~~~iSRmtivv   50 (84)
T PRK13562          3 RILKL--QVADQVST-----LNRITSAFVRLQYNIDTLHVTHSE--QPGISNMEIQV   50 (84)
T ss_pred             EEEEE--EEECCCCH-----HHHHHHHHhccCcCeeeEEecccC--CCCceEEEEEE
Confidence            34554  59999984     578999999999999999998885  55555555443

>PRK06737 acetolactate synthase 1 regulatory subunit; Validated

Probab=84.38  E-value=3.7  Score=29.66  Aligned_cols=42  Identities=19%  Similarity=0.142  Sum_probs=32.8

Q ss_pred             EeecCcCCCCchHHHHHHHHHHhCCCeEEEEEeCCCCCCCCCcceEEEe
Q psy3546          64 RTPNVKGFEGSRSRDLITSMLTRAGFRFQEFLLSPTQFGTSLYTEWLRN  112 (164)
Q Consensus        64 l~ENVkGf~~s~~~d~I~s~L~~~GY~v~~~lLnatdfGVPQ~Rr~~i~  112 (164)
                      +++|-||     ....|+..|.+.||++...-+.|+.  .|...|..++
T Consensus         8 ~v~n~pG-----VL~Ri~~lf~rRgfNI~Sl~vg~te--~~~~sriti~   49 (76)
T PRK06737          8 VIHNDPS-----VLLRISGIFARRGYYISSLNLNERD--TSGVSEMKLT   49 (76)
T ss_pred             EEecCCC-----HHHHHHHHHhccCcceEEEEecccC--CCCeeEEEEE
Confidence            5999998     4578999999999999988888775  5555454444

>PRK08178 acetolactate synthase 1 regulatory subunit; Reviewed

Probab=82.59  E-value=4.1  Score=31.01  Aligned_cols=43  Identities=16%  Similarity=0.179  Sum_probs=33.6

Q ss_pred             EeecCcCCCCchHHHHHHHHHHhCCCeEEEEEeCCCCCCCCCcceEEEec
Q psy3546          64 RTPNVKGFEGSRSRDLITSMLTRAGFRFQEFLLSPTQFGTSLYTEWLRNK  113 (164)
Q Consensus        64 l~ENVkGf~~s~~~d~I~s~L~~~GY~v~~~lLnatdfGVPQ~Rr~~i~~  113 (164)
                      ++||.||.     ...|...|++.||.+......|+.  .|...|+.|+.
T Consensus        14 lv~N~pGV-----L~RIaglFsRRgyNIeSLtvg~te--~~~iSRmtivv   56 (96)
T PRK08178         14 TVRNHPGV-----MSHVCGLFARRAFNVEGILCLPIQ--DGDKSRIWLLV   56 (96)
T ss_pred             EEECCcCH-----HHHHHHHHhcCCcCeeeEEEeecC--CCCceEEEEEE
Confidence            59999984     578999999999999988777764  67765555544

>COG4747 ACT domain-containing protein [General function prediction only]

Probab=80.87  E-value=2.6  Score=34.22  Aligned_cols=39  Identities=23%  Similarity=0.387  Sum_probs=30.5

Q ss_pred             ccceEEEeecCcCCCCchHHHHHHHHHHhCCCeEEEE-EeCCCCCCC
Q psy3546          58 KLSGIFRTPNVKGFEGSRSRDLITSMLTRAGFRFQEF-LLSPTQFGT  103 (164)
Q Consensus        58 ~~~~iFl~ENVkGf~~s~~~d~I~s~L~~~GY~v~~~-lLnatdfGV  103 (164)
                      |.|.|  +||-||=     +-..++.|.++|-++..+ +-++.+||+
T Consensus         5 QISvF--lENk~GR-----L~~~~~~L~eagINiRA~tiAdt~dFGI   44 (142)
T COG4747           5 QISVF--LENKPGR-----LASVANKLKEAGINIRAFTIADTGDFGI   44 (142)
T ss_pred             EEEEE--ecCCcch-----HHHHHHHHHHcCCceEEEEeccccCcce
Confidence            56655  9999973     345678889999999766 678999997

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	164
1g55_A	343	Structure Of Human Dnmt2, An Enigmatic Dna Methyltr		8e-08
4h0n_A	333	Crystal Structure Of Spodoptera Frugiperda Dnmt2 E2		3e-04

>pdb|1G55|A Chain A, Structure Of Human Dnmt2, An Enigmatic Dna Methyltransferase Homologue Length = 343

Iteration: 1
 Score = 53.1 bits (126), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 31/88 (35%), Positives = 45/88 (51%), Gaps = 18/88 (20%)
Query: 15  GLQKDIADARCTALSYLIETIPANFPGDRLDHYTTQAVKGWKRKLSGIFRTPNVKGFEGS 74
           G Q D+ D+R  +  ++++ +P      RL            +KL       NVKGFE S
Sbjct: 85  GRQGDMTDSRTNSFLHILDILP------RL------------QKLPKYILLENVKGFEVS 126
Query: 75  RSRDLITSMLTRAGFRFQEFLLSPTQFG 102
            +RDL+   +   GF++QEFLLSPT  G
Sbjct: 127 STRDLLIQTIENXGFQYQEFLLSPTSLG 154

>pdb|4H0N|A Chain A, Crystal Structure Of Spodoptera Frugiperda Dnmt2 E260a/e261a/k263a Mutant Length = 333

Iteration: 1
 Score = 40.8 bits (94), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 18/37 (48%), Positives = 21/37 (56%)
Query: 67  NVKGFEGSRSRDLITSMLTRAGFRFQEFLLSPTQFGT 103
           NVKGFE S  R+L    L    F +QEFLL P+  G 
Sbjct: 119 NVKGFENSTVRNLFIDKLKECNFIYQEFLLCPSTVGV 155

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	164
3qv2_A	327	5-cytosine DNA methyltransferase; DNMT2, ehmeth; H	3e-06
1g55_A	343	DNA cytosine methyltransferase DNMT2; human DNA me	3e-06
3lvg_D	190	LCB, clathrin light chain B; SELF assembly, coated	3e-06
3lvg_D	190	LCB, clathrin light chain B; SELF assembly, coated	3e-05
4ady_A	963	RPN2, 26S proteasome regulatory subunit RPN2; prot	7e-06
4ady_A	963	RPN2, 26S proteasome regulatory subunit RPN2; prot	4e-05
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	5e-04
1qy5_A	269	Endoplasmin; GRP94, NECA, HSP90, chaperone; HET: N	8e-04

>3qv2_A 5-cytosine DNA methyltransferase; DNMT2, ehmeth; HET: SAH; 2.15A {Entamoeba histolytica} Length = 327

 Score = 44.8 bits (106), Expect = 3e-06
 Identities = 22/157 (14%), Positives = 41/157 (26%), Gaps = 22/157 (14%)

Query: 10  SDPGTGLQKDIADARCTALSYLIETIPANFPGDRLDHYTTQAVKGWKRKLSGIFRTPNVK 69
           ++      KDI D R  ++ +L   I                   +           NV 
Sbjct: 90  NNSIMSKHKDINDPRAKSVLHLYRDI-----------------LPYLINKPKHIFIENVP 132

Query: 70  GFEGSRSRDLITSMLTRAGFRFQEFLLSPTQFGTS-----LYTEWLRNKKKKRKEKKKKK 124
            F+ S     I ++L +  +  ++ + SP   G        Y        K   +  ++K
Sbjct: 133 LFKESLVFKEIYNILIKNQYYIKDIICSPIDIGIPNSRTRYYVMARLTPFKNEIQLHQEK 192

Query: 125 DKKKKKEEKKKEKRKEEKKKKEEEKKKKKKKKKKKKN 161
           +                       KK        K +
Sbjct: 193 ESMISNYLDNNVNESYSIPSDLILKKGMLFDIVGKDD 229

>1g55_A DNA cytosine methyltransferase DNMT2; human DNA methyltransferase homologue; HET: DNA SAH; 1.80A {Homo sapiens} SCOP: c.66.1.26 Length = 343

 Score = 44.8 bits (106), Expect = 3e-06
 Identities = 24/98 (24%), Positives = 41/98 (41%), Gaps = 5/98 (5%)

Query: 67  NVKGFEGSRSRDLITSMLTRAGFRFQEFLLSPTQFGTS-----LYTEWLRNKKKKRKEKK 121
           NVKGFE S +RDL+   +   GF++QEFLLSPT  G        +       +    +  
Sbjct: 119 NVKGFEVSSTRDLLIQTIENCGFQYQEFLLSPTSLGIPNSRLRYFLIAKLQSEPLPFQAP 178

Query: 122 KKKDKKKKKEEKKKEKRKEEKKKKEEEKKKKKKKKKKK 159
            +   +  K E  ++ +++     +  K   +      
Sbjct: 179 GQVLMEFPKIEIHRKNQQDSDLSVKMLKDFLEDDTDVN 216

>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic vesicle, membrane, Ca structural protein; 7.94A {Bos taurus} Length = 190

 Score = 44.0 bits (103), Expect = 3e-06
 Identities = 13/56 (23%), Positives = 31/56 (55%), Gaps = 2/56 (3%)

Query: 108 EWLRNKKKKRKEKKKKKDKKKKKEEKKK-EKRKEEKKKKEEEKKKKKKKKKKKKNA 162
           +W R +++KR ++     K  ++E ++K +K  EE  +++ E+ +K K   +  + 
Sbjct: 89  KW-REEQRKRLQELDAASKVMEQEWREKAKKDLEEWNQRQSEQVEKNKINNRIADK 143

>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic vesicle, membrane, Ca structural protein; 7.94A {Bos taurus} Length = 190

 Score = 41.3 bits (96), Expect = 3e-05
 Identities = 13/53 (24%), Positives = 28/53 (52%), Gaps = 4/53 (7%)

Query: 113 KKKKRKEKKKKKDKKKKKEEKKKEKRKEEKKKKEEE----KKKKKKKKKKKKN 161
             +K +E+++K+ ++     K  E+   EK KK+ E    ++ ++ +K K  N
Sbjct: 86  SIRKWREEQRKRLQELDAASKVMEQEWREKAKKDLEEWNQRQSEQVEKNKINN 138

>4ady_A RPN2, 26S proteasome regulatory subunit RPN2; protein binding, PC repeat; 2.70A {Saccharomyces cerevisiae} Length = 963

 Score = 44.0 bits (103), Expect = 7e-06
 Identities = 17/50 (34%), Positives = 31/50 (62%)

Query: 111 RNKKKKRKEKKKKKDKKKKKEEKKKEKRKEEKKKKEEEKKKKKKKKKKKK 160
              KK +KEK   +++KKK+ E+K+++R+  KK  +E K+  ++  K K 
Sbjct: 823 ARAKKTKKEKGPNEEEKKKEHEEKEKERETNKKGIKETKENDEEFYKNKY 872

>4ady_A RPN2, 26S proteasome regulatory subunit RPN2; protein binding, PC repeat; 2.70A {Saccharomyces cerevisiae} Length = 963

 Score = 41.7 bits (97), Expect = 4e-05
 Identities = 17/48 (35%), Positives = 31/48 (64%)

Query: 113 KKKKRKEKKKKKDKKKKKEEKKKEKRKEEKKKKEEEKKKKKKKKKKKK 160
            + K + KK KK+K   +EEKKKE  ++EK+++  +K  K+ K+  ++
Sbjct: 819 ARAKARAKKTKKEKGPNEEEKKKEHEEKEKERETNKKGIKETKENDEE 866

>2dfs_A Myosin-5A; myosin-V, inhibited state, cryoelectron tomograp contractIle protein-transport protein complex; 24.00A {Gallus gallus} Length = 1080

 Score = 38.6 bits (90), Expect = 5e-04
 Identities = 10/55 (18%), Positives = 17/55 (30%)

Query: 110 LRNKKKKRKEKKKKKDKKKKKEEKKKEKRKEEKKKKEEEKKKKKKKKKKKKNALD 164
              + K   EK    +     E +K     E  +  EEE K    +    +  + 
Sbjct: 940 QNKEYKSLLEKMNNLEITYSTETEKLRSDVERLRMSEEEAKNATNRVLSLQEEIA 994

>1qy5_A Endoplasmin; GRP94, NECA, HSP90, chaperone; HET: NEC; 1.75A {Canis lupus familiaris} SCOP: d.122.1.1 PDB: 1qy8_A* 1qye_A* 1u0y_A* 1yt2_A* Length = 269

 Score = 37.6 bits (88), Expect = 8e-04
 Identities = 11/49 (22%), Positives = 29/49 (59%)

Query: 110 LRNKKKKRKEKKKKKDKKKKKEEKKKEKRKEEKKKKEEEKKKKKKKKKK 158
           + + K +  E+  ++++  K+E++  +     ++++EE+K K KK +K 
Sbjct: 213 VWSSKTETVEEPMEEEEAAKEEKEDSDDEAAVEEEEEEKKPKTKKVEKT 261

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	164
3ubt_Y	331	Modification methylase HAEIII; protein-DNA complex	99.95
4h0n_A	333	DNMT2; SAH binding, transferase; HET: SAH; 2.71A {	99.93
1g55_A	343	DNA cytosine methyltransferase DNMT2; human DNA me	99.93
3qv2_A	327	5-cytosine DNA methyltransferase; DNMT2, ehmeth; H	99.93
2c7p_A	327	Modification methylase HHAI; DNA methyltransferase	99.93
4ft4_B	784	DNA (cytosine-5)-methyltransferase 1; chromodomain	99.92
3g7u_A	376	Cytosine-specific methyltransferase; DNA-binding,	99.91
4dkj_A	403	Cytosine-specific methyltransferase; CG-specificit	99.91
3me5_A	482	Cytosine-specific methyltransferase; structural ge	99.85
3swr_A	1002	DNA (cytosine-5)-methyltransferase 1; epigenetics,	99.84
3av4_A	1330	DNA (cytosine-5)-methyltransferase 1; CXXC-type zi	99.83
2qrv_A	295	DNA (cytosine-5)-methyltransferase 3A; DNA methylt	99.81
2qrv_B	230	DNA (cytosine-5)-methyltransferase 3-like; DNA met	99.74
2pv0_B	386	DNA (cytosine-5)-methyltransferase 3-like; DNMT3L,	99.73
2igt_A	332	SAM dependent methyltransferase; alpha-beta sandwi	85.67

>3ubt_Y Modification methylase HAEIII; protein-DNA complex, DNA cytosine-5 methyltransferase, DNA B S-adenosyl methionine binding; HET: ATP 2PE; 2.50A {Haemophilus aegyptius} PDB: 1dct_A*

Probab=99.95  E-value=3.2e-29  Score=204.05  Aligned_cols=94  Identities=18%  Similarity=0.179  Sum_probs=84.3

Q ss_pred             CcCCCCCcccccCcCCCCCCccchHHHHHHHhccccCCCCCCCchhhhhhhccccccceEEEeecCcCCCC---chHHHH
Q psy3546           3 SIDYASNSDPGTGLQKDIADARCTALSYLIETIPANFPGDRLDHYTTQAVKGWKRKLSGIFRTPNVKGFEG---SRSRDL   79 (164)
Q Consensus         3 ~~~fPCQ~FS~aG~rkd~~D~R~~L~~~~iriI~~~~p~~~P~~~~~~~~~~~~~~~~~iFl~ENVkGf~~---s~~~d~   79 (164)
                      +-|||||+||.+|++++.+|+|+.||.+++++|.+++    |+                +|+||||+||.+   +..++.
T Consensus        66 ~ggpPCQ~fS~ag~~~g~~d~R~~L~~~~~r~i~~~~----Pk----------------~~~~ENV~gl~~~~~~~~~~~  125 (331)
T 3ubt_Y           66 IGGPPSQSWSEGGSLRGIDDPRGKLFYEYIRILKQKK----PI----------------FFLAENVKGMMAQRHNKAVQE  125 (331)
T ss_dssp             ECCCCGGGTEETTEECCTTCGGGHHHHHHHHHHHHHC----CS----------------EEEEEECCGGGGCTTSHHHHH
T ss_pred             EecCCCCCcCCCCCccCCCCchhHHHHHHHHHHhccC----Ce----------------EEEeeeecccccccccchhhh
Confidence            4689999999999999999999999999999999998    68                559999999975   468999


Q ss_pred             HHHHHHhCCCeEEEEEeCCCCCCCCCcceEEEecccc
Q psy3546          80 ITSMLTRAGFRFQEFLLSPTQFGTSLYTEWLRNKKKK  116 (164)
Q Consensus        80 I~s~L~~~GY~v~~~lLnatdfGVPQ~Rr~~i~~rkk  116 (164)
                      |++.|.++||.+.+.+|||+||||||.|+|+++.+.+
T Consensus       126 i~~~l~~~GY~v~~~vlna~~yGvPQ~R~Rvfivg~r  162 (331)
T 3ubt_Y          126 FIQEFDNAGYDVHIILLNANDYGVAQDRKRVFYIGFR  162 (331)
T ss_dssp             HHHHHHHHTEEEEEEEEEGGGTTCSBCCEEEEEEEEE
T ss_pred             hhhhhccCCcEEEEEecccccCCCCcccceEEEEEEc
Confidence            9999999999999999999999999999555554444

>4h0n_A DNMT2; SAH binding, transferase; HET: SAH; 2.71A {Spodoptera frugiperda}

Probab=99.93  E-value=6.3e-27  Score=198.89  Aligned_cols=93  Identities=28%  Similarity=0.399  Sum_probs=84.5

Q ss_pred             CcCCCCCcccccCcCCCCCCccchHHHHHHHhccccCCCCCCCchhhhhhhccccccceEEEeecCcCCCCchHHHHHHH
Q psy3546           3 SIDYASNSDPGTGLQKDIADARCTALSYLIETIPANFPGDRLDHYTTQAVKGWKRKLSGIFRTPNVKGFEGSRSRDLITS   82 (164)
Q Consensus         3 ~~~fPCQ~FS~aG~rkd~~D~R~~L~~~~iriI~~~~p~~~P~~~~~~~~~~~~~~~~~iFl~ENVkGf~~s~~~d~I~s   82 (164)
                      .-|||||+||.+|.+++.+|+|+.||.+++++|.+++   +|+                +|+||||+||.++..++.|++
T Consensus        74 ~ggpPCQ~fS~ag~~~~~~d~r~~L~~~~~r~i~~~~---~P~----------------~~vlENV~gl~~~~~~~~i~~  134 (333)
T 4h0n_A           74 LMSPPCQPFTRNGKYLDDNDPRTNSFLYLIGILDQLD---NVD----------------YILMENVKGFENSTVRNLFID  134 (333)
T ss_dssp             EECCCCCCSEETTEECCTTCTTSCCHHHHHHHGGGCT---TCC----------------EEEEEECTTGGGSHHHHHHHH
T ss_pred             EecCCCcchhhhhhccCCcCcccccHHHHHHHHHHhc---CCC----------------EEEEecchhhhhhhHHHHHHH
Confidence            4589999999999999999999999999999999996   167                559999999999999999999


Q ss_pred             HHHhCCCeEEEEEeCCCCCCCCCcc-eEEEecc
Q psy3546          83 MLTRAGFRFQEFLLSPTQFGTSLYT-EWLRNKK  114 (164)
Q Consensus        83 ~L~~~GY~v~~~lLnatdfGVPQ~R-r~~i~~r  114 (164)
                      .|+++||.+.+.+|||.+|||||.| |+|+++.
T Consensus       135 ~l~~~GY~v~~~vl~a~~~GvPQ~R~R~fiva~  167 (333)
T 4h0n_A          135 KLKECNFIYQEFLLCPSTVGVPNSRLRYYCTAR  167 (333)
T ss_dssp             HHHHTTEEEEEEEECTTTTTCSCCCCEEEEEEE
T ss_pred             HHHhCCCeEEEEEecHHHcCCCccceEEEEEEE
Confidence            9999999999999999999999999 5555554

>1g55_A DNA cytosine methyltransferase DNMT2; human DNA methyltransferase homologue; HET: DNA SAH; 1.80A {Homo sapiens} SCOP: c.66.1.26

Probab=99.93  E-value=1.1e-26  Score=196.06  Aligned_cols=96  Identities=29%  Similarity=0.393  Sum_probs=67.7

Q ss_pred             CcCCCCCcccccCcCCCCCCccchHHHHHHHhccccCCCCCCCchhhhhhhccccccceEEEeecCcCCCCchHHHHHHH
Q psy3546           3 SIDYASNSDPGTGLQKDIADARCTALSYLIETIPANFPGDRLDHYTTQAVKGWKRKLSGIFRTPNVKGFEGSRSRDLITS   82 (164)
Q Consensus         3 ~~~fPCQ~FS~aG~rkd~~D~R~~L~~~~iriI~~~~p~~~P~~~~~~~~~~~~~~~~~iFl~ENVkGf~~s~~~d~I~s   82 (164)
                      ..|+|||+||.+|.+++.+|+|+.||.+++++|.+++  .+|+                +|+||||+||..+.+++.|++
T Consensus        73 ~~gpPCq~fS~ag~~~g~~d~r~~l~~~~~~~i~~~~--~~P~----------------~~~~ENV~~l~~~~~~~~i~~  134 (343)
T 1g55_A           73 LMSPPCQPFTRIGRQGDMTDSRTNSFLHILDILPRLQ--KLPK----------------YILLENVKGFEVSSTRDLLIQ  134 (343)
T ss_dssp             EECCC------------------CHHHHHHHHGGGCS--SCCS----------------EEEEEEETTGGGSHHHHHHHH
T ss_pred             EEcCCCcchhhcCCcCCccCccchHHHHHHHHHHHhc--CCCC----------------EEEEeCCccccCHHHHHHHHH
Confidence            4699999999999999999999999999999999997  1367                459999999998899999999


Q ss_pred             HHHhCCCeEEEEEeCCCCCCCCCcceEEEecccc
Q psy3546          83 MLTRAGFRFQEFLLSPTQFGTSLYTEWLRNKKKK  116 (164)
Q Consensus        83 ~L~~~GY~v~~~lLnatdfGVPQ~Rr~~i~~rkk  116 (164)
                      .|.++||.+.+.+|||.||||||.|+|+++.+.+
T Consensus       135 ~l~~~GY~v~~~vl~a~~~GvPQ~R~R~~iv~~~  168 (343)
T 1g55_A          135 TIENCGFQYQEFLLSPTSLGIPNSRLRYFLIAKL  168 (343)
T ss_dssp             HHHHTTEEEEEEEECGGGGTCSCCCCEEEEEEEE
T ss_pred             HHHHCCCeeEEEEEEHHHCCCCCcccEEEEEEEe
Confidence            9999999999999999999999999444444443

>3qv2_A 5-cytosine DNA methyltransferase; DNMT2, ehmeth; HET: SAH; 2.15A {Entamoeba histolytica}

Probab=99.93  E-value=3.4e-26  Score=194.35  Aligned_cols=92  Identities=17%  Similarity=0.176  Sum_probs=84.2

Q ss_pred             CcCCCCCcc--cccCcCCCCCCccchHHHHHHH-hcccc--CCCCCCCchhhhhhhccccccceEEEeecCcCCCCchHH
Q psy3546           3 SIDYASNSD--PGTGLQKDIADARCTALSYLIE-TIPAN--FPGDRLDHYTTQAVKGWKRKLSGIFRTPNVKGFEGSRSR   77 (164)
Q Consensus         3 ~~~fPCQ~F--S~aG~rkd~~D~R~~L~~~~ir-iI~~~--~p~~~P~~~~~~~~~~~~~~~~~iFl~ENVkGf~~s~~~   77 (164)
                      ..|+|||+|  |.+|.+++.+|+|++||.++++ +|.++  +    |+                +|+||||+||..+..+
T Consensus        81 ~ggpPCQ~fs~S~ag~~~~~~d~r~~L~~~~~r~~i~~~~~~----P~----------------~~~lENV~gl~~~~~~  140 (327)
T 3qv2_A           81 FMSPPCQPYNNSIMSKHKDINDPRAKSVLHLYRDILPYLINK----PK----------------HIFIENVPLFKESLVF  140 (327)
T ss_dssp             EECCCCTTCSHHHHTTTCTTTCGGGHHHHHHHHTTGGGCSSC----CS----------------EEEEEECGGGGGSHHH
T ss_pred             EecCCccCcccccCCCCCCCccccchhHHHHHHHHHHHhccC----CC----------------EEEEEchhhhcChHHH
Confidence            458999999  9999999999999999999999 99998  5    78                5599999999999999


Q ss_pred             HHHHHHHHhCCCeEEEEEeCCCCCCCCCcc-eEEEecc
Q psy3546          78 DLITSMLTRAGFRFQEFLLSPTQFGTSLYT-EWLRNKK  114 (164)
Q Consensus        78 d~I~s~L~~~GY~v~~~lLnatdfGVPQ~R-r~~i~~r  114 (164)
                      +.|++.|+++||.+.+.+|||.+|||||.| |+|+++.
T Consensus       141 ~~i~~~l~~~GY~v~~~vl~a~~yGvPQ~R~R~fivg~  178 (327)
T 3qv2_A          141 KEIYNILIKNQYYIKDIICSPIDIGIPNSRTRYYVMAR  178 (327)
T ss_dssp             HHHHHHHHHTTCEEEEEEECGGGGTCSBCCCEEEEEEE
T ss_pred             HHHHHHHHhCCCEEEEEEEeHHHcCCCccceEEEEEEE
Confidence            999999999999999999999999999999 5555543

>2c7p_A Modification methylase HHAI; DNA methyltransferase, methyltransferase, base flipping, restriction system, transferase; HET: 5CM A1P SAH EPE CIT; 1.7A {Haemophilus haemolyticus} SCOP: c.66.1.26 PDB: 10mh_A* 1m0e_A* 1mht_A* 1hmy_A* 1skm_A* 2c7o_A* 2c7q_A* 2hmy_B* 2hr1_A* 3eeo_A* 3mht_A* 4mht_A* 5mht_A* 6mht_A* 7mht_A* 8mht_A* 9mht_A* 2zcj_A* 2z6u_A* 2z6q_A* ...

Probab=99.93  E-value=2.4e-26  Score=194.27  Aligned_cols=94  Identities=15%  Similarity=0.229  Sum_probs=83.8

Q ss_pred             CcCCCCCcccccCcCCCCCCccchHHHHHHHhccccCCCCCCCchhhhhhhccccccceEEEeecCcCCCC---chHHHH
Q psy3546           3 SIDYASNSDPGTGLQKDIADARCTALSYLIETIPANFPGDRLDHYTTQAVKGWKRKLSGIFRTPNVKGFEG---SRSRDL   79 (164)
Q Consensus         3 ~~~fPCQ~FS~aG~rkd~~D~R~~L~~~~iriI~~~~p~~~P~~~~~~~~~~~~~~~~~iFl~ENVkGf~~---s~~~d~   79 (164)
                      ..|+|||+||.+|.+++.+|+|+.||.+++++|.+++    |+                +|+||||+||..   +..++.
T Consensus        76 ~~gpPCQ~fS~ag~~~g~~d~r~~L~~~~~r~i~~~~----P~----------------~~~~ENV~gl~~~~~~~~~~~  135 (327)
T 2c7p_A           76 CAGFPCQAFSISGKQKGFEDSRGTLFFDIARIVREKK----PK----------------VVFMENVKNFASHDNGNTLEV  135 (327)
T ss_dssp             EEECCCTTTCTTSCCCGGGSTTSCHHHHHHHHHHHHC----CS----------------EEEEEEEGGGGTGGGGHHHHH
T ss_pred             EECCCCCCcchhcccCCCcchhhHHHHHHHHHHHhcc----Cc----------------EEEEeCcHHHHhccccHHHHH
Confidence            4689999999999999999999999999999999998    68                559999999975   357999


Q ss_pred             HHHHHHhCCCeEEEEEeCCCCCCCCCcceEEEecccc
Q psy3546          80 ITSMLTRAGFRFQEFLLSPTQFGTSLYTEWLRNKKKK  116 (164)
Q Consensus        80 I~s~L~~~GY~v~~~lLnatdfGVPQ~Rr~~i~~rkk  116 (164)
                      |++.|.++||.+.+.+|||++|||||.|+|+++.+.+
T Consensus       136 i~~~l~~~GY~v~~~vl~a~~~GvPQ~R~R~~iv~~~  172 (327)
T 2c7p_A          136 VKNTMNELDYSFHAKVLNALDYGIPQKRERIYMICFR  172 (327)
T ss_dssp             HHHHHHHTTBCCEEEEEEGGGGTCSBCCEEEEEEEEB
T ss_pred             HHHHHHhCCCEEEEEEEEHHHcCCCccceEEEEEEEe
Confidence            9999999999999999999999999999555544443

>4ft4_B DNA (cytosine-5)-methyltransferase 1; chromodomain, BAH domain, DNA methyltransferase domain, H3K9 binding, methylation, transferase; HET: DNA MLY SAH; 2.70A {Zea mays} PDB: 4ft2_A* 4fsx_A*

Probab=99.92  E-value=2.4e-25  Score=202.47  Aligned_cols=93  Identities=8%  Similarity=-0.006  Sum_probs=81.6

Q ss_pred             cCCCCCcccccCcCCC----CCCccchHHHHHHHhccccCCCCCCCchhhhhhhccccccceEEEeecCcCCCC---chH
Q psy3546           4 IDYASNSDPGTGLQKD----IADARCTALSYLIETIPANFPGDRLDHYTTQAVKGWKRKLSGIFRTPNVKGFEG---SRS   76 (164)
Q Consensus         4 ~~fPCQ~FS~aG~rkd----~~D~R~~L~~~~iriI~~~~p~~~P~~~~~~~~~~~~~~~~~iFl~ENVkGf~~---s~~   76 (164)
                      -|||||+||.+|++++    .+|+|++||.+|+++|.+++    |+                +|+||||+||..   +..
T Consensus       385 GGpPCQ~FS~aG~~kg~~~~~~D~R~~L~~~~~riv~~~r----Pk----------------~fvlENV~glls~~~g~~  444 (784)
T 4ft4_B          385 GGPPCQGISGFNRYRNRDEPLKDEKNKQMVTFMDIVAYLK----PK----------------YVLMENVVDILKFADGYL  444 (784)
T ss_dssp             ECCCCCSSSGGGGGSCTTSTTTSTTCHHHHHHHHHHHHHC----CS----------------EEEEEEEGGGGTGGGGHH
T ss_pred             ecCCCcchhhhhcccCcCccccCchhHHHHHHHHHHHHHC----CC----------------EEEEEecCCccccccchH
Confidence            3899999999998765    67999999999999999998    68                559999999975   467


Q ss_pred             HHHHHHHHHhCCCeEEEEEeCCCCCCCCCcceEEEecccc
Q psy3546          77 RDLITSMLTRAGFRFQEFLLSPTQFGTSLYTEWLRNKKKK  116 (164)
Q Consensus        77 ~d~I~s~L~~~GY~v~~~lLnatdfGVPQ~Rr~~i~~rkk  116 (164)
                      ++.|++.|..+||.+.+.+|||.+|||||.|+|+++.+.+
T Consensus       445 ~~~il~~l~~lGY~v~~~vLnA~dyGVPQ~R~Rvfivg~r  484 (784)
T 4ft4_B          445 GKYALSCLVAMKYQARLGMMVAGCYGLPQFRMRVFLWGAL  484 (784)
T ss_dssp             HHHHHHHHHHTTCEEEEEEEEGGGGTCSSCCEEEEEEEEC
T ss_pred             HHHHHHHHHhCCCeeeeeecCHHHcCCCcccccceeeeec
Confidence            9999999999999999999999999999999555544433

>3g7u_A Cytosine-specific methyltransferase; DNA-binding, NAD-binding, structural GENO protein structure initiative, PSI; 1.75A {Escherichia coli O157}

Probab=99.91  E-value=2.2e-25  Score=191.79  Aligned_cols=93  Identities=12%  Similarity=0.068  Sum_probs=75.6

Q ss_pred             CcCCCCCcccccCcCCCCCCccchHHHHHHHhccccCCCCCCCchhhhhhhccccccceEEEeecCcCCCCc---hHHHH
Q psy3546           3 SIDYASNSDPGTGLQKDIADARCTALSYLIETIPANFPGDRLDHYTTQAVKGWKRKLSGIFRTPNVKGFEGS---RSRDL   79 (164)
Q Consensus         3 ~~~fPCQ~FS~aG~rkd~~D~R~~L~~~~iriI~~~~p~~~P~~~~~~~~~~~~~~~~~iFl~ENVkGf~~s---~~~d~   79 (164)
                      ..|+|||+||.+|++ +.+|+|+.||.+++++|..++    |+                +|+||||+||.+.   ..++.
T Consensus        76 ~ggpPCQ~fS~ag~~-~~~d~r~~L~~~~~~~v~~~~----P~----------------~~v~ENV~gl~s~~~~~~~~~  134 (376)
T 3g7u_A           76 IGGPPCQGFSSIGKG-NPDDSRNQLYMHFYRLVSELQ----PL----------------FFLAENVPGIMQEKYSGIRNK  134 (376)
T ss_dssp             EECCCCCTTC--------CHHHHHHHHHHHHHHHHHC----CS----------------EEEEEECTTTTCGGGHHHHHH
T ss_pred             EecCCCCCcccccCC-CCCCchHHHHHHHHHHHHHhC----CC----------------EEEEecchHhhccCcHHHHHH
Confidence            469999999999976 889999999999999999998    68                5599999999864   47899


Q ss_pred             HHHHHHhCCCeE-EEEEeCCCCCCCCCcceEEEecccch
Q psy3546          80 ITSMLTRAGFRF-QEFLLSPTQFGTSLYTEWLRNKKKKR  117 (164)
Q Consensus        80 I~s~L~~~GY~v-~~~lLnatdfGVPQ~Rr~~i~~rkk~  117 (164)
                      |+ .|.++||.+ .+.+|||.||||||.|+|+++.+.+.
T Consensus       135 i~-~l~~~GY~v~~~~vl~a~dyGvPQ~R~R~~iig~r~  172 (376)
T 3g7u_A          135 AF-NLVSGDYDILDPIKVKASDYGAPTIRTRYFFIGVKK  172 (376)
T ss_dssp             HH-HHHHTTEEECCCEEEEGGGGTCSBCCEEEEEEEEEG
T ss_pred             HH-HHHcCCCccCcEEEEEHhhCCCCCCCcEEEEEEEeC
Confidence            99 999999999 99999999999999996555555443

>4dkj_A Cytosine-specific methyltransferase; CG-specificity, DNA intercalation, CPG sequence, cytosine C5 methylation; HET: DNA C37 5CM SAH; 2.15A {Mycoplasma penetrans}

Probab=99.91  E-value=6.9e-25  Score=191.88  Aligned_cols=94  Identities=17%  Similarity=0.240  Sum_probs=82.2

Q ss_pred             CcCCCCCcccccCcCCCCCC---ccchHHHHHHHhccc--------cCCCCCCCchhhhhhhccccccceEEEeecCcCC
Q psy3546           3 SIDYASNSDPGTGLQKDIAD---ARCTALSYLIETIPA--------NFPGDRLDHYTTQAVKGWKRKLSGIFRTPNVKGF   71 (164)
Q Consensus         3 ~~~fPCQ~FS~aG~rkd~~D---~R~~L~~~~iriI~~--------~~p~~~P~~~~~~~~~~~~~~~~~iFl~ENVkGf   71 (164)
                      .-|||||+||.+|.+++.+|   +|+.||.+++++|.+        .+    |+                +|+||||+||
T Consensus       130 ~ggpPCQ~fS~ag~~~g~~d~~~~r~~L~~~~~rii~~~~~k~~~~~~----Pk----------------~~l~ENV~gl  189 (403)
T 4dkj_A          130 TYSFPCQDLSVQGLQKGIDKELNTRSGLLWEIERILEEIKNSFSKEEM----PK----------------YLLMENVKNL  189 (403)
T ss_dssp             EECCCCTTTCTTSCCCCCCGGGCCSGGGHHHHHHHHHHHHHHSCGGGS----CS----------------EEEEEEEGGG
T ss_pred             EEeCCCCCHHHhCCCCCCCccccccchhHHHHHHHHHHhhhhhccccC----CC----------------EEEEecchhh
Confidence            45899999999999999887   999999999999998        55    78                5599999999


Q ss_pred             CCc---hHHHHHHHHHHhCCCeEEEEEeCCCCCCCCCcceEEEecccc
Q psy3546          72 EGS---RSRDLITSMLTRAGFRFQEFLLSPTQFGTSLYTEWLRNKKKK  116 (164)
Q Consensus        72 ~~s---~~~d~I~s~L~~~GY~v~~~lLnatdfGVPQ~Rr~~i~~rkk  116 (164)
                      ..+   ..++.|++.|+++||.+.+.+|||.+|||||.|+|+++.+.+
T Consensus       190 ~~~~~~~~~~~i~~~l~~~GY~v~~~vl~a~~~GvPQ~R~R~fiva~r  237 (403)
T 4dkj_A          190 LSHKNKKNYNTWLKQLEKFGYKSKTYLLNSKNFDNCQNRERVFCLSIR  237 (403)
T ss_dssp             GSHHHHHHHHHHHHHHHHTTEEEEEEEEEGGGTTCSBCCEEEEEEEEE
T ss_pred             hhhccchHHHHHHHHHHhCCCeEEEEEecHHHcCCCccceEEEEEEEc
Confidence            875   478999999999999999999999999999999555444443

>3me5_A Cytosine-specific methyltransferase; structural genomics, protein structure initiative, NEW YORK structural genomix research consortium; 1.75A {Shigella flexneri 2A} PDB: 3lx6_A

Probab=99.85  E-value=4.2e-22  Score=178.13  Aligned_cols=94  Identities=17%  Similarity=0.228  Sum_probs=72.7

Q ss_pred             CcCCCCCcccccCcCCC--------C-CCccchHHHHHHHhccccCCCCCCCchhhhhhhccccccceEEEeecCcCCCC
Q psy3546           3 SIDYASNSDPGTGLQKD--------I-ADARCTALSYLIETIPANFPGDRLDHYTTQAVKGWKRKLSGIFRTPNVKGFEG   73 (164)
Q Consensus         3 ~~~fPCQ~FS~aG~rkd--------~-~D~R~~L~~~~iriI~~~~p~~~P~~~~~~~~~~~~~~~~~iFl~ENVkGf~~   73 (164)
                      .-|||||+||.+|.+++        + +|+|++||.+++++|..++    |+                +|+||||+||.+
T Consensus       174 ~gGpPCQ~FS~AG~~k~~~~g~~~G~~~D~R~~Lf~e~~riI~~~r----Pk----------------~fvlENV~gl~s  233 (482)
T 3me5_A          174 LAGFPCQPFSLAGVSKKNSLGRAHGFACDTQGTLFFDVVRIIDARR----PA----------------MFVLENVKNLKS  233 (482)
T ss_dssp             EEECCCCCC------------------CTTTTSHHHHHHHHHHHHC----CS----------------EEEEEEETTTTT
T ss_pred             EecCCCcchhhhCcccccccccccccccCccccHHHHHHHHHHHcC----Cc----------------EEEEeCcHHHhc
Confidence            35899999999996542        2 3899999999999999998    68                559999999976


Q ss_pred             ---chHHHHHHHHHHhCCCeEE---------EEEeCCCCCCCCCcceEEEecccch
Q psy3546          74 ---SRSRDLITSMLTRAGFRFQ---------EFLLSPTQFGTSLYTEWLRNKKKKR  117 (164)
Q Consensus        74 ---s~~~d~I~s~L~~~GY~v~---------~~lLnatdfGVPQ~Rr~~i~~rkk~  117 (164)
                         +..++.|++.|.++||.+.         +.||||.+| |||.|+++++.+.++
T Consensus       234 ~~~g~~f~~i~~~L~~lGY~v~~~~~~g~~~~~vlnA~~~-vPQ~R~R~fivg~r~  288 (482)
T 3me5_A          234 HDKGKTFRIIMQTLDELGYDVADAEDNGPDDPKIIDGKHF-LPQHRERIVLVGFRR  288 (482)
T ss_dssp             GGGGHHHHHHHHHHHHTTEEETTTTCCSTTCTTEEEGGGT-SSBCCEEEEEEEEEG
T ss_pred             ccCCcHHHHHHHHHhcCCcEEEeccccCcccceeeecccc-CCccceEEEEEEEec
Confidence               4589999999999999997         579999999 999995555544443

>3swr_A DNA (cytosine-5)-methyltransferase 1; epigenetics, DNA methyltransferase fold, maintenance methyla transferase; HET: DNA SFG MES; 2.49A {Homo sapiens} PDB: 3pta_A* 3pt6_A* 3pt9_A* 4da4_A*

Probab=99.84  E-value=6e-22  Score=190.57  Aligned_cols=93  Identities=14%  Similarity=0.072  Sum_probs=80.2

Q ss_pred             CcCCCCCcccccCcCC--CCCCccchHHHHHHHhccccCCCCCCCchhhhhhhccccccceEEEeecCcCCCC---chHH
Q psy3546           3 SIDYASNSDPGTGLQK--DIADARCTALSYLIETIPANFPGDRLDHYTTQAVKGWKRKLSGIFRTPNVKGFEG---SRSR   77 (164)
Q Consensus         3 ~~~fPCQ~FS~aG~rk--d~~D~R~~L~~~~iriI~~~~p~~~P~~~~~~~~~~~~~~~~~iFl~ENVkGf~~---s~~~   77 (164)
                      .-|+|||+||.+|.+.  +.+|+|+.||.+|+++|.+++    |+                +|+||||+||..   +..+
T Consensus       623 ~GGpPCQ~FS~ag~~~~~~~~d~R~~L~~~~~riv~~~r----Pk----------------~~llENV~glls~~~~~~~  682 (1002)
T 3swr_A          623 CGGPPCQGFSGMNRFNSRTYSKFKNSLVVSFLSYCDYYR----PR----------------FFLLENVRNFVSFKRSMVL  682 (1002)
T ss_dssp             EECCCCTTCCSSSCCCHHHHHHHTTSHHHHHHHHHHHHC----CS----------------EEEEEEEGGGGTTGGGHHH
T ss_pred             EEcCCCcchhhhCCCCCCcccchhhHHHHHHHHHHHHhC----CC----------------EEEEeccHHHhccCcchHH
Confidence            3589999999999753  457899999999999999998    68                559999999975   4579


Q ss_pred             HHHHHHHHhCCCeEEEEEeCCCCCCCCCcceEEEeccc
Q psy3546          78 DLITSMLTRAGFRFQEFLLSPTQFGTSLYTEWLRNKKK  115 (164)
Q Consensus        78 d~I~s~L~~~GY~v~~~lLnatdfGVPQ~Rr~~i~~rk  115 (164)
                      +.|++.|.++||.+.+.||||.+|||||.|+|+++.+.
T Consensus       683 ~~i~~~L~~lGY~v~~~vLnA~dyGvPQ~R~R~fiva~  720 (1002)
T 3swr_A          683 KLTLRCLVRMGYQCTFGVLQAGQYGVAQTRRRAIILAA  720 (1002)
T ss_dssp             HHHHHHHHHHTCEEEEEEEEGGGGTCSBCCEEEEEEEE
T ss_pred             HHHHHHHHhcCCeEEEEEEEHHHCCCCccceEEEEEEE
Confidence            99999999999999999999999999999955444443

>3av4_A DNA (cytosine-5)-methyltransferase 1; CXXC-type zinc finger/C5-methyltransferase family; HET: DNA; 2.75A {Mus musculus} PDB: 3av5_A* 3av6_A*

Probab=99.83  E-value=1.2e-21  Score=192.97  Aligned_cols=94  Identities=14%  Similarity=0.076  Sum_probs=81.0

Q ss_pred             CcCCCCCcccccCcC--CCCCCccchHHHHHHHhccccCCCCCCCchhhhhhhccccccceEEEeecCcCCCC---chHH
Q psy3546           3 SIDYASNSDPGTGLQ--KDIADARCTALSYLIETIPANFPGDRLDHYTTQAVKGWKRKLSGIFRTPNVKGFEG---SRSR   77 (164)
Q Consensus         3 ~~~fPCQ~FS~aG~r--kd~~D~R~~L~~~~iriI~~~~p~~~P~~~~~~~~~~~~~~~~~iFl~ENVkGf~~---s~~~   77 (164)
                      .-|||||+||.+|++  ++.+|+|+.||.+|+++|..++    |+                +|+||||+||..   +..+
T Consensus       934 ~GGpPCQ~FS~agr~~~~~~~d~R~~L~~~~lriv~~~r----Pk----------------~fv~ENV~glls~~~g~~~  993 (1330)
T 3av4_A          934 CGGPPCQGFSGMNRFNSRTYSKFKNSLVVSFLSYCDYYR----PR----------------FFLLENVRNFVSYRRSMVL  993 (1330)
T ss_dssp             EECCCCTTTCSSSCCCHHHHHHHHHSHHHHHHHHHHHHC----CS----------------EEEEEEEGGGGTTTTTHHH
T ss_pred             EecCCCcccccccccccccccchhhHHHHHHHHHHHHhc----Cc----------------EEEEeccHHHhccCccHHH
Confidence            358999999999975  3457999999999999999998    68                559999999975   3579


Q ss_pred             HHHHHHHHhCCCeEEEEEeCCCCCCCCCcceEEEecccc
Q psy3546          78 DLITSMLTRAGFRFQEFLLSPTQFGTSLYTEWLRNKKKK  116 (164)
Q Consensus        78 d~I~s~L~~~GY~v~~~lLnatdfGVPQ~Rr~~i~~rkk  116 (164)
                      +.|+..|..+||.+.+.||||.+|||||.|+|+++.+.+
T Consensus       994 ~~il~~L~~lGY~v~~~vLnA~dyGVPQ~R~Rvfivg~r 1032 (1330)
T 3av4_A          994 KLTLRCLVRMGYQCTFGVLQAGQYGVAQTRRRAIILAAA 1032 (1330)
T ss_dssp             HHHHHHHHHHTCEEEEEEEEGGGGSCSBCCEEEEEEEEC
T ss_pred             HHHHHHHHhcCCeeeEEEecHHHcCCCccccEEEEEEec
Confidence            999999999999999999999999999999555554443

>2qrv_A DNA (cytosine-5)-methyltransferase 3A; DNA methyltransferase 3A (DNMT3A) and ITS regulatory factor; HET: DNA SAH; 2.89A {Homo sapiens}

Probab=99.81  E-value=1.8e-20  Score=157.49  Aligned_cols=89  Identities=11%  Similarity=0.034  Sum_probs=72.2

Q ss_pred             CcCCCCCcccccC-cCCCCCCccchHHHHHHHhccccCCC---CCCCchhhhhhhccccccceEEEeecCcCCCCchHHH
Q psy3546           3 SIDYASNSDPGTG-LQKDIADARCTALSYLIETIPANFPG---DRLDHYTTQAVKGWKRKLSGIFRTPNVKGFEGSRSRD   78 (164)
Q Consensus         3 ~~~fPCQ~FS~aG-~rkd~~D~R~~L~~~~iriI~~~~p~---~~P~~~~~~~~~~~~~~~~~iFl~ENVkGf~~s~~~d   78 (164)
                      .-|||||+||.+| .+++.+|+|+.||.+++++|.+++|.   ++|.                +|+||||+||..+. ..
T Consensus        88 ~ggpPCQ~fS~ag~~r~g~~d~r~~L~~~~~rii~~~~P~~~~~~P~----------------~~l~ENV~gl~~~~-~~  150 (295)
T 2qrv_A           88 IGGSPCNDLSIVNPARKGLYEGTGRLFFEFYRLLHDARPKEGDDRPF----------------FWLFENVVAMGVSD-KR  150 (295)
T ss_dssp             EECCCCGGGBTTCTTCCTTTSTTTTHHHHHHHHHHHHSCCTTCCCCC----------------EEEEEEESSBCHHH-HH
T ss_pred             EecCCCccccccCccccccccccchhHHHHHHHHHHhCcccccCCcc----------------EEEEEcCcchhhcC-cc
Confidence            4589999999999 78899999999999999999999974   3566                56999999998654 23


Q ss_pred             HHHHHHHhCCCeEEEEEeCCCCCCCCCcceEEEecc
Q psy3546          79 LITSMLTRAGFRFQEFLLSPTQFGTSLYTEWLRNKK  114 (164)
Q Consensus        79 ~I~s~L~~~GY~v~~~lLnatdfGVPQ~Rr~~i~~r  114 (164)
                      .|.+.|+.     .+.+|||.+|| ||.|+|++++.
T Consensus       151 ~~~~~l~~-----~~~vl~a~~~~-PQ~R~R~~i~~  180 (295)
T 2qrv_A          151 DISRFLES-----NPVMIDAKEVS-AAHRARYFWGN  180 (295)
T ss_dssp             HHHHHHTS-----CCCCEEGGGTS-SBCCEEEEEEC
T ss_pred             HHHHHHhc-----CcEEeecceEC-CccCcEEEEEE
Confidence            46666653     46899999996 99996655554

>2qrv_B DNA (cytosine-5)-methyltransferase 3-like; DNA methyltransferase 3A (DNMT3A) and ITS regulatory factor; HET: DNA SAH; 2.89A {Homo sapiens}

Probab=99.74  E-value=1.3e-18  Score=145.00  Aligned_cols=81  Identities=7%  Similarity=-0.041  Sum_probs=60.4

Q ss_pred             cCCCCCcccccCcCCCCCCccchHHHHHHHhccccCCC---CCCCchhhhhhhccccccceEEEeecCcCCCCchHHHHH
Q psy3546           4 IDYASNSDPGTGLQKDIADARCTALSYLIETIPANFPG---DRLDHYTTQAVKGWKRKLSGIFRTPNVKGFEGSRSRDLI   80 (164)
Q Consensus         4 ~~fPCQ~FS~aG~rkd~~D~R~~L~~~~iriI~~~~p~---~~P~~~~~~~~~~~~~~~~~iFl~ENVkGf~~s~~~d~I   80 (164)
                      =|||||+||.+|       +|++||.+|+|+|.+++|.   .+|.                +|+||||+||..+. .+.|
T Consensus        87 GG~PCQ~FS~ag-------~rg~Lf~ef~Riv~~~rPk~~~~~P~----------------~fv~ENV~gL~~~~-~~~i  142 (230)
T 2qrv_B           87 GATPPLGHTCDR-------PPSWYLFQFHRLLQYARPKPGSPRPF----------------FWMFVDNLVLNKED-LDVA  142 (230)
T ss_dssp             EECCCTTTSSCS-------CTHHHHHHHHHHHHHHCCCSSCCSCC----------------EEEEEECSCSCHHH-HHHH
T ss_pred             ECCCCCcccccC-------CCchHHHHHHHHHHHHCcCcccCCCc----------------EEEEeccHHhhhcc-HHHH
Confidence            389999999887       4899999999999999973   2455                66999999996543 3556


Q ss_pred             HHHHHhCCCeEEEEEeCCCCCCCCCcceEEEec
Q psy3546          81 TSMLTRAGFRFQEFLLSPTQFGTSLYTEWLRNK  113 (164)
Q Consensus        81 ~s~L~~~GY~v~~~lLnatdfGVPQ~Rr~~i~~  113 (164)
                      ...|+     +.+.||||.+|||||.|++|+..
T Consensus       143 ~~~l~-----~~~~vLnA~dfgvpQrRr~f~g~  170 (230)
T 2qrv_B          143 SRFLE-----MEPVTIPDVHGGSLQNAVRVWSN  170 (230)
T ss_dssp             HHHHT-----SCCEECCCCCSCC----CEEEEC
T ss_pred             HHHHc-----CCcEEEEcccCCcCcccEEEEee
Confidence            55553     35678999999999999888743

>2pv0_B DNA (cytosine-5)-methyltransferase 3-like; DNMT3L, unmethylated H3K4, de novo DNA methylation, transferase regulator; HET: DNA; 3.30A {Homo sapiens} PDB: 2pvc_B*

Probab=99.73  E-value=1.8e-18  Score=153.20  Aligned_cols=81  Identities=6%  Similarity=-0.056  Sum_probs=65.0

Q ss_pred             cCCCCCcccccCcCCCCCCccchHHHHHHHhccccCCC---CCCCchhhhhhhccccccceEEEeecCcCCCCchHHHHH
Q psy3546           4 IDYASNSDPGTGLQKDIADARCTALSYLIETIPANFPG---DRLDHYTTQAVKGWKRKLSGIFRTPNVKGFEGSRSRDLI   80 (164)
Q Consensus         4 ~~fPCQ~FS~aG~rkd~~D~R~~L~~~~iriI~~~~p~---~~P~~~~~~~~~~~~~~~~~iFl~ENVkGf~~s~~~d~I   80 (164)
                      =|||||+||.+|       +|++||++|+|+|.+++|.   .+|.                +|+||||+||. +.....|
T Consensus       243 GG~PCQ~FS~A~-------~Rg~Lf~ef~Riv~~~rPk~~~~~P~----------------~fv~ENV~gL~-~~~~~~i  298 (386)
T 2pv0_B          243 GATPPLGHTCDR-------PPSWYLFQFHRLLQYARPKPGSPGPF----------------FWMFVDNLVLN-KEDLDVA  298 (386)
T ss_dssp             EECCCTTTCSCS-------CTHHHHHHHHHHHHHHSCCSSCCSCC----------------EEEEEECSCSC-HHHHHHH
T ss_pred             ECCCCCcccccC-------CcchHHHHHHHHHHHhCCCcccCCCc----------------EEEEEechhhh-hcchHHH
Confidence            389999999884       6899999999999999983   3455                66999999994 3334456


Q ss_pred             HHHHHhCCCeEEEEEeCCCCCCCCCcceEEEec
Q psy3546          81 TSMLTRAGFRFQEFLLSPTQFGTSLYTEWLRNK  113 (164)
Q Consensus        81 ~s~L~~~GY~v~~~lLnatdfGVPQ~Rr~~i~~  113 (164)
                      ...|+     +.+.||||.+|||||.|++|+..
T Consensus       299 ~~~L~-----v~~~VLnA~dyGVPQrRrRf~g~  326 (386)
T 2pv0_B          299 SRFLE-----MEPVTIPDVHGGSLQNAVRVWSN  326 (386)
T ss_dssp             HHHTT-----SCCCEEECCCSSSCCCEEEEEEC
T ss_pred             HHHHc-----CCeEEEEccccCccccccEEEEE
Confidence            55553     56789999999999999887744

>2igt_A SAM dependent methyltransferase; alpha-beta sandwich, beta-barrel, structural genomics, PSI-2 structure initiative; HET: MSE SAM GOL; 1.89A {Agrobacterium tumefaciens str} SCOP: c.66.1.51

Probab=85.67  E-value=0.42  Score=39.85  Aligned_cols=46  Identities=11%  Similarity=-0.055  Sum_probs=31.6

Q ss_pred             eEEEeecCcCCCC-ch-HHHHHHHHHHhCCCeEEEEEeCCCCCCCCCc
Q psy3546          61 GIFRTPNVKGFEG-SR-SRDLITSMLTRAGFRFQEFLLSPTQFGTSLY  106 (164)
Q Consensus        61 ~iFl~ENVkGf~~-s~-~~d~I~s~L~~~GY~v~~~lLnatdfGVPQ~  106 (164)
                      ++|++++.....- .. ..+.|.+.+..+||.+....+.-..+++||.
T Consensus       266 G~lli~~~~~~~~~~~~~~~~l~~a~~~~g~~v~~~e~~~p~~~~~q~  313 (332)
T 2igt_A          266 ALGLVLTAYSIRASFYSMHELMRETMRGAGGVVASGELVIREAGLDGK  313 (332)
T ss_dssp             CCEEEEEECCTTSCHHHHHHHHHHHTTTSCSEEEEEEEEEECCCSSSC
T ss_pred             cEEEEEECCCCCCCHHHHHHHHHHHHHHcCCeEEEEEEecccCCcccc
Confidence            5557777665432 22 3444445677899999877777788899998

---

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	164
d1y2oa1	248	a.238.1.3 (A:1-248) BAP2/IRSp53 N-terminal domain	0.001

>d1y2oa1 a.238.1.3 (A:1-248) BAP2/IRSp53 N-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 248

class: All alpha proteins
fold: BAR/IMD domain-like
superfamily: BAR/IMD domain-like
family: IMD domain
domain: BAP2/IRSp53 N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 35.8 bits (82), Expect = 0.001
 Identities = 16/90 (17%), Positives = 36/90 (40%)

Query: 73  GSRSRDLITSMLTRAGFRFQEFLLSPTQFGTSLYTEWLRNKKKKRKEKKKKKDKKKKKEE 132
            S+    +  +L +     ++      +   S + E L   ++K +   +      KK +
Sbjct: 65  ESQGSKELGDVLFQMAEVHRQIQNQLEEMLKSFHNELLTQLEQKVELDSRYLSAALKKYQ 124

Query: 133 KKKEKRKEEKKKKEEEKKKKKKKKKKKKNA 162
            ++  + +   K + E KK +KK +  KN 
Sbjct: 125 TEQRSKGDALDKCQAELKKLRKKSQGSKNP 154

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	164
d1g55a_	343	DNMT2 {Human (Homo sapiens) [TaxId: 9606]}	99.95
d1dcta_	324	DNA methylase HaeIII {Haemophilus aegyptius [TaxId	99.94
d2c7pa1	327	DNA methylase HhaI {Haemophilus haemolyticus [TaxI	99.94
d2f06a2	70	Hypothetical protein BT0572 {Bacteroides thetaiota	93.98
d2f1fa1	76	Acetolactate synthase small subunit, IlvH {Escheri	87.17
d2pc6a2	77	Acetolactate synthase small subunit, IlvH {Nitroso	86.02
d2fgca2	78	Acetolactate synthase small subunit, IlvH {Thermot	84.7

>d1g55a_ c.66.1.26 (A:) DNMT2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: S-adenosyl-L-methionine-dependent methyltransferases
superfamily: S-adenosyl-L-methionine-dependent methyltransferases
family: C5 cytosine-specific DNA methylase, DCM
domain: DNMT2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.95  E-value=2.8e-29  Score=198.43  Aligned_cols=96  Identities=29%  Similarity=0.393  Sum_probs=67.6

Q ss_pred             CcCCCCCcccccCcCCCCCCccchHHHHHHHhccccCCCCCCCchhhhhhhccccccceEEEeecCcCCCCchHHHHHHH
Q psy3546           3 SIDYASNSDPGTGLQKDIADARCTALSYLIETIPANFPGDRLDHYTTQAVKGWKRKLSGIFRTPNVKGFEGSRSRDLITS   82 (164)
Q Consensus         3 ~~~fPCQ~FS~aG~rkd~~D~R~~L~~~~iriI~~~~p~~~P~~~~~~~~~~~~~~~~~iFl~ENVkGf~~s~~~d~I~s   82 (164)
                      .-|||||+||.+|.+++.+|+|+.|+.+++++|.++.  .+|+                +|+||||+||..+..++.|++
T Consensus        73 ~ggpPCq~fS~ag~~~~~~d~r~~l~~~~~~~i~~~~--~kPk----------------~~i~ENV~~l~~~~~~~~i~~  134 (343)
T d1g55a_          73 LMSPPCQPFTRIGRQGDMTDSRTNSFLHILDILPRLQ--KLPK----------------YILLENVKGFEVSSTRDLLIQ  134 (343)
T ss_dssp             EECCC------------------CHHHHHHHHGGGCS--SCCS----------------EEEEEEETTGGGSHHHHHHHH
T ss_pred             EeecccccccccccccccccccccccchhhhhHhhhc--CCCc----------------eeeeeccCCcccchhhHHHHh
Confidence            4589999999999999999999999999999999884  1488                559999999999999999999


Q ss_pred             HHHhCCCeEEEEEeCCCCCCCCCcceEEEecccc
Q psy3546          83 MLTRAGFRFQEFLLSPTQFGTSLYTEWLRNKKKK  116 (164)
Q Consensus        83 ~L~~~GY~v~~~lLnatdfGVPQ~Rr~~i~~rkk  116 (164)
                      .|.++||.+.+.+|||.+|||||.|+|+++.+.+
T Consensus       135 ~l~~~GY~v~~~vlna~dyGvPQ~R~Rvfivg~r  168 (343)
T d1g55a_         135 TIENCGFQYQEFLLSPTSLGIPNSRLRYFLIAKL  168 (343)
T ss_dssp             HHHHTTEEEEEEEECGGGGTCSCCCCEEEEEEEE
T ss_pred             hhhccccccceeeeeccccCCcccceeEEEEEEe
Confidence            9999999999999999999999999554444443

>d1dcta_ c.66.1.26 (A:) DNA methylase HaeIII {Haemophilus aegyptius [TaxId: 197575]}

class: Alpha and beta proteins (a/b)
fold: S-adenosyl-L-methionine-dependent methyltransferases
superfamily: S-adenosyl-L-methionine-dependent methyltransferases
family: C5 cytosine-specific DNA methylase, DCM
domain: DNA methylase HaeIII
species: Haemophilus aegyptius [TaxId: 197575]

Probab=99.94  E-value=1.7e-28  Score=191.90  Aligned_cols=95  Identities=17%  Similarity=0.164  Sum_probs=84.4

Q ss_pred             CCcCCCCCcccccCcCCCCCCccchHHHHHHHhccccCCCCCCCchhhhhhhccccccceEEEeecCcCCCCc---hHHH
Q psy3546           2 ASIDYASNSDPGTGLQKDIADARCTALSYLIETIPANFPGDRLDHYTTQAVKGWKRKLSGIFRTPNVKGFEGS---RSRD   78 (164)
Q Consensus         2 ~~~~fPCQ~FS~aG~rkd~~D~R~~L~~~~iriI~~~~p~~~P~~~~~~~~~~~~~~~~~iFl~ENVkGf~~s---~~~d   78 (164)
                      .+-|||||+||.+|++++.+|+|+.||.+++++|.+++    |+                +|++|||+||.++   ..++
T Consensus        65 l~~g~PCq~fS~ag~~~g~~d~r~~l~~~~~~~i~~~~----Pk----------------~~~lENV~~~~~~~~~~~~~  124 (324)
T d1dcta_          65 IIGGPPCQSWSEGGSLRGIDDPRGKLFYEYIRILKQKK----PI----------------FFLAENVKGMMAQRHNKAVQ  124 (324)
T ss_dssp             EEECCCCTTTSSSSCCCCSSSHHHHHHHHHHHHHHHHC----CS----------------EEEEEEEGGGGSGGGHHHHH
T ss_pred             EeecccccccccccccccccccccchHHHHHHHHHhhC----Cc----------------eeeccccccccccccchhhH
Confidence            35699999999999999999999999999999999998    68                4599999999864   4688


Q ss_pred             HHHHHHHhCCCeEEEEEeCCCCCCCCCcceEEEecccc
Q psy3546          79 LITSMLTRAGFRFQEFLLSPTQFGTSLYTEWLRNKKKK  116 (164)
Q Consensus        79 ~I~s~L~~~GY~v~~~lLnatdfGVPQ~Rr~~i~~rkk  116 (164)
                      .++..|..+||.+++.+||+.+|||||.|+|+++.+.+
T Consensus       125 ~~l~~l~~lGY~v~~~vlna~~~GvPQ~R~R~fiv~~r  162 (324)
T d1dcta_         125 EFIQEFDNAGYDVHIILLNANDYGVAQDRKRVFYIGFR  162 (324)
T ss_dssp             HHHHHHHHHHEEEEEEEEEGGGGTCSBCCEEEEEEEEE
T ss_pred             HHHhHHhhCCCccceeeeecccccCchhhceeeEeeec
Confidence            99999999999999999999999999999555555544

>d2c7pa1 c.66.1.26 (A:1-327) DNA methylase HhaI {Haemophilus haemolyticus [TaxId: 726]}

class: Alpha and beta proteins (a/b)
fold: S-adenosyl-L-methionine-dependent methyltransferases
superfamily: S-adenosyl-L-methionine-dependent methyltransferases
family: C5 cytosine-specific DNA methylase, DCM
domain: DNA methylase HhaI
species: Haemophilus haemolyticus [TaxId: 726]

Probab=99.94  E-value=4.6e-28  Score=192.95  Aligned_cols=95  Identities=15%  Similarity=0.220  Sum_probs=84.2

Q ss_pred             CCcCCCCCcccccCcCCCCCCccchHHHHHHHhccccCCCCCCCchhhhhhhccccccceEEEeecCcCCCCc---hHHH
Q psy3546           2 ASIDYASNSDPGTGLQKDIADARCTALSYLIETIPANFPGDRLDHYTTQAVKGWKRKLSGIFRTPNVKGFEGS---RSRD   78 (164)
Q Consensus         2 ~~~~fPCQ~FS~aG~rkd~~D~R~~L~~~~iriI~~~~p~~~P~~~~~~~~~~~~~~~~~iFl~ENVkGf~~s---~~~d   78 (164)
                      .+-|||||+||.+|++++.+|+|+.||.+++++|.+++    |+                +|+||||+||...   ..++
T Consensus        75 l~ggpPCq~fS~ag~~~g~~d~r~~l~~~~~~~i~~~k----P~----------------~~~lENV~~~~~~~~~~~~~  134 (327)
T d2c7pa1          75 LCAGFPCQAFSISGKQKGFEDSRGTLFFDIARIVREKK----PK----------------VVFMENVKNFASHDNGNTLE  134 (327)
T ss_dssp             EEEECCCTTTCTTSCCCGGGSTTSCHHHHHHHHHHHHC----CS----------------EEEEEEEGGGGTGGGGHHHH
T ss_pred             eecccccchhhhhhhhcCCcccchhHHHHHHHHHhccC----Cc----------------EEecccchhhhhhccchhhH
Confidence            35699999999999999999999999999999999998    68                5599999999754   5789


Q ss_pred             HHHHHHHhCCCeEEEEEeCCCCCCCCCcceEEEecccc
Q psy3546          79 LITSMLTRAGFRFQEFLLSPTQFGTSLYTEWLRNKKKK  116 (164)
Q Consensus        79 ~I~s~L~~~GY~v~~~lLnatdfGVPQ~Rr~~i~~rkk  116 (164)
                      .|++.|+++||.+.+.+|||++|||||.|+|+++.+.+
T Consensus       135 ~i~~~l~~lGY~~~~~vl~a~~~GvPQ~R~R~fivg~r  172 (327)
T d2c7pa1         135 VVKNTMNELDYSFHAKVLNALDYGIPQKRERIYMICFR  172 (327)
T ss_dssp             HHHHHHHHTTBCCEEEEEEGGGGTCSBCCEEEEEEEEB
T ss_pred             HhhhHHHhcCCcceeeEecHHHcCCCchhhhheeeeec
Confidence            99999999999999999999999999999555444443

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

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

Probab=93.98  E-value=0.027  Score=37.10  Aligned_cols=41  Identities=20%  Similarity=0.348  Sum_probs=32.8

Q ss_pred             cccceEEEeecCcCCCCchHHHHHHHHHHhCCCeEEEE-EeCCCCCCCC
Q psy3546          57 RKLSGIFRTPNVKGFEGSRSRDLITSMLTRAGFRFQEF-LLSPTQFGTS  104 (164)
Q Consensus        57 ~~~~~iFl~ENVkGf~~s~~~d~I~s~L~~~GY~v~~~-lLnatdfGVP  104 (164)
                      +|||.+  +||=||     .+..++..|.+.||++... +.+..+||+.
T Consensus         4 ~QisV~--~eNkpG-----~L~~v~~~~~~~~inI~sl~v~~t~~~~i~   45 (70)
T d2f06a2           4 KQLSIF--LENKSG-----RLTEVTEVLAKENINLSALCIAENADFGIL   45 (70)
T ss_dssp             EEEEEE--ECSSSS-----HHHHHHHHHHHTTCCEEEEEEEECSSCEEE
T ss_pred             EEEEEE--EeCCCc-----HHHHHHHHHHHCCCCEEEEEEeecCCCCEE
Confidence            677766  999998     4578999999999999876 5666777763

>d2f1fa1 d.58.18.6 (A:2-77) Acetolactate synthase small subunit, IlvH {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: ACT-like
family: IlvH-like
domain: Acetolactate synthase small subunit, IlvH
species: Escherichia coli [TaxId: 562]

Probab=87.17  E-value=0.47  Score=31.63  Aligned_cols=42  Identities=12%  Similarity=0.279  Sum_probs=33.1

Q ss_pred             EeecCcCCCCchHHHHHHHHHHhCCCeEEEEEeCCCCCCCCCcceEEEe
Q psy3546          64 RTPNVKGFEGSRSRDLITSMLTRAGFRFQEFLLSPTQFGTSLYTEWLRN  112 (164)
Q Consensus        64 l~ENVkGf~~s~~~d~I~s~L~~~GY~v~~~lLnatdfGVPQ~Rr~~i~  112 (164)
                      ++||-||+     ...|...|.+.||.+......|++  .|-..|+-|+
T Consensus         7 ~v~N~~GV-----L~RisglF~rRg~NI~Sl~v~~te--~~~iSR~tiv   48 (76)
T d2f1fa1           7 LLENESGA-----LSRVIGLFSQRGYNIESLTVAPTD--DPTLSRMTIQ   48 (76)
T ss_dssp             EEECCTTH-----HHHHHHHHHTTTCCCSEEEEEECS--CSSEEEEEEE
T ss_pred             EEECCCcH-----HHHHHHHHHhcCcceEEEEEcccC--CCCeeEEEEE
Confidence            59999984     578999999999999999988887  4555444444

>d2pc6a2 d.58.18.6 (A:1-77) Acetolactate synthase small subunit, IlvH {Nitrosomonas europaea [TaxId: 915]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: ACT-like
family: IlvH-like
domain: Acetolactate synthase small subunit, IlvH
species: Nitrosomonas europaea [TaxId: 915]

Probab=86.02  E-value=0.25  Score=33.14  Aligned_cols=42  Identities=12%  Similarity=0.279  Sum_probs=32.5

Q ss_pred             EeecCcCCCCchHHHHHHHHHHhCCCeEEEEEeCCCCCCCCCcceEEEe
Q psy3546          64 RTPNVKGFEGSRSRDLITSMLTRAGFRFQEFLLSPTQFGTSLYTEWLRN  112 (164)
Q Consensus        64 l~ENVkGf~~s~~~d~I~s~L~~~GY~v~~~lLnatdfGVPQ~Rr~~i~  112 (164)
                      ++||.||     .+..|...|.+.||.++.....|++  .|-..|+-++
T Consensus         8 ~veN~pG-----vL~Ris~lF~rRg~NI~Sltv~~te--~~~iSRmtiv   49 (77)
T d2pc6a2           8 LMENEAG-----ALSRVAGLFSARGYNIESLSVAPTE--DPTLSRMTLV   49 (77)
T ss_dssp             EEECSTT-----HHHHHHHHHHHHTCCCCEEEEEECS--STTEEEEEEE
T ss_pred             EEECCcc-----HHHHHHHHHhccCcceEEEEEeccC--CCCeEEEEEE
Confidence            5999998     4578999999999999999988876  3444344443

>d2fgca2 d.58.18.6 (A:27-104) Acetolactate synthase small subunit, IlvH {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: ACT-like
family: IlvH-like
domain: Acetolactate synthase small subunit, IlvH
species: Thermotoga maritima [TaxId: 2336]

Probab=84.70  E-value=0.6  Score=31.23  Aligned_cols=33  Identities=15%  Similarity=0.320  Sum_probs=28.4

Q ss_pred             EeecCcCCCCchHHHHHHHHHHhCCCeEEEEEeCCCCC
Q psy3546          64 RTPNVKGFEGSRSRDLITSMLTRAGFRFQEFLLSPTQF  101 (164)
Q Consensus        64 l~ENVkGf~~s~~~d~I~s~L~~~GY~v~~~lLnatdf  101 (164)
                      ++||-||     .+..|...|.+.||.+......|+.-
T Consensus         9 lv~n~pG-----vL~Ri~~lF~rRg~NI~SL~v~~te~   41 (78)
T d2fgca2           9 LVHNKPG-----VMRKVANLFARRGFNISSITVGESET   41 (78)
T ss_dssp             EEECCTT-----HHHHHHHHHHTTTCEEEEEEEEECSS
T ss_pred             EEeCCCc-----HHHHHHHHHhhCCcceEEEEEeecCC
Confidence            5999998     45789999999999999988888753