Citrus Sinensis ID: 038964

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-
Protein Sequence
MKRIDWETYFLYDRGSLVNDEVFGDIPTFDTTYQTNAYSKPFVVIVGINQHIETISFLFGLLTSETKYTNTYLLETFLRAMNRKNSLRVIINGDQIMSKAMATTFLDSTHK
Secondary Structure (PSIPRED)
cccccccEEEEEcccccHHHHHcccEEEEccccccccccccEEEEEEcccccHHHHHHHHHcccccccHHHHHHHHHHHHHcccccEEEEEccHHHHHHHHHHHccccccc
Secondary Structure Prediction (SSPRO)
ccccccccEEEEcccHHHHHHHcccEEEEEccccccccccccEEEEEEcccccEEEEEEHEHccccHHHHHHHHHHHHHHHcccccEEEEEccHHHHHHHHHHHccccccc
Coil and Loop (DISEMBL)
mkridwetyflydrgslvndevfgdiptfdttyqtnayskPFVVIVGINQHIETISFLFGLLTSETKYTNTYLLETFLRAMNRKNSLRVIINGDQIMSKAMATTFLDSTHK
Flexible Loop (DISEMBL)
mkridwetyflydrgslvndevFGDIPTFDTTYQTNAYSKPFVVIVGINQHIETISFLFGLLTSETKYTNTYLLETFLRAMNRKNSLRVIINGDQIMSKAMAttfldsthk
Low Complexity Region (SEG)
MKRIDWETYFLYDRGSLVNDEVFGDIPTFDTTYQTNAYSKPFVVIVGINQHIETISFLFGLLTSETKYTNTYLLETFLRAMNRKNSLRVIINGDQIMSKAMATTFLDSTHK
Disordered region (IsUnstruct)
***IDWETYFLYDRGSLVNDEVFGDIPTFDTTYQTNAYSKPFVVIVGINQHIETISFLFGLLTSETKYTNTYLLETFLRAMNRKNSLRVIINGDQIMSKAM**********
Disordered Region (DISOPRED)
****DWETYFLYDRGSLVNDEVFGDIPTFDTTYQTNAYSKPFVVIVGINQHIETISFLFGLLTSETKYTNTYLLETFLRAMNRKNSLRVIINGDQIMSKAMATTFLDSTHK
Disordered Region (DISEMBL)
MKRIDWETYFLYDRGSLVNDEVFGDIPTFDTTYQTNAYSKPFVVIVGINQHIETISFLFGLLTSETKYTNTYLLETFLRAMNRKNSLRVIINGDQIMSKAMATTFLDSTHK
Disordered Region (DISPRO)
*KRIDWETYFLYDRGSLVNDEVFGDIPTFDTTYQTNAYSKPFVVIVGINQHIETISFLFGLLTSETKYTNTYLLETFLRAMNRKNSLRVIINGDQIMSKAMATTFLD****
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MKRIDWETYFLYDRGSLVNDEVFGDIPTFDTTYQTNAYSKPFVVIVGINQHIETISFLFGLLTSETKYTNTYLLETFLRAMNRKNSLRVIINGDQIMSKAMATTFLDSTHK
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	111	2.2.26 [Sep-21-2011]
Q9SZL8	788	Protein FAR1-RELATED SEQU	yes	no	0.918	0.129	0.303	2e-09
Q3E7I5	788	Protein FAR1-RELATED SEQU	no	no	0.801	0.112	0.303	2e-09
Q9LIE5	839	Protein FAR-RED ELONGATED	no	no	0.909	0.120	0.316	3e-09
Q9M8J3	764	Protein FAR1-RELATED SEQU	no	no	0.801	0.116	0.314	4e-09
Q9ZVC9	851	Protein FAR1-RELATED SEQU	no	no	0.909	0.118	0.306	9e-08
Q6NQJ7	732	Protein FAR1-RELATED SEQU	no	no	0.648	0.098	0.333	2e-07
Q9S793	725	Protein FAR1-RELATED SEQU	no	no	0.801	0.122	0.348	3e-07
Q9SZL7	545	Protein FAR1-RELATED SEQU	no	no	0.909	0.185	0.284	2e-06
Q3EBQ3	807	Protein FAR1-RELATED SEQU	no	no	0.792	0.109	0.272	9e-06
Q9SWG3	827	Protein FAR-RED IMPAIRED	no	no	0.792	0.106	0.261	2e-05

>sp|Q9SZL8|FRS5_ARATH Protein FAR1-RELATED SEQUENCE 5 OS=Arabidopsis thaliana GN=FRS5 PE=2 SV=1

 Score = 61.6 bits (148), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 31/102 (30%), Positives = 54/102 (52%)

Query: 10  FLYDRGSLVNDEVFGDIPTFDTTYQTNAYSKPFVVIVGINQHIETISFLFGLLTSETKYT 69
           F  D  ++++   FGD  TFDTTY++N Y  PF    G+N H + I F    + +ET+ +
Sbjct: 283 FWADPKAIMDFTHFGDTVTFDTTYRSNRYRLPFAPFTGVNHHGQPILFGCAFIINETEAS 342

Query: 70  NTYLLETFLRAMNRKNSLRVIINGDQIMSKAMATTFLDSTHK 111
             +L  T+L AM+    + +  + D ++  A+   F  + H+
Sbjct: 343 FVWLFNTWLAAMSAHPPVSITTDHDAVIRAAIMHVFPGARHR 384

Putative transcription activator involved in regulating light control of development.
Arabidopsis thaliana (taxid: 3702)

>sp|Q3E7I5|FRS12_ARATH Protein FAR1-RELATED SEQUENCE 12 OS=Arabidopsis thaliana GN=FRS12 PE=2 SV=1

 Score = 61.2 bits (147), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 27/89 (30%), Positives = 49/89 (55%)

Query: 23  FGDIPTFDTTYQTNAYSKPFVVIVGINQHIETISFLFGLLTSETKYTNTYLLETFLRAMN 82
           FGD   FDT+Y+  +YS PF  I+G N H + +     ++  E+K    +L +T+LRAM+
Sbjct: 396 FGDSVVFDTSYRKGSYSVPFATIIGFNHHRQPVLLGCAMVADESKEAFLWLFQTWLRAMS 455

Query: 83  RKNSLRVIINGDQIMSKAMATTFLDSTHK 111
            +    ++ + D  + +A+   F  + H+
Sbjct: 456 GRRPRSIVADQDLPIQQALVQVFPGAHHR 484

Putative transcription activator involved in regulating light control of development.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9LIE5|FHY3_ARATH Protein FAR-RED ELONGATED HYPOCOTYL 3 OS=Arabidopsis thaliana GN=FHY3 PE=1 SV=1

 Score = 60.5 bits (145), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 32/101 (31%), Positives = 53/101 (52%)

Query: 10  FLYDRGSLVNDEVFGDIPTFDTTYQTNAYSKPFVVIVGINQHIETISFLFGLLTSETKYT 69
           F  D  S  N   F D+ + DTTY  N Y  P  + VG+NQH + +     L++ E+  T
Sbjct: 268 FWVDAKSRHNYGSFCDVVSLDTTYVRNKYKMPLAIFVGVNQHYQYMVLGCALISDESAAT 327

Query: 70  NTYLLETFLRAMNRKNSLRVIINGDQIMSKAMATTFLDSTH 110
            ++L+ET+LRA+  +    +I   D +M+  +   F ++ H
Sbjct: 328 YSWLMETWLRAIGGQAPKVLITELDVVMNSIVPEIFPNTRH 368

Transcription activator that recognizes and binds to the DNA consensus sequence 5'-CACGCGC-3'. Activates the expression of FHY1 and FHL involved in light responses. When associated with PHYA, protects it from being recognized and degraded by the COP1/SPA complex.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9M8J3|FRS7_ARATH Protein FAR1-RELATED SEQUENCE 7 OS=Arabidopsis thaliana GN=FRS7 PE=2 SV=1

 Score = 60.1 bits (144), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 28/89 (31%), Positives = 49/89 (55%)

Query: 23  FGDIPTFDTTYQTNAYSKPFVVIVGINQHIETISFLFGLLTSETKYTNTYLLETFLRAMN 82
           FGD   FDT+Y+   YS PF   +G N H + +     L+  E+K   ++L +T+LRAM+
Sbjct: 372 FGDAVVFDTSYRKGDYSVPFATFIGFNHHRQPVLLGGALVADESKEAFSWLFQTWLRAMS 431

Query: 83  RKNSLRVIINGDQIMSKAMATTFLDSTHK 111
            +    ++ + D  + +A+A  F  + H+
Sbjct: 432 GRRPRSMVADQDLPIQQAVAQVFPGTHHR 460

Putative transcription activator involved in regulating light control of development.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9ZVC9|FRS3_ARATH Protein FAR1-RELATED SEQUENCE 3 OS=Arabidopsis thaliana GN=FRS3 PE=2 SV=2

 Score = 55.5 bits (132), Expect = 9e-08,   Method: Composition-based stats.
 Identities = 31/101 (30%), Positives = 48/101 (47%)

Query: 10  FLYDRGSLVNDEVFGDIPTFDTTYQTNAYSKPFVVIVGINQHIETISFLFGLLTSETKYT 69
           F  D  S V    FGD  T DT Y+ N +  PF    G+N H + I F   L+  E+  +
Sbjct: 230 FWADSRSRVAYTHFGDTVTLDTRYRCNQFRVPFAPFTGVNHHGQAILFGCALILDESDTS 289

Query: 70  NTYLLETFLRAMNRKNSLRVIINGDQIMSKAMATTFLDSTH 110
             +L +TFL AM  +  + ++ + D+ +  A    F  + H
Sbjct: 290 FIWLFKTFLTAMRDQPPVSLVTDQDRAIQIAAGQVFPGARH 330

Putative transcription activator involved in regulating light control of development.

Arabidopsis thaliana (taxid: 3702)

>sp|Q6NQJ7|FRS4_ARATH Protein FAR1-RELATED SEQUENCE 4 OS=Arabidopsis thaliana GN=FRS4 PE=2 SV=2

 Score = 54.3 bits (129), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 24/72 (33%), Positives = 43/72 (59%)

Query: 10  FLYDRGSLVNDEVFGDIPTFDTTYQTNAYSKPFVVIVGINQHIETISFLFGLLTSETKYT 69
           F  D   + + + F D+ +F+T+Y  + Y  P V+ VG+N H++ +    GLL  +T YT
Sbjct: 196 FWVDAKGIEDYKSFSDVVSFETSYFVSKYKVPLVLFVGVNHHVQPVLLGCGLLADDTVYT 255

Query: 70  NTYLLETFLRAM 81
             +L++++L AM
Sbjct: 256 YVWLMQSWLVAM 267

Putative transcription activator involved in regulating light control of development.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9S793|FRS8_ARATH Protein FAR1-RELATED SEQUENCE 8 OS=Arabidopsis thaliana GN=FRS8 PE=2 SV=2

 Score = 53.5 bits (127), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 31/89 (34%), Positives = 44/89 (49%)

Query: 23  FGDIPTFDTTYQTNAYSKPFVVIVGINQHIETISFLFGLLTSETKYTNTYLLETFLRAMN 82
           FGD+  FDTT  +NAY  P V  VGIN H +TI    GLL  ++  T  +L   +L  M 
Sbjct: 318 FGDVLLFDTTCLSNAYELPLVAFVGINHHGDTILLGCGLLADQSFETYVWLFRAWLTCML 377

Query: 83  RKNSLRVIINGDQIMSKAMATTFLDSTHK 111
            +     I    + M  A++  F  + H+
Sbjct: 378 GRPPQIFITEQCKAMRTAVSEVFPRAHHR 406

Putative transcription activator involved in regulating light control of development. May have a role in controlling flowering time.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9SZL7|FRS9_ARATH Protein FAR1-RELATED SEQUENCE 9 OS=Arabidopsis thaliana GN=FRS9 PE=2 SV=2

 Score = 50.8 bits (120), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 29/102 (28%), Positives = 50/102 (49%), Gaps = 1/102 (0%)

Query: 5   DWETYFLYDRGSLVNDEVFGDIPTFDTTYQTNA-YSKPFVVIVGINQHIETISFLFGLLT 63
           D    F  D    +N   FGD   FDTTY+    Y  PF    G N H + + F   L+ 
Sbjct: 42  DCGNVFWADPTCRLNYTYFGDTLVFDTTYRRGKRYQVPFAAFTGFNHHGQPVLFGCALIL 101

Query: 64  SETKYTNTYLLETFLRAMNRKNSLRVIINGDQIMSKAMATTF 105
           +E++ +  +L +T+L+AM+      + +  D+++  A++  F
Sbjct: 102 NESESSFAWLFQTWLQAMSAPPPPSITVEPDRLIQVAVSRVF 143

Putative transcription activator involved in regulating light control of development. May act as a negative regulator specific to phyB signaling.

Arabidopsis thaliana (taxid: 3702)

>sp|Q3EBQ3|FRS2_ARATH Protein FAR1-RELATED SEQUENCE 2 OS=Arabidopsis thaliana GN=FRS2 PE=2 SV=1

 Score = 48.9 bits (115), Expect = 9e-06,   Method: Composition-based stats.
 Identities = 24/88 (27%), Positives = 45/88 (51%)

Query: 23  FGDIPTFDTTYQTNAYSKPFVVIVGINQHIETISFLFGLLTSETKYTNTYLLETFLRAMN 82
           F D+  FDT Y  N Y  PF   +G++ H + +     L+   ++ T ++L  T+L+A+ 
Sbjct: 216 FSDVVLFDTFYVRNGYRIPFAPFIGVSHHRQYVLLGCALIGEVSESTYSWLFRTWLKAVG 275

Query: 83  RKNSLRVIINGDQIMSKAMATTFLDSTH 110
            +    +I + D+++S  +   F D  H
Sbjct: 276 GQAPGVMITDQDKLLSDIVVEVFPDVRH 303

Putative transcription activator involved in regulating light control of development.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9SWG3|FAR1_ARATH Protein FAR-RED IMPAIRED RESPONSE 1 OS=Arabidopsis thaliana GN=FAR1 PE=1 SV=1

 Score = 47.8 bits (112), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 23/88 (26%), Positives = 46/88 (52%)

Query: 23  FGDIPTFDTTYQTNAYSKPFVVIVGINQHIETISFLFGLLTSETKYTNTYLLETFLRAMN 82
           F D+ +FDTTY       P  + +G+N H + +     L+  E+  T  +L++T+LRAM 
Sbjct: 272 FNDVVSFDTTYVKFNDKLPLALFIGVNHHSQPMLLGCALVADESMETFVWLIKTWLRAMG 331

Query: 83  RKNSLRVIINGDQIMSKAMATTFLDSTH 110
            +    ++ + D+ +  A++    ++ H
Sbjct: 332 GRAPKVILTDQDKFLMSAVSELLPNTRH 359

Transcription activator that recognizes and binds to the DNA consensus sequence 5'-CACGCGC-3'. Activates the expression of FHY1 and FHL involved in light responses.

Arabidopsis thaliana (taxid: 3702)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	111
147765294	934	hypothetical protein VITISV_003778 [Viti	0.918	0.109	0.509	9e-21
147767877	400	hypothetical protein VITISV_015952 [Viti	0.918	0.255	0.509	2e-20
147783613	612	hypothetical protein VITISV_035651 [Viti	0.918	0.166	0.5	7e-20
147845651	332	hypothetical protein VITISV_040474 [Viti	0.918	0.307	0.470	8e-17
147777005	782	hypothetical protein VITISV_011051 [Viti	0.918	0.130	0.431	1e-16
147772141	876	hypothetical protein VITISV_026047 [Viti	0.801	0.101	0.471	3e-16
147768008	837	hypothetical protein VITISV_003923 [Viti	0.918	0.121	0.421	5e-16
357116523	666	PREDICTED: protein FAR1-RELATED SEQUENCE	0.918	0.153	0.411	9e-16
357128873	832	PREDICTED: protein FAR1-RELATED SEQUENCE	0.918	0.122	0.392	5e-15
147787970	742	hypothetical protein VITISV_029735 [Viti	0.918	0.137	0.411	7e-15

>gi|147765294|emb|CAN77889.1| hypothetical protein VITISV_003778 [Vitis vinifera]

 Score =  103 bits (258), Expect = 9e-21,   Method: Compositional matrix adjust.
 Identities = 52/102 (50%), Positives = 66/102 (64%)

Query: 10  FLYDRGSLVNDEVFGDIPTFDTTYQTNAYSKPFVVIVGINQHIETISFLFGLLTSETKYT 69
           F  D  S ++   FGD+  FDTTY+TNAY KP V++VGIN H +TI F   LL  E+  T
Sbjct: 400 FWADSTSKLDYSCFGDVLAFDTTYRTNAYKKPLVILVGINHHHQTIVFGCALLVDESVST 459

Query: 70  NTYLLETFLRAMNRKNSLRVIINGDQIMSKAMATTFLDSTHK 111
            T++LETFL AMN K  L VI +GD+ M KA+   F DS H+
Sbjct: 460 YTWVLETFLDAMNNKKPLSVITDGDKAMRKAIKRIFPDSCHR 501

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147767877|emb|CAN69010.1| hypothetical protein VITISV_015952 [Vitis vinifera]

 Score =  102 bits (255), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 52/102 (50%), Positives = 65/102 (63%)

Query: 10  FLYDRGSLVNDEVFGDIPTFDTTYQTNAYSKPFVVIVGINQHIETISFLFGLLTSETKYT 69
           F  D  S ++   FGD+  FDTTY+TNAY KP V++V IN H +TI F   LL  E+  T
Sbjct: 180 FWADSTSKLDYSCFGDVLAFDTTYRTNAYKKPLVILVDINHHHQTIVFGCALLVDESVST 239

Query: 70  NTYLLETFLRAMNRKNSLRVIINGDQIMSKAMATTFLDSTHK 111
            T++LETFL AMN K  L VI NGD+ M KA+   F DS H+
Sbjct: 240 YTWVLETFLDAMNNKKPLSVITNGDKAMRKAIKRIFPDSCHQ 281

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147783613|emb|CAN68134.1| hypothetical protein VITISV_035651 [Vitis vinifera]

 Score =  100 bits (250), Expect = 7e-20,   Method: Composition-based stats.
 Identities = 51/102 (50%), Positives = 66/102 (64%)

Query: 10  FLYDRGSLVNDEVFGDIPTFDTTYQTNAYSKPFVVIVGINQHIETISFLFGLLTSETKYT 69
           F  D  S ++   FGD+  FDTTY+TNAY KP V++VGIN H +TI F   LL  E+  T
Sbjct: 60  FWADSTSKLDYSCFGDVLAFDTTYRTNAYKKPLVILVGINHHHQTIVFGCALLVDESVST 119

Query: 70  NTYLLETFLRAMNRKNSLRVIINGDQIMSKAMATTFLDSTHK 111
            T++LETFL AMN K  + VI +GD+ M KA+   F DS H+
Sbjct: 120 YTWVLETFLDAMNNKKPISVITDGDKAMRKAIKRIFPDSCHR 161

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147845651|emb|CAN80592.1| hypothetical protein VITISV_040474 [Vitis vinifera]

 Score = 90.9 bits (224), Expect = 8e-17,   Method: Compositional matrix adjust.
 Identities = 48/102 (47%), Positives = 62/102 (60%)

Query: 10  FLYDRGSLVNDEVFGDIPTFDTTYQTNAYSKPFVVIVGINQHIETISFLFGLLTSETKYT 69
           F  D  S ++    GD+ +FDTTYQTNAY  P V++VGIN H +TI     LL  E+  T
Sbjct: 21  FWVDXTSRLDYTCLGDVLSFDTTYQTNAYKNPLVILVGINHHHQTIVIGCVLLVYESAST 80

Query: 70  NTYLLETFLRAMNRKNSLRVIINGDQIMSKAMATTFLDSTHK 111
            T++LETFL AMN K  L +I  GD+ M KA+   F  S H+
Sbjct: 81  YTWILETFLDAMNNKRPLSIITYGDKAMXKAIKRIFSYSYHR 122

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147777005|emb|CAN63412.1| hypothetical protein VITISV_011051 [Vitis vinifera]

 Score = 90.5 bits (223), Expect = 1e-16,   Method: Composition-based stats.
 Identities = 44/102 (43%), Positives = 63/102 (61%)

Query: 10  FLYDRGSLVNDEVFGDIPTFDTTYQTNAYSKPFVVIVGINQHIETISFLFGLLTSETKYT 69
           F  D  + ++   FGD+  FDTTY+TNAY KP VV+VG+N H +T+ F   LL  E+  T
Sbjct: 271 FWADSTARMDYACFGDVLAFDTTYRTNAYKKPLVVLVGVNHHHQTVVFGCALLIDESVGT 330

Query: 70  NTYLLETFLRAMNRKNSLRVIINGDQIMSKAMATTFLDSTHK 111
             ++LETFL AM  K  + V+ +GD+ M KA+     D+ H+
Sbjct: 331 YEWVLETFLEAMMNKRPISVVTDGDKAMRKAIKKVLPDTCHR 372

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147772141|emb|CAN64548.1| hypothetical protein VITISV_026047 [Vitis vinifera]

 Score = 89.4 bits (220), Expect = 3e-16,   Method: Composition-based stats.
 Identities = 42/89 (47%), Positives = 57/89 (64%)

Query: 23  FGDIPTFDTTYQTNAYSKPFVVIVGINQHIETISFLFGLLTSETKYTNTYLLETFLRAMN 82
           FGD+  FDTTY+TNAY KP VV+VG+N H  T+ F   LL  E+  T  ++LETFL AM 
Sbjct: 273 FGDVLAFDTTYRTNAYKKPLVVLVGVNHHHXTVVFGCALLIDESVGTYEWVLETFLEAMM 332

Query: 83  RKNSLRVIINGDQIMSKAMATTFLDSTHK 111
            K  + V+ +GD+ M KA+     D+ H+
Sbjct: 333 NKRPISVVTDGDKAMRKAIKKVLPDTCHR 361

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147768008|emb|CAN60610.1| hypothetical protein VITISV_003923 [Vitis vinifera]

 Score = 88.2 bits (217), Expect = 5e-16,   Method: Composition-based stats.
 Identities = 43/102 (42%), Positives = 61/102 (59%)

Query: 10  FLYDRGSLVNDEVFGDIPTFDTTYQTNAYSKPFVVIVGINQHIETISFLFGLLTSETKYT 69
           F  D    ++   FGD+  FDTTY+TNAY KP VV+VG+N H +T+ F   LL  E+  T
Sbjct: 353 FWXDSTXRMDYACFGDVLAFDTTYRTNAYKKPLVVLVGVNHHHQTVVFGCALLIDESVGT 412

Query: 70  NTYLLETFLRAMNRKNSLRVIINGDQIMSKAMATTFLDSTHK 111
             ++LETFL AM  K  + V+ +GD+ M  A+     D+ H+
Sbjct: 413 YEWVLETFLDAMMNKKPIXVVTDGDKAMRXAIKKVLPDTCHR 454

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357116523|ref|XP_003560030.1| PREDICTED: protein FAR1-RELATED SEQUENCE 5-like [Brachypodium distachyon]

 Score = 87.4 bits (215), Expect = 9e-16,   Method: Composition-based stats.
 Identities = 42/102 (41%), Positives = 64/102 (62%)

Query: 10  FLYDRGSLVNDEVFGDIPTFDTTYQTNAYSKPFVVIVGINQHIETISFLFGLLTSETKYT 69
           F  D  S ++ EVFGD+  FD+TY+TN Y+ PFV  VG+N H  TI F  G+++ ET  +
Sbjct: 169 FWADSQSRLDYEVFGDVVVFDSTYKTNKYNLPFVPFVGLNHHRSTIIFGCGIISHETSES 228

Query: 70  NTYLLETFLRAMNRKNSLRVIINGDQIMSKAMATTFLDSTHK 111
             ++L TF  AM +K+ + VI +GD  M +A+   + D+ H+
Sbjct: 229 YEWMLRTFSAAMAQKHPISVITDGDLAMQRAIRVVWPDTIHR 270

Source: Brachypodium distachyon

Species: Brachypodium distachyon

Genus: Brachypodium

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357128873|ref|XP_003566094.1| PREDICTED: protein FAR1-RELATED SEQUENCE 5-like [Brachypodium distachyon]

 Score = 85.1 bits (209), Expect = 5e-15,   Method: Composition-based stats.
 Identities = 40/102 (39%), Positives = 61/102 (59%)

Query: 10  FLYDRGSLVNDEVFGDIPTFDTTYQTNAYSKPFVVIVGINQHIETISFLFGLLTSETKYT 69
           F  D  S ++ E FGD+  FD+TY+ N Y+ PFV  +G+N H  TI F  G+++ ET  +
Sbjct: 219 FWADSQSQIDYEAFGDLVVFDSTYRVNRYNLPFVPFIGVNHHRSTIVFGVGIVSDETVSS 278

Query: 70  NTYLLETFLRAMNRKNSLRVIINGDQIMSKAMATTFLDSTHK 111
           + +LL++FL AM+ KN   VI +GD    KA+      + H+
Sbjct: 279 HEWLLQSFLEAMSHKNPRSVITDGDAATRKAIKKVMPRTDHR 320

Source: Brachypodium distachyon

Species: Brachypodium distachyon

Genus: Brachypodium

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147787970|emb|CAN62918.1| hypothetical protein VITISV_029735 [Vitis vinifera]

 Score = 84.7 bits (208), Expect = 7e-15,   Method: Composition-based stats.
 Identities = 42/102 (41%), Positives = 61/102 (59%)

Query: 10  FLYDRGSLVNDEVFGDIPTFDTTYQTNAYSKPFVVIVGINQHIETISFLFGLLTSETKYT 69
           F  D  + ++   FGD+  FDTTY+TNAY KP VV+VG+N H +T+ F   LL  E+  T
Sbjct: 240 FWADSTARMDYACFGDVLAFDTTYRTNAYKKPLVVLVGVNHHHQTVVFGCALLIDESVGT 299

Query: 70  NTYLLETFLRAMNRKNSLRVIINGDQIMSKAMATTFLDSTHK 111
             ++L TFL AM  K  + V+ + D+ M KA+     D+ H+
Sbjct: 300 YEWVLGTFLDAMMNKRPISVVTDEDKAMRKAIKKVLPDTCHR 341

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	111
TAIR|locus:2121060	788	FRS5 "FAR1-related sequence 5"	0.918	0.129	0.303	5.6e-09
TAIR|locus:2144930	788	FRS12 "FAR1-related sequence 1	0.801	0.112	0.303	1.2e-08
TAIR|locus:2082420	764	FRS7 "FAR1-related sequence 7"	0.801	0.116	0.314	1.9e-08
TAIR|locus:2090394	839	FHY3 "far-red elongated hypoco	0.909	0.120	0.316	2.1e-08
TAIR|locus:2014639	732	FRS4 "FAR1-related sequence 4"	0.909	0.137	0.267	2.2e-08
TAIR|locus:2059304	851	FRS3 "FAR1-related sequence 3"	0.909	0.118	0.306	5.2e-07
TAIR|locus:2121003	545	FRS9 "FAR1-related sequence 9"	0.909	0.185	0.284	6e-07
TAIR|locus:2016259	725	FRS8 "FAR1-related sequence 8"	0.801	0.122	0.348	1.1e-06
TAIR|locus:2062606	807	FRS2 "FAR1-related sequence 2"	0.792	0.109	0.272	2e-05
TAIR|locus:2129665	827	FAR1 "FAR-RED IMPAIRED RESPONS	0.792	0.106	0.261	2e-05

TAIR|locus:2121060 FRS5 "FAR1-related sequence 5" [Arabidopsis thaliana (taxid:3702)]

 Score = 145 (56.1 bits), Expect = 5.6e-09, P = 5.6e-09
 Identities = 31/102 (30%), Positives = 54/102 (52%)

Query:    10 FLYDRGSLVNDEVFGDIPTFDTTYQTNAYSKPFVVIVGINQHIETISFLFGLLTSETKYT 69
             F  D  ++++   FGD  TFDTTY++N Y  PF    G+N H + I F    + +ET+ +
Sbjct:   283 FWADPKAIMDFTHFGDTVTFDTTYRSNRYRLPFAPFTGVNHHGQPILFGCAFIINETEAS 342

Query:    70 NTYLLETFLRAMNRKNSLRVIINGDQIMSKAMATTFLDSTHK 111
               +L  T+L AM+    + +  + D ++  A+   F  + H+
Sbjct:   343 FVWLFNTWLAAMSAHPPVSITTDHDAVIRAAIMHVFPGARHR 384

GO:0005634 "nucleus" evidence=ISM

GO:0008270 "zinc ion binding" evidence=IEA

GO:0009639 "response to red or far red light" evidence=ISS

TAIR|locus:2144930 FRS12 "FAR1-related sequence 12" [Arabidopsis thaliana (taxid:3702)]

 Score = 142 (55.0 bits), Expect = 1.2e-08, P = 1.2e-08
 Identities = 27/89 (30%), Positives = 49/89 (55%)

Query:    23 FGDIPTFDTTYQTNAYSKPFVVIVGINQHIETISFLFGLLTSETKYTNTYLLETFLRAMN 82
             FGD   FDT+Y+  +YS PF  I+G N H + +     ++  E+K    +L +T+LRAM+
Sbjct:   396 FGDSVVFDTSYRKGSYSVPFATIIGFNHHRQPVLLGCAMVADESKEAFLWLFQTWLRAMS 455

Query:    83 RKNSLRVIINGDQIMSKAMATTFLDSTHK 111
              +    ++ + D  + +A+   F  + H+
Sbjct:   456 GRRPRSIVADQDLPIQQALVQVFPGAHHR 484

GO:0005634 "nucleus" evidence=ISM

GO:0008270 "zinc ion binding" evidence=IEA

GO:0009639 "response to red or far red light" evidence=ISS

TAIR|locus:2082420 FRS7 "FAR1-related sequence 7" [Arabidopsis thaliana (taxid:3702)]

 Score = 140 (54.3 bits), Expect = 1.9e-08, P = 1.9e-08
 Identities = 28/89 (31%), Positives = 49/89 (55%)

Query:    23 FGDIPTFDTTYQTNAYSKPFVVIVGINQHIETISFLFGLLTSETKYTNTYLLETFLRAMN 82
             FGD   FDT+Y+   YS PF   +G N H + +     L+  E+K   ++L +T+LRAM+
Sbjct:   372 FGDAVVFDTSYRKGDYSVPFATFIGFNHHRQPVLLGGALVADESKEAFSWLFQTWLRAMS 431

Query:    83 RKNSLRVIINGDQIMSKAMATTFLDSTHK 111
              +    ++ + D  + +A+A  F  + H+
Sbjct:   432 GRRPRSMVADQDLPIQQAVAQVFPGTHHR 460

GO:0005634 "nucleus" evidence=ISM

GO:0008270 "zinc ion binding" evidence=IEA

GO:0009639 "response to red or far red light" evidence=ISS

TAIR|locus:2090394 FHY3 "far-red elongated hypocotyls 3" [Arabidopsis thaliana (taxid:3702)]

 Score = 140 (54.3 bits), Expect = 2.1e-08, P = 2.1e-08
 Identities = 32/101 (31%), Positives = 53/101 (52%)

Query:    10 FLYDRGSLVNDEVFGDIPTFDTTYQTNAYSKPFVVIVGINQHIETISFLFGLLTSETKYT 69
             F  D  S  N   F D+ + DTTY  N Y  P  + VG+NQH + +     L++ E+  T
Sbjct:   268 FWVDAKSRHNYGSFCDVVSLDTTYVRNKYKMPLAIFVGVNQHYQYMVLGCALISDESAAT 327

Query:    70 NTYLLETFLRAMNRKNSLRVIINGDQIMSKAMATTFLDSTH 110
              ++L+ET+LRA+  +    +I   D +M+  +   F ++ H
Sbjct:   328 YSWLMETWLRAIGGQAPKVLITELDVVMNSIVPEIFPNTRH 368

GO:0004553 "hydrolase activity, hydrolyzing O-glycosyl compounds" evidence=IEA

GO:0005634 "nucleus" evidence=ISM;IDA

GO:0005975 "carbohydrate metabolic process" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0009585 "red, far-red light phototransduction" evidence=IMP

GO:0007623 "circadian rhythm" evidence=IMP

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

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

GO:0010218 "response to far red light" evidence=IMP

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

GO:0042753 "positive regulation of circadian rhythm" evidence=IMP

GO:0000956 "nuclear-transcribed mRNA catabolic process" evidence=RCA

GO:0006487 "protein N-linked glycosylation" evidence=RCA

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

GO:0009630 "gravitropism" evidence=RCA

GO:0009639 "response to red or far red light" evidence=RCA

TAIR|locus:2014639 FRS4 "FAR1-related sequence 4" [Arabidopsis thaliana (taxid:3702)]

 Score = 139 (54.0 bits), Expect = 2.2e-08, P = 2.2e-08
 Identities = 27/101 (26%), Positives = 55/101 (54%)

Query:    10 FLYDRGSLVNDEVFGDIPTFDTTYQTNAYSKPFVVIVGINQHIETISFLFGLLTSETKYT 69
             F  D   + + + F D+ +F+T+Y  + Y  P V+ VG+N H++ +    GLL  +T YT
Sbjct:   196 FWVDAKGIEDYKSFSDVVSFETSYFVSKYKVPLVLFVGVNHHVQPVLLGCGLLADDTVYT 255

Query:    70 NTYLLETFLRAMNRKNSLRVIINGDQIMSKAMATTFLDSTH 110
               +L++++L AM  +    ++ + +  +  A+A    ++ H
Sbjct:   256 YVWLMQSWLVAMGGQKPKVMLTDQNNAIKAAIAAVLPETRH 296

GO:0005634 "nucleus" evidence=ISM

GO:0008270 "zinc ion binding" evidence=IEA

GO:0009639 "response to red or far red light" evidence=ISS

TAIR|locus:2059304 FRS3 "FAR1-related sequence 3" [Arabidopsis thaliana (taxid:3702)]

 Score = 127 (49.8 bits), Expect = 5.2e-07, P = 5.2e-07
 Identities = 31/101 (30%), Positives = 48/101 (47%)

Query:    10 FLYDRGSLVNDEVFGDIPTFDTTYQTNAYSKPFVVIVGINQHIETISFLFGLLTSETKYT 69
             F  D  S V    FGD  T DT Y+ N +  PF    G+N H + I F   L+  E+  +
Sbjct:   230 FWADSRSRVAYTHFGDTVTLDTRYRCNQFRVPFAPFTGVNHHGQAILFGCALILDESDTS 289

Query:    70 NTYLLETFLRAMNRKNSLRVIINGDQIMSKAMATTFLDSTH 110
               +L +TFL AM  +  + ++ + D+ +  A    F  + H
Sbjct:   290 FIWLFKTFLTAMRDQPPVSLVTDQDRAIQIAAGQVFPGARH 330

GO:0005634 "nucleus" evidence=ISM

GO:0008270 "zinc ion binding" evidence=IEA

GO:0009639 "response to red or far red light" evidence=ISS

GO:0009506 "plasmodesma" evidence=IDA

GO:0006635 "fatty acid beta-oxidation" evidence=RCA

GO:0016558 "protein import into peroxisome matrix" evidence=RCA

TAIR|locus:2121003 FRS9 "FAR1-related sequence 9" [Arabidopsis thaliana (taxid:3702)]

 Score = 124 (48.7 bits), Expect = 6.0e-07, P = 6.0e-07
 Identities = 29/102 (28%), Positives = 50/102 (49%)

Query:     5 DWETYFLYDRGSLVNDEVFGDIPTFDTTYQTNA-YSKPFVVIVGINQHIETISFLFGLLT 63
             D    F  D    +N   FGD   FDTTY+    Y  PF    G N H + + F   L+ 
Sbjct:    42 DCGNVFWADPTCRLNYTYFGDTLVFDTTYRRGKRYQVPFAAFTGFNHHGQPVLFGCALIL 101

Query:    64 SETKYTNTYLLETFLRAMNRKNSLRVIINGDQIMSKAMATTF 105
             +E++ +  +L +T+L+AM+      + +  D+++  A++  F
Sbjct:   102 NESESSFAWLFQTWLQAMSAPPPPSITVEPDRLIQVAVSRVF 143

GO:0005634 "nucleus" evidence=ISM

GO:0008270 "zinc ion binding" evidence=IEA

GO:0009639 "response to red or far red light" evidence=ISS

TAIR|locus:2016259 FRS8 "FAR1-related sequence 8" [Arabidopsis thaliana (taxid:3702)]

 Score = 123 (48.4 bits), Expect = 1.1e-06, P = 1.1e-06
 Identities = 31/89 (34%), Positives = 44/89 (49%)

Query:    23 FGDIPTFDTTYQTNAYSKPFVVIVGINQHIETISFLFGLLTSETKYTNTYLLETFLRAMN 82
             FGD+  FDTT  +NAY  P V  VGIN H +TI    GLL  ++  T  +L   +L  M 
Sbjct:   318 FGDVLLFDTTCLSNAYELPLVAFVGINHHGDTILLGCGLLADQSFETYVWLFRAWLTCML 377

Query:    83 RKNSLRVIINGDQIMSKAMATTFLDSTHK 111
              +     I    + M  A++  F  + H+
Sbjct:   378 GRPPQIFITEQCKAMRTAVSEVFPRAHHR 406

GO:0005634 "nucleus" evidence=ISM

GO:0008270 "zinc ion binding" evidence=IEA

GO:0009639 "response to red or far red light" evidence=ISS

GO:0010228 "vegetative to reproductive phase transition of meristem" evidence=RCA

GO:0016926 "protein desumoylation" evidence=RCA

GO:0050665 "hydrogen peroxide biosynthetic process" evidence=RCA

TAIR|locus:2062606 FRS2 "FAR1-related sequence 2" [Arabidopsis thaliana (taxid:3702)]

 Score = 112 (44.5 bits), Expect = 2.0e-05, P = 2.0e-05
 Identities = 24/88 (27%), Positives = 45/88 (51%)

Query:    23 FGDIPTFDTTYQTNAYSKPFVVIVGINQHIETISFLFGLLTSETKYTNTYLLETFLRAMN 82
             F D+  FDT Y  N Y  PF   +G++ H + +     L+   ++ T ++L  T+L+A+ 
Sbjct:   216 FSDVVLFDTFYVRNGYRIPFAPFIGVSHHRQYVLLGCALIGEVSESTYSWLFRTWLKAVG 275

Query:    83 RKNSLRVIINGDQIMSKAMATTFLDSTH 110
              +    +I + D+++S  +   F D  H
Sbjct:   276 GQAPGVMITDQDKLLSDIVVEVFPDVRH 303

GO:0005634 "nucleus" evidence=ISM

GO:0008270 "zinc ion binding" evidence=IEA

GO:0009639 "response to red or far red light" evidence=ISS

TAIR|locus:2129665 FAR1 "FAR-RED IMPAIRED RESPONSE 1" [Arabidopsis thaliana (taxid:3702)]

 Score = 112 (44.5 bits), Expect = 2.0e-05, P = 2.0e-05
 Identities = 23/88 (26%), Positives = 46/88 (52%)

Query:    23 FGDIPTFDTTYQTNAYSKPFVVIVGINQHIETISFLFGLLTSETKYTNTYLLETFLRAMN 82
             F D+ +FDTTY       P  + +G+N H + +     L+  E+  T  +L++T+LRAM 
Sbjct:   272 FNDVVSFDTTYVKFNDKLPLALFIGVNHHSQPMLLGCALVADESMETFVWLIKTWLRAMG 331

Query:    83 RKNSLRVIINGDQIMSKAMATTFLDSTH 110
              +    ++ + D+ +  A++    ++ H
Sbjct:   332 GRAPKVILTDQDKFLMSAVSELLPNTRH 359

GO:0005634 "nucleus" evidence=ISM;IDA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0009639 "response to red or far red light" evidence=IMP

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

GO:0010018 "far-red light signaling pathway" evidence=IMP

GO:0005515 "protein binding" evidence=IPI

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

GO:0010218 "response to far red light" evidence=IMP

GO:0045893 "positive regulation of transcription, DNA-dependent" evidence=RCA;IDA

GO:0042753 "positive regulation of circadian rhythm" evidence=IMP

GO:0000278 "mitotic cell cycle" evidence=RCA

GO:0000724 "double-strand break repair via homologous recombination" evidence=RCA

GO:0006396 "RNA processing" evidence=RCA

GO:0009410 "response to xenobiotic stimulus" evidence=RCA

GO:0009630 "gravitropism" evidence=RCA

GO:0009640 "photomorphogenesis" evidence=RCA

GO:0010212 "response to ionizing radiation" evidence=RCA

GO:0010388 "cullin deneddylation" evidence=RCA

GO:0016567 "protein ubiquitination" evidence=RCA

GO:0016571 "histone methylation" evidence=RCA

GO:0016579 "protein deubiquitination" evidence=RCA

GO:0048522 "positive regulation of cellular process" evidence=RCA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	111
PLN03097	846	PLN03097, FHY3, Protein FAR-RED ELONGATED HYPOCOTY	1e-13
pfam10551	88	pfam10551, MULE, MULE transposase domain	3e-09

>gnl|CDD|178645 PLN03097, FHY3, Protein FAR-RED ELONGATED HYPOCOTYL 3; Provisional

 Score = 65.0 bits (158), Expect = 1e-13
 Identities = 29/88 (32%), Positives = 51/88 (57%)

Query: 23  FGDIPTFDTTYQTNAYSKPFVVIVGINQHIETISFLFGLLTSETKYTNTYLLETFLRAMN 82
           F D+ +FDTTY  N Y  P  + VG+NQH + +     L++ E+  T ++L++T+LRAM 
Sbjct: 285 FSDVVSFDTTYVRNKYKMPLALFVGVNQHYQFMLLGCALISDESAATYSWLMQTWLRAMG 344

Query: 83  RKNSLRVIINGDQIMSKAMATTFLDSTH 110
            +    +I + D+ M   ++  F ++ H
Sbjct: 345 GQAPKVIITDQDKAMKSVISEVFPNAHH 372

Length = 846

>gnl|CDD|220806 pfam10551, MULE, MULE transposase domain

 Score = 49.7 bits (119), Expect = 3e-09
 Identities = 23/80 (28%), Positives = 42/80 (52%), Gaps = 4/80 (5%)

Query: 31  TTYQTNAYSKPFVVIVGINQHIETISFLFGLLTSETKYTNTYLLETFLRAMNRKNSLRVI 90
            TY TN Y       VG++ H +     F L++ E++ + T+ LE   +A+  +  L +I
Sbjct: 1   GTYLTNKY----KGAVGVDHHGQGFPLAFALVSDESEESWTWFLEGLKKALGGRPPLTII 56

Query: 91  INGDQIMSKAMATTFLDSTH 110
            +GD+ + KA+   F ++ H
Sbjct: 57  SDGDKGLKKAIKEVFPNARH 76

This domain was identified by Babu and colleagues. Length = 88

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	111
PLN03097	846	FHY3 Protein FAR-RED ELONGATED HYPOCOTYL 3; Provis	100.0
PF10551	93	MULE: MULE transposase domain; InterPro: IPR018289	99.91
PF00872	381	Transposase_mut: Transposase, Mutator family; Inte	98.7
COG3328	379	Transposase and inactivated derivatives [DNA repli	97.4
PF13610	140	DDE_Tnp_IS240: DDE domain	96.86
PF00665	120	rve: Integrase core domain; InterPro: IPR001584 In	96.43
COG3316	215	Transposase and inactivated derivatives [DNA repli	93.37
PF01610	249	DDE_Tnp_ISL3: Transposase; InterPro: IPR002560 Aut	90.95

>PLN03097 FHY3 Protein FAR-RED ELONGATED HYPOCOTYL 3; Provisional

Probab=100.00  E-value=6.4e-44  Score=298.14  Aligned_cols=110  Identities=29%  Similarity=0.490  Sum_probs=108.5

Q ss_pred             ccceeeEEEEechhchhhhhhCCCeEEEecccccCCCCCceeEEEEEccCCceEEEEeeeccccccchhhHHHHHHHHHh
Q 038964            2 KRIDWETYFLYDRGSLVNDEVFGDIPTFDTTYQTNAYSKPFVVIVGINQHIETISFLFGLLTSETKYTNTYLLETFLRAM   81 (111)
Q Consensus         2 ~~~~l~~ifw~~~~~~~~~~~f~dvv~~D~Ty~tn~y~~pl~~~~g~n~~~~~~~~~~~ll~~E~~es~~W~l~~f~~~~   81 (111)
                      .+++|++|||+|++|+.+|.+|||||+||+||+||+|+|||+.|+|+|||+|+++||||||.||+.|||.|||++|+++|
T Consensus       264 e~~~l~niFWaD~~sr~~Y~~FGDvV~fDTTY~tN~y~~Pfa~FvGvNhH~qtvlfGcaLl~dEt~eSf~WLf~tfl~aM  343 (846)
T PLN03097        264 EDQRLKNLFWVDAKSRHDYGNFSDVVSFDTTYVRNKYKMPLALFVGVNQHYQFMLLGCALISDESAATYSWLMQTWLRAM  343 (846)
T ss_pred             cCCCeeeEEeccHHHHHHHHhcCCEEEEeceeeccccCcEEEEEEEecCCCCeEEEEEEEcccCchhhHHHHHHHHHHHh
Confidence            46899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCceEEEeeCcHHHHHHHHHhCCCCCCC
Q 038964           82 NRKNSLRVIINGDQIMSKAMATTFLDSTHK  111 (111)
Q Consensus        82 ~~~~p~~iiTD~d~a~~~Ai~~vfP~~~Hr  111 (111)
                      +|+.|++||||+|.+|++||++|||+|.||
T Consensus       344 ~gk~P~tIiTDqd~am~~AI~~VfP~t~Hr  373 (846)
T PLN03097        344 GGQAPKVIITDQDKAMKSVISEVFPNAHHC  373 (846)
T ss_pred             CCCCCceEEecCCHHHHHHHHHHCCCceeh
Confidence            999999999999999999999999999998

>PF10551 MULE: MULE transposase domain; InterPro: IPR018289 This entry represents a domain found in Mutator-like elements (MULE)-encoded tranposases, some of which also contain a zinc-finger motif [, ]

Probab=99.91  E-value=1.1e-24  Score=138.69  Aligned_cols=79  Identities=30%  Similarity=0.497  Sum_probs=75.8

Q ss_pred             cccccCCCCCceeE---EEEEccCCceEEEEeeeccccccchhhHHHHHHHHHhcCCCceEEEeeCcHHHHHHHHHhCCC
Q 038964           31 TTYQTNAYSKPFVV---IVGINQHIETISFLFGLLTSETKYTNTYLLETFLRAMNRKNSLRVIINGDQIMSKAMATTFLD  107 (111)
Q Consensus        31 ~Ty~tn~y~~pl~~---~~g~n~~~~~~~~~~~ll~~E~~es~~W~l~~f~~~~~~~~p~~iiTD~d~a~~~Ai~~vfP~  107 (111)
                      +||+||+| +|++.   ++|+|++++.+++|++++.+|+.++|.|+|+.+++.+..+ |.+|+||+|.++.+||+++||+
T Consensus         1 ~T~~tn~~-~~l~~~~~~~~~d~~~~~~~v~~~l~~~e~~~~~~~~l~~~~~~~~~~-p~~ii~D~~~~~~~Ai~~vfP~   78 (93)
T PF10551_consen    1 GTYKTNKY-GPLLYLMIAVGIDGNGRGFPVAFALVSSESEESYEWFLEKLKEAMPQK-PKVIISDFDKALINAIKEVFPD   78 (93)
T ss_pred             Cccccccc-cccceeceEEEEcCCCCEEEEEEEEEcCCChhhhHHHHHHhhhccccC-ceeeeccccHHHHHHHHHHCCC
Confidence            69999999 88885   9999999999999999999999999999999999999887 9999999999999999999999


Q ss_pred             CCCC
Q 038964          108 STHK  111 (111)
Q Consensus       108 ~~Hr  111 (111)
                      +.|+
T Consensus        79 ~~~~   82 (93)
T PF10551_consen   79 ARHQ   82 (93)
T ss_pred             ceEe
Confidence            9985

This domain is also found in a transposase for the insertion sequence element IS256 in transposon Tn4001 [].

>PF00872 Transposase_mut: Transposase, Mutator family; InterPro: IPR001207 Autonomous mobile genetic elements such as transposon or insertion sequences (IS) encode an enzyme, transposase, that is required for excising and inserting the mobile element

Probab=98.70  E-value=3.5e-09  Score=83.06  Aligned_cols=85  Identities=19%  Similarity=0.181  Sum_probs=75.0

Q ss_pred             CeEEEecccccCCC-----CCceeEEEEEccCCceEEEEeeeccccccchhhHHHHHHHHHhcCCCceEEEeeCcHHHHH
Q 038964           25 DIPTFDTTYQTNAY-----SKPFVVIVGINQHIETISFLFGLLTSETKYTNTYLLETFLRAMNRKNSLRVIINGDQIMSK   99 (111)
Q Consensus        25 dvv~~D~Ty~tn~y-----~~pl~~~~g~n~~~~~~~~~~~ll~~E~~es~~W~l~~f~~~~~~~~p~~iiTD~d~a~~~   99 (111)
                      ++|.+|++|.+-+.     +.+++.++|+|..|+-.++|+.+-..|+.++|.=+|+.+++. |-+.|..|++|..+++.+
T Consensus       163 ~~l~iD~~~~kvr~~~~~~~~~~~v~iGi~~dG~r~vLg~~~~~~Es~~~W~~~l~~L~~R-Gl~~~~lvv~Dg~~gl~~  241 (381)
T PF00872_consen  163 PYLWIDGTYFKVREDGRVVKKAVYVAIGIDEDGRREVLGFWVGDRESAASWREFLQDLKER-GLKDILLVVSDGHKGLKE  241 (381)
T ss_pred             cceeeeeeecccccccccccchhhhhhhhhcccccceeeeecccCCccCEeeecchhhhhc-cccccceeeccccccccc
Confidence            57889999987553     467899999999999999999999999999999888888765 335699999999999999


Q ss_pred             HHHHhCCCCCC
Q 038964          100 AMATTFLDSTH  110 (111)
Q Consensus       100 Ai~~vfP~~~H  110 (111)
                      ||+++||++.|
T Consensus       242 ai~~~fp~a~~  252 (381)
T PF00872_consen  242 AIREVFPGAKW  252 (381)
T ss_pred             cccccccchhh
Confidence            99999999875

Transposases have been grouped into various families [, , ]. The mutator family of transposases consists of a number of elements that include, mutator from maize, IsT2 from Thiobacillus ferrooxidans, Is256 from Staphylococcus aureus, Is1201 from Lactobacillus helveticus, Is1081 from Mycobacterium bovis, IsRm3 from Rhizobium meliloti and others. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated

>COG3328 Transposase and inactivated derivatives [DNA replication, recombination, and repair]

Probab=97.40  E-value=0.00031  Score=55.55  Aligned_cols=84  Identities=13%  Similarity=0.137  Sum_probs=65.6

Q ss_pred             CeEEEecccccCC--CCCceeEEEEEccCCceEEEEeeeccccccchhhHHHHHHHHHhcCCCceEEEeeCcHHHHHHHH
Q 038964           25 DIPTFDTTYQTNA--YSKPFVVIVGINQHIETISFLFGLLTSETKYTNTYLLETFLRAMNRKNSLRVIINGDQIMSKAMA  102 (111)
Q Consensus        25 dvv~~D~Ty~tn~--y~~pl~~~~g~n~~~~~~~~~~~ll~~E~~es~~W~l~~f~~~~~~~~p~~iiTD~d~a~~~Ai~  102 (111)
                      .++.+|++|.+=+  -+..++..+|++.+|+-.+.|.-+=..|. ..|.-++..|... +-..-..+++|..+++.+||.
T Consensus       146 ~~v~~D~~~~k~r~v~~~~~~ia~Gv~~eG~reilg~~~~~~e~-~~w~~~l~~l~~r-gl~~v~l~v~Dg~~gl~~aI~  223 (379)
T COG3328         146 PYVYLDAKYVKVRSVRNKAVYIAIGVTEEGRREILGIWVGVRES-KFWLSFLLDLKNR-GLSDVLLVVVDGLKGLPEAIS  223 (379)
T ss_pred             eEEEEecceeehhhhhhheeeeeeccCcccchhhhceeeecccc-hhHHHHHHHHHhc-cccceeEEecchhhhhHHHHH
Confidence            4678999999988  35688899999999999999988888888 6665333334332 223445667799999999999


Q ss_pred             HhCCCCCC
Q 038964          103 TTFLDSTH  110 (111)
Q Consensus       103 ~vfP~~~H  110 (111)
                      .+||.+.|
T Consensus       224 ~v~p~a~~  231 (379)
T COG3328         224 AVFPQAAV  231 (379)
T ss_pred             HhccHhhh
Confidence            99998765

>PF13610 DDE_Tnp_IS240: DDE domain

Probab=96.86  E-value=0.00036  Score=47.53  Aligned_cols=80  Identities=15%  Similarity=0.079  Sum_probs=61.7

Q ss_pred             CCeEEEecccccCCCCCceeEEEEEccCCceEEEEeeeccccccchhhHHHHHHHHHhcCCCceEEEeeCcHHHHHHHHH
Q 038964           24 GDIPTFDTTYQTNAYSKPFVVIVGINQHIETISFLFGLLTSETKYTNTYLLETFLRAMNRKNSLRVIINGDQIMSKAMAT  103 (111)
Q Consensus        24 ~dvv~~D~Ty~tn~y~~pl~~~~g~n~~~~~~~~~~~ll~~E~~es~~W~l~~f~~~~~~~~p~~iiTD~d~a~~~Ai~~  103 (111)
                      |+.+.+|=||-+=+ |--...+-.+|.+++  ++.+=|-...+...=..+|+..++... ..|.+|+||+.++...|+++
T Consensus         1 ~~~w~~DEt~iki~-G~~~yl~~aiD~~~~--~l~~~ls~~Rd~~aA~~Fl~~~l~~~~-~~p~~ivtDk~~aY~~A~~~   76 (140)
T PF13610_consen    1 GDSWHVDETYIKIK-GKWHYLWRAIDAEGN--ILDFYLSKRRDTAAAKRFLKRALKRHR-GEPRVIVTDKLPAYPAAIKE   76 (140)
T ss_pred             CCEEEEeeEEEEEC-CEEEEEEEeeccccc--chhhhhhhhcccccceeeccccceeec-cccceeecccCCccchhhhh
Confidence            68899999997643 345667888899988  555556666666666666666666544 78999999999999999999


Q ss_pred             hCCC
Q 038964          104 TFLD  107 (111)
Q Consensus       104 vfP~  107 (111)
                      +.|+
T Consensus        77 l~~~   80 (140)
T PF13610_consen   77 LNPE   80 (140)
T ss_pred             cccc
Confidence            9997

>PF00665 rve: Integrase core domain; InterPro: IPR001584 Integrase comprises three domains capable of folding independently and whose three-dimensional structures are known

Probab=96.43  E-value=0.04  Score=35.23  Aligned_cols=74  Identities=14%  Similarity=0.062  Sum_probs=51.0

Q ss_pred             CCeEEEeccccc-CCCCCceeEEEEEccCCceEEEEeeeccccccchhhHHHHHHHHHhcCCCceEEEeeCcHHHH
Q 038964           24 GDIPTFDTTYQT-NAYSKPFVVIVGINQHIETISFLFGLLTSETKYTNTYLLETFLRAMNRKNSLRVIINGDQIMS   98 (111)
Q Consensus        24 ~dvv~~D~Ty~t-n~y~~pl~~~~g~n~~~~~~~~~~~ll~~E~~es~~W~l~~f~~~~~~~~p~~iiTD~d~a~~   98 (111)
                      ++.+.+|.+... ...+.....++.+|...+-.. +..+-..++.+.+.-+++...+..++..|++|+||+..+..
T Consensus         6 ~~~~~~D~~~~~~~~~~~~~~~~~~iD~~S~~~~-~~~~~~~~~~~~~~~~l~~~~~~~~~~~p~~i~tD~g~~f~   80 (120)
T PF00665_consen    6 GERWQIDFTPMPIPDKGGRVYLLVFIDDYSRFIY-AFPVSSKETAEAALRALKRAIEKRGGRPPRVIRTDNGSEFT   80 (120)
T ss_dssp             TTEEEEEEEEETGGCTT-CEEEEEEEETTTTEEE-EEEESSSSHHHHHHHHHHHHHHHHS-SE-SEEEEESCHHHH
T ss_pred             CCEEEEeeEEEecCCCCccEEEEEEEECCCCcEE-EEEeecccccccccccccccccccccccceecccccccccc
Confidence            578889998444 445557888888888877544 55555555766776666666665555559999999999886

However, the manner in which the N-terminal, catalytic, and C-terminal domains interact in the holoenzyme remains obscure. Numerous studies indicate that the enzyme functions as a multimer, minimally a dimer. The integrase proteins from Human immunodeficiency virus 1 (HIV-1) and Avian sarcoma virus (ASV) have been studied most carefully with respect to the structural basis of catalysis. Although the active site of ASV integrase does not undergo significant conformational changes on binding the required metal cofactor, that of HIV-1 does. This active site-mediated conformational change in HIV-1 reorganises the catalytic core and C-terminal domains and appears to promote an interaction that is favourable for catalysis []. Retroviral integrase is synthesised as part of the POL polyprotein that contains; an aspartyl protease, a reverse transcriptase, RNase H and integrase. POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. The presence of retrovirus integrase-related gene sequences in eukaryotes is known. Bacterial transposases involved in the transposition of the insertion sequence also belong to this group. HIV integrase catalyses the incorporation of virally derived DNA into the human genome. This unique step in the virus life cycle provides a variety of points for intervention and hence is an attractive target for the development of new therapeutics for the treatment of AIDS []. Substrate recognition by the retroviral integrase enzyme is critical for retroviral integration. To catalyse this recombination event, integrase must recognise and act on two types of substrates, viral DNA and host DNA, yet the necessary interactions exhibit markedly different degrees of specificity [].; GO: 0015074 DNA integration; PDB: 3AO3_A 3OVN_A 3AO5_A 3AO4_A 3AO1_A 1C6V_D 3HPG_A 3HPH_A 3OYD_A 3OYF_B ....

>COG3316 Transposase and inactivated derivatives [DNA replication, recombination, and repair]

Probab=93.37  E-value=0.24  Score=36.54  Aligned_cols=84  Identities=14%  Similarity=0.111  Sum_probs=54.6

Q ss_pred             CCCeEEEecccccCCCCCceeEEEEEccCCceEEEEeeeccccccchhhHHHHHHHHHhcCCCceEEEeeCcHHHHHHHH
Q 038964           23 FGDIPTFDTTYQTNAYSKPFVVIVGINQHIETISFLFGLLTSETKYTNTYLLETFLRAMNRKNSLRVIINGDQIMSKAMA  102 (111)
Q Consensus        23 f~dvv~~D~Ty~tn~y~~pl~~~~g~n~~~~~~~~~~~ll~~E~~es~~W~l~~f~~~~~~~~p~~iiTD~d~a~~~Ai~  102 (111)
                      =++..-+|=||-+-+=+- ....-.||..|++.-+-  |-..-+...=.=++..+++..  ..|.+|+||+.+....|++
T Consensus        69 ~~~~w~vDEt~ikv~gkw-~ylyrAid~~g~~Ld~~--L~~rRn~~aAk~Fl~kllk~~--g~p~v~vtDka~s~~~A~~  143 (215)
T COG3316          69 AGDSWRVDETYIKVNGKW-HYLYRAIDADGLTLDVW--LSKRRNALAAKAFLKKLLKKH--GEPRVFVTDKAPSYTAALR  143 (215)
T ss_pred             cccceeeeeeEEeeccEe-eehhhhhccCCCeEEEE--EEcccCcHHHHHHHHHHHHhc--CCCceEEecCccchHHHHH
Confidence            357788899987655333 23344556667765542  222222222233445555543  6789999999999999999


Q ss_pred             HhCCCCCCC
Q 038964          103 TTFLDSTHK  111 (111)
Q Consensus       103 ~vfP~~~Hr  111 (111)
                      ++-++..||
T Consensus       144 ~l~~~~ehr  152 (215)
T COG3316         144 KLGSEVEHR  152 (215)
T ss_pred             hcCcchhee
Confidence            999988886

>PF01610 DDE_Tnp_ISL3: Transposase; InterPro: IPR002560 Autonomous mobile genetic elements such as transposon or insertion sequences (IS) encode an enzyme, transposase, that is required for excising and inserting the mobile element

Probab=90.95  E-value=0.45  Score=34.63  Aligned_cols=49  Identities=18%  Similarity=0.184  Sum_probs=37.2

Q ss_pred             eccccccchhhHHHHHH-HHHhcCCCceEEEeeCcHHHHHHHHHhCCCCCC
Q 038964           61 LLTSETKYTNTYLLETF-LRAMNRKNSLRVIINGDQIMSKAMATTFLDSTH  110 (111)
Q Consensus        61 ll~~E~~es~~W~l~~f-~~~~~~~~p~~iiTD~d~a~~~Ai~~vfP~~~H  110 (111)
                      ++.+-+.+++.=.|..+ -.. .....++|.+|-..+..+|+++.||+|.+
T Consensus        32 i~~~r~~~~l~~~~~~~~~~~-~~~~v~~V~~Dm~~~y~~~~~~~~P~A~i   81 (249)
T PF01610_consen   32 ILPGRDKETLKDFFRSLYPEE-ERKNVKVVSMDMSPPYRSAIREYFPNAQI   81 (249)
T ss_pred             EcCCccHHHHHHHHHHhCccc-cccceEEEEcCCCcccccccccccccccc
Confidence            67787877774444433 222 34678899999999999999999999874

Transposases have been grouped into various families [, , ]. This family includes the IS204 [], IS1001 [], IS1096 [] and IS1165 [] transposases. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

No hit with e-value below 0.005

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	111
3kks_A	152	Integrase, IN; beta-strands flanked by alpha-helic	93.56
3hph_A	219	Integrase, IN; protein-protein complex, tetramer,	90.16
1c0m_A	238	Protein (integrase); HIV, X-RAY crystallography, p	87.82
1cxq_A	162	Avian sarcoma virus integrase; mixed beta-sheet su	84.72
3l3u_A	163	POL polyprotein; DNA integration, AIDS, integrase,	83.48

>3kks_A Integrase, IN; beta-strands flanked by alpha-helices, DNA binding protein; 2.20A {Bovine immunodeficiency virus} PDB: 3kkr_A

Probab=93.56  E-value=0.38  Score=30.51  Aligned_cols=66  Identities=9%  Similarity=0.122  Sum_probs=43.4

Q ss_pred             CCeEEEecccccCCCCCceeEEEEEccCCceEEEEeeeccccccchhhHHHHHHHHHhcCCCceEEEeeCcHHHHH
Q 038964           24 GDIPTFDTTYQTNAYSKPFVVIVGINQHIETISFLFGLLTSETKYTNTYLLETFLRAMNRKNSLRVIINGDQIMSK   99 (111)
Q Consensus        24 ~dvv~~D~Ty~tn~y~~pl~~~~g~n~~~~~~~~~~~ll~~E~~es~~W~l~~f~~~~~~~~p~~iiTD~d~a~~~   99 (111)
                      +++..+|.|+..++     ..++-+|...+-. .+.. +.+++.+...-++..+....+   |++|.||+......
T Consensus         2 n~~w~~D~t~~~~~-----y~~~~iD~~sr~~-~~~~-~~~~~~~~~~~~l~~~~~~~g---p~~i~sDnG~~f~s   67 (152)
T 3kks_A            2 SHLWQMDNTHWNKT-----IIWVAVETNSGLV-EAQV-IPEETALQVALCILQLIQRYT---VLHLHSDNGPCFTA   67 (152)
T ss_dssp             CCEEEEEEEEETTE-----EEEEEEETTTCCE-EEEE-ESSSCHHHHHHHHHHHHHHSC---CSEEEECSCHHHHS
T ss_pred             CcEEEEeeeeeCCE-----EEEEEEEcCCCcE-EEEE-eCCcCHHHHHHHHHHHHHHhC---CcEEecCCchHhhH
Confidence            46788999988543     4556667666544 3443 456666666555555555444   99999999987754

>3hph_A Integrase, IN; protein-protein complex, tetramer, DNA integration, endonucl magnesium, metal-binding, multifunctional enzyme; 2.64A {Maedi visna virus} PDB: 3hpg_A

Probab=90.16  E-value=1.2  Score=30.34  Aligned_cols=65  Identities=11%  Similarity=0.055  Sum_probs=42.9

Q ss_pred             CeEEEecccccCCCCCceeEEEEEccCCceEEEEeeeccccccchhhHHHHHHHHHhcCCCceEEEeeCcHHHHH
Q 038964           25 DIPTFDTTYQTNAYSKPFVVIVGINQHIETISFLFGLLTSETKYTNTYLLETFLRAMNRKNSLRVIINGDQIMSK   99 (111)
Q Consensus        25 dvv~~D~Ty~tn~y~~pl~~~~g~n~~~~~~~~~~~ll~~E~~es~~W~l~~f~~~~~~~~p~~iiTD~d~a~~~   99 (111)
                      +++.+|.|+..++     ..++-+|...+-. .+. .+.+++.+...-++..+....+   |++|.||+......
T Consensus        61 ~~w~~D~t~~~~~-----y~~~~iD~~Sr~~-~~~-~~~~~~~~~~~~~l~~~~~~~g---p~~i~sDnG~~F~s  125 (219)
T 3hph_A           61 DHWQVDYTHYEDK-----IILVWVETNSGLI-YAE-RVKGETGQEFRVQTMKWYAMFA---PKSLQSDNGPAFVA  125 (219)
T ss_dssp             CEEEEEEEEETTE-----EEEEEEETTTCCE-EEE-EESCCCHHHHHHHHHHHHHHHC---CCEEEECCCHHHHS
T ss_pred             ceEEEEEecCCCE-----EEEEEEeCCCCcE-EEE-EeCCCCHHHHHHHHHHHHHHhC---CcEEEeCCCchhhh
Confidence            6778999977554     4556667766654 333 3566666665555555555444   99999999988753

>1c0m_A Protein (integrase); HIV, X-RAY crystallography, protein structure, transferase; 2.53A {Rous sarcoma virus} SCOP: b.34.7.1 c.55.3.2 PDB: 1c1a_A

Probab=87.82  E-value=3.4  Score=28.69  Aligned_cols=71  Identities=10%  Similarity=0.015  Sum_probs=46.1

Q ss_pred             CCeEEEecccccCCCCCceeEEEEEccCCceEEEEeeeccccccchhhHHHHHHHHHhcCCCceEEEeeCcHHHHH
Q 038964           24 GDIPTFDTTYQTNAYSKPFVVIVGINQHIETISFLFGLLTSETKYTNTYLLETFLRAMNRKNSLRVIINGDQIMSK   99 (111)
Q Consensus        24 ~dvv~~D~Ty~tn~y~~pl~~~~g~n~~~~~~~~~~~ll~~E~~es~~W~l~~f~~~~~~~~p~~iiTD~d~a~~~   99 (111)
                      ++++.+|.||.....+. ...++-+|...+-.. |+.+ .+++.+...-+|+......+  .|++|.||+......
T Consensus        10 ~~~w~~D~~~~~~~~g~-~yl~~~iD~~Sr~i~-~~~~-~~~~~~~v~~~l~~~~~~~g--~p~~i~sDnG~~f~s   80 (238)
T 1c0m_A           10 LQIWQTDFTLEPRMAPR-SWLAVTVDTASSAIV-VTQH-GRVTSVAVQHHWATAIAVLG--RPKAIKTDNGSCFTS   80 (238)
T ss_dssp             TSEEEEEEEECGGGCSS-CEEEEEEETTTCCEE-EEEE-SSCCHHHHHHHHHHHHHHHC--CCSEEEECSCHHHHS
T ss_pred             CCEEEEeeccccccCCC-EEEEEEEECCCCCEE-EEEc-cCCCHHHHHHHHHHHHHHhC--CCcEEEECCCCcccc
Confidence            46889999986654443 445666777665443 5544 36666666555555555444  488999999988743

>1cxq_A Avian sarcoma virus integrase; mixed beta-sheet surrounded by alpha-helices, transferase; HET: EPE; 1.02A {Avian sarcoma virus} SCOP: c.55.3.2 PDB: 1cxu_A* 1czb_A* 1cz9_A* 1asu_A* 1asw_A* 1asv_A 1a5v_A* 1a5w_A* 1a5x_A* 1vsf_A* 1vse_A* 3o4n_A* 1vsm_A 3o4q_A* 1vsd_A* 1vsh_A* 1vsi_A* 1vsj_A* 1vsk_A 1vsl_A

Probab=84.72  E-value=5.9  Score=25.41  Aligned_cols=71  Identities=10%  Similarity=0.022  Sum_probs=44.7

Q ss_pred             CCeEEEecccccCCCCCceeEEEEEccCCceEEEEeeeccccccchhhHHHHHHHHHhcCCCceEEEeeCcHHHHH
Q 038964           24 GDIPTFDTTYQTNAYSKPFVVIVGINQHIETISFLFGLLTSETKYTNTYLLETFLRAMNRKNSLRVIINGDQIMSK   99 (111)
Q Consensus        24 ~dvv~~D~Ty~tn~y~~pl~~~~g~n~~~~~~~~~~~ll~~E~~es~~W~l~~f~~~~~~~~p~~iiTD~d~a~~~   99 (111)
                      .+++.+|.||.....+. ....+.+|...+-. +|+.+ .+++.+...-+++......  ..|++|.||+......
T Consensus        11 ~~~~~~D~~~~~~~~g~-~yl~~~iD~~Sr~i-~~~~~-~~~~~~~v~~~l~~~~~~~--g~p~~i~sDnG~~f~s   81 (162)
T 1cxq_A           11 LQIWQTDFTLEPRMAPR-SWLAVTVDTASSAI-VVTQH-GRVTSVAAQHHWATAIAVL--GRPKAIKTDNGSCFTS   81 (162)
T ss_dssp             CCEEEEEEEECGGGTTS-CEEEEEEETTTCCE-EEEEE-SSCCHHHHHHHHHHHHHHH--CCCSEEECCSCHHHHS
T ss_pred             CCEEEeeeeecccCCCC-EEEEEEEEcCCCeE-EEEEC-CCccHHHHHHHHHHHHHHH--CCCeEEEeCCchhhhh
Confidence            56889999986554444 44566777776644 34444 3555555444444444443  3588999999987743

>3l3u_A POL polyprotein; DNA integration, AIDS, integrase, endonuclease, polynucleotidyl transferase, DNA binding, viral protein; 1.40A {Human immunodeficiency virus 1} PDB: 3ao1_A 3l3v_A* 3ovn_A* 3ao2_A* 3ao3_A* 3ao4_A* 3ao5_A* 2itg_A 1biz_A 1biu_A 1b9d_A 4dmn_A* 2b4j_A 1itg_A 1b92_A 1bl3_A 1bi4_A 1bis_A 1b9f_A 1bi4_B ...

Probab=83.48  E-value=3  Score=26.73  Aligned_cols=64  Identities=17%  Similarity=0.108  Sum_probs=41.7

Q ss_pred             CCeEEEecccccCCCCCceeEEEEEccCCceEEEEeeeccccccchhhHHHHHHHHHhcCCCceEEEeeCcHHH
Q 038964           24 GDIPTFDTTYQTNAYSKPFVVIVGINQHIETISFLFGLLTSETKYTNTYLLETFLRAMNRKNSLRVIINGDQIM   97 (111)
Q Consensus        24 ~dvv~~D~Ty~tn~y~~pl~~~~g~n~~~~~~~~~~~ll~~E~~es~~W~l~~f~~~~~~~~p~~iiTD~d~a~   97 (111)
                      .+++.+|.||..++     ..++-+|...+-. .+.. +.+++.+...-++..+...++   +++|.||+....
T Consensus         9 ~~~w~~D~t~~~g~-----y~~~~iD~~sr~~-~~~~-~~~~~~~~~~~~l~~~~~~~~---~~~i~sD~G~~f   72 (163)
T 3l3u_A            9 PGIWQLDCTHLEGK-----VILVAVHVASGYI-EAEV-IPAETGQETAYFLLKLAGRWP---VKTVHTDNGSNF   72 (163)
T ss_dssp             TTEEEEEEEEETTE-----EEEEEEETTTCCE-EEEE-ESSCCHHHHHHHHHHHHHHSC---CCEEEECCCGGG
T ss_pred             CCEEEEEecccCCc-----EEEEEEecCCCcE-EEEE-eCCCcHHHHHHHHHHHHHHcC---CcEEeecChHhh
Confidence            46788999998654     3556667766643 3443 456666666555555544443   589999998765

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

No hit with e-value below 0.005

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	111
d1exqa_	154	Retroviral integrase, catalytic domain {Human immu	92.93
d1cxqa_	147	Retroviral integrase, catalytic domain {Rous sarco	91.7
d1c6va_	159	Retroviral integrase, catalytic domain {Simian imm	84.3

>d1exqa_ c.55.3.2 (A:) Retroviral integrase, catalytic domain {Human immunodeficiency virus type 1 [TaxId: 11676]}

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Ribonuclease H-like
family: Retroviral integrase, catalytic domain
domain: Retroviral integrase, catalytic domain
species: Human immunodeficiency virus type 1 [TaxId: 11676]

Probab=92.93  E-value=0.067  Score=33.78  Aligned_cols=65  Identities=14%  Similarity=0.088  Sum_probs=43.7

Q ss_pred             eEEEecccccCCCCCceeEEEEEccCCceEEEEeeeccccccchhhHHHHHHHHHhcCCCceEEEeeCcHHHHHH
Q 038964           26 IPTFDTTYQTNAYSKPFVVIVGINQHIETISFLFGLLTSETKYTNTYLLETFLRAMNRKNSLRVIINGDQIMSKA  100 (111)
Q Consensus        26 vv~~D~Ty~tn~y~~pl~~~~g~n~~~~~~~~~~~ll~~E~~es~~W~l~~f~~~~~~~~p~~iiTD~d~a~~~A  100 (111)
                      +..+|.|+..|+|     .++.+|...+- +.+. .+.+++.+...-++..+...   ..|++|.||+.....++
T Consensus         5 ~W~~D~~~~~~k~-----ilv~vD~~Sr~-~~~~-~~~~~~~~~v~~~l~~~~~~---~~p~~I~sDnG~eF~s~   69 (154)
T d1exqa_           5 IWQLDCTHLEGKV-----ILVAVHVASGY-IEAE-VIPAETGQETAYFLLKLAGR---WPVKTIHTDNGSNFTGA   69 (154)
T ss_dssp             EEEEEEEEETTEE-----EEEEEETTTTE-EEEE-EESSSSHHHHHHHHHHHHHH---SCCCEEECCCCGGGTSH
T ss_pred             ceeeEEEEECCEE-----EEEEEECcCCc-EEEE-EecCcchHHHHhhhhhheec---cCCCEEEEcCCccccch
Confidence            6678999988764     45778888663 3443 45667766665555554433   34899999999877543

>d1cxqa_ c.55.3.2 (A:) Retroviral integrase, catalytic domain {Rous sarcoma virus RSV [TaxId: 11886]}

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Ribonuclease H-like
family: Retroviral integrase, catalytic domain
domain: Retroviral integrase, catalytic domain
species: Rous sarcoma virus RSV [TaxId: 11886]

Probab=91.70  E-value=0.65  Score=28.42  Aligned_cols=70  Identities=9%  Similarity=0.043  Sum_probs=42.9

Q ss_pred             CCeEEEecccccCCCCCceeEEEEEccCCceEEEEeeeccccccchhhHHHHHHHHHhcCCCceEEEeeCcHHHH
Q 038964           24 GDIPTFDTTYQTNAYSKPFVVIVGINQHIETISFLFGLLTSETKYTNTYLLETFLRAMNRKNSLRVIINGDQIMS   98 (111)
Q Consensus        24 ~dvv~~D~Ty~tn~y~~pl~~~~g~n~~~~~~~~~~~ll~~E~~es~~W~l~~f~~~~~~~~p~~iiTD~d~a~~   98 (111)
                      ++++.+|-|+.....+... ..+.+|...+- +.++ .+.+++.+...-.+......++  .|+.|.||+.....
T Consensus         7 ~~~w~~D~~~~~~~~~~~~-l~v~vD~~Sr~-i~~~-~~~~~t~~~~~~~l~~~~~~~g--~p~~i~sDnG~~F~   76 (147)
T d1cxqa_           7 LQIWQTDFTLEPRMAPRSW-LAVTVDTASSA-IVVT-QHGRVTSVAAQHHWATAIAVLG--RPKAIKTDNGSCFT   76 (147)
T ss_dssp             CCEEEEEEEECGGGTTSCE-EEEEEETTTCC-EEEE-EESSCCHHHHHHHHHHHHHHHC--CCSEEECCSCHHHH
T ss_pred             CCEEEEEEEEecCCCCeEE-EEEEEecccce-eccc-ccCccchHHHHHHHHHHHHHhC--CCeEEEeccccccc
Confidence            4678899888765555543 34555665543 3333 4566666555444444444433  69999999988774

>d1c6va_ c.55.3.2 (A:) Retroviral integrase, catalytic domain {Simian immunodeficiency virus [TaxId: 11723]}

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Ribonuclease H-like
family: Retroviral integrase, catalytic domain
domain: Retroviral integrase, catalytic domain
species: Simian immunodeficiency virus [TaxId: 11723]

Probab=84.30  E-value=1.1  Score=27.62  Aligned_cols=62  Identities=15%  Similarity=0.043  Sum_probs=38.4

Q ss_pred             eEEEecccccCCCCCceeEEEEEccCCceEEEEeeeccccccchhhHHHHHHHHHhcCCCceEEEeeCcHHH
Q 038964           26 IPTFDTTYQTNAYSKPFVVIVGINQHIETISFLFGLLTSETKYTNTYLLETFLRAMNRKNSLRVIINGDQIM   97 (111)
Q Consensus        26 vv~~D~Ty~tn~y~~pl~~~~g~n~~~~~~~~~~~ll~~E~~es~~W~l~~f~~~~~~~~p~~iiTD~d~a~   97 (111)
                      +-.+|.||..++|     .++.+|...+- +.+. .+.+++.+...-++....   ....|++|.||+....
T Consensus         6 ~W~~D~t~~~~k~-----il~~vD~~Sr~-~~~~-~~~~~~a~~v~~~l~~~~---~~~~~~~I~sDnG~~F   67 (159)
T d1c6va_           6 TWQMDCTHLEGKI-----VIVAVHVASGF-IEAE-VIPQETGRQTALFLLKLA---GRWPITHLHTDNGANF   67 (159)
T ss_dssp             EEEEEEEEETTEE-----EEEEECTTSCC-EEEE-ECSSCSHHHHHHHHHHHH---TTSCCCEEECCCCSST
T ss_pred             ceeeEEEEECCEE-----EEEEEECCCCe-EEEE-EeeccCHHHHHHHHHHHh---hccCCceeEecCCCcc
Confidence            4568999987764     44556766554 3343 567777766554444433   2233568999998765