Citrus Sinensis ID: 028759

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200----
Protein Sequence
MCSLQSQHFLNSPLLIFPKFNDNRKFHLNRTRNFGQRIGALSSVEEFLPNATRRKKDSLWRGGFSLGVDLGLSRTGLALSKGFCVRPLTVLKLRGEKLELQLLEIAQREETDEFIIGLPKSWDGSETPQSNKVRSVAGRLAVRAAERGWRVYLLDEHRTSAEAVDRMINMGLSKSARQTKTDAYAAVVRQESITFGHLMNIIFW
Secondary Structure (PSIPRED)
cccccccccccccccccccccccHHHHHcccccccccccccccccccccccccccccccccccEEEEEEccccEEEEEEccccEEEEEEEEEEccccHHHHHHHHHHHHcccEEEEEccccccccccHHHHHHHHHHHHHHHHHccccccEEEEccccHHHHHHHHHHHcccccccccHHHHHHHHHHHHHHHHHccccccccc
Secondary Structure Prediction (SSPRO)
cccccccccccccEEEccccccccEEEEcccccccccEEEEccHHHccccHHHccccccccccEEEEEEcccEEEEEEEccccEEcccEEEEcccccHHHHHHHHHHHccccEEEEEccccccccccHHHHHHHHHHHHHHHHHHcccccEEEEcccccHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHHHHHHHEEcc
Coil and Loop (DISEMBL)
mcslqsqhflnspllifpkfndnrkfHLNRTRNFGQRIGALSSVEeflpnatrrkkdslwrggfslgvdlglsrtglalskgfcvrpltVLKLRGEKLELQLLEIAQReetdefiiglpkswdgsetpqsnkvrSVAGRLAVRAAERGWRVYLLDEHRTSAEAVDRMINMGLSKSARQTKTDAYAAVVRQESITFGHLMNIIFW
Flexible Loop (DISEMBL)
mcslqsqhflnspllifPKFNDNRKFHLNRTRNFgqrigalssveeflpnatrrkkdslwrgGFSLGVDLGLSrtglalskgfcvRPLTVLKLRGEKLELQLLEiaqreetdeFIIGlpkswdgsetpqsnkvrsvagRLAVRAAERGWRVYLLDEHRTSAEAVDRMINMGLSKSARQTKTDAYAAVVRQesitfghlmniifw
Low Complexity Region (SEG)
MCSLQSQHFLNSPLLIFPKFNDNRKFHLNRTRNFGQRIGALSSVEEFLPNATRRKKDSLWRGGFSLGVDLGLSRTGLALSKGFCVRPLTVLKLRGEKLELQLLEIAQREETDEFIIGLPKSWDGSETPQSNKVRSVAGRLAVRAAERGWRVYLLDEHRTSAEAVDRMINMGLSKSARQTKTDAYAAVVRQESITFGHLMNIIFW
Disordered region (IsUnstruct)
********FLNSPLLIFPKFNDNRKFHLNRTRNFGQRIGALSSVEEFLPNATRRKKDSLWRGGFSLGVDLGLSRTGLALSKGFCVRPLTVLKLRGEKLELQLLEIAQREETDEFIIGLPKSW*************VAGRLAVRAAERGWRVYLLDEHRTSAEAVDRMINM**********TDAYAAVVRQESITFGHLMNIIFW
Disordered Region (DISOPRED)
*******HFLNSPLLIFPKFNDNRKF*************************************FSLGVDLGLSRTGLALSKGFCVRPLTVLKLRGEKLELQLLEIAQREETDEFIIGLPKSWDGSETPQSNKVRSVAGRLAVRAAERGWRVYLLDEHRTSAEAV*****************DAYAAVVRQESITFGHLMNIIFW
Disordered Region (DISEMBL)
MCSLQSQHFLNSPLLIFPKFNDNRKFHLNRTRNFGQRIGALSSVEEFLPNATRRKKDSLWRGGFSLGVDLGLSRTGLALSKGFCVRPLTVLKLRGEKLELQLLEIAQREETDEFIIGLPKSWD************VAGRLAVRAAERGWRVYLLDEHRTSAEAVDRMINMGLSKSARQTKTDAYAAVVRQESITFGHLMNIIFW
Disordered Region (DISPRO)
*C*LQSQHFLNSPLLIFPKFNDNRKFHLNRTRNFGQRIGALSSVEEFLPNATRRKKDSLWRGGFSLGVDLGLSRTGLALSKGFCVRPLTVLKLRGEKLELQLLEIAQREETDEFIIGLPKSWDGSETPQSNKVRSVAGRLAVRAAERGWRVYLLDEHRTSAEAVDRMINMGLSKSARQTKTDAYAAVVRQESITFGHLMNIIFW
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MCSLQSQHFLNSPLLIFPKFNDNRKFHLNRTRNFGQRIGALSSVEEFLPNATRRKKDSLWRGGFSLGVDLGLSRTGLALSKGFCVRPLTVLKLRGEKLELQLLEIAQREETDEFIIGLPKSWDGSETPQSNKVRSVAGRLAVRAAERGWRVYLLDEHRTSAEAVDRMINMGLSKSARQTKTDAYAAVVRQESITFGHLMNIIFW
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	204	2.2.26 [Sep-21-2011]
A1SJC8	156	Putative Holliday junctio	yes	no	0.622	0.814	0.348	9e-10
Q2IQC1	137	Putative Holliday junctio	yes	no	0.593	0.883	0.370	2e-09
B4UH04	137	Putative Holliday junctio	yes	no	0.593	0.883	0.370	7e-09
B8JDZ9	137	Putative Holliday junctio	yes	no	0.593	0.883	0.370	7e-09
A7HDE0	137	Putative Holliday junctio	yes	no	0.588	0.875	0.373	2e-08
Q2RHZ7	140	Putative Holliday junctio	yes	no	0.578	0.842	0.330	4e-08
A7MJR8	138	Putative Holliday junctio	yes	no	0.622	0.920	0.315	2e-07
Q3SFS3	145	Putative Holliday junctio	yes	no	0.588	0.827	0.367	3e-07
C6C125	135	Putative Holliday junctio	yes	no	0.607	0.918	0.315	3e-07
B7NI12	138	Putative Holliday junctio	yes	no	0.622	0.920	0.308	4e-07

>sp|A1SJC8|RUVX_NOCSJ Putative Holliday junction resolvase OS=Nocardioides sp. (strain BAA-499 / JS614) GN=Noca_2408 PE=3 SV=1

 Score = 63.5 bits (153), Expect = 9e-10,   Method: Compositional matrix adjust.
 Identities = 47/135 (34%), Positives = 70/135 (51%), Gaps = 8/135 (5%)

Query: 60  WRGGFSLGVDLGLSRTGLALS--KGFCVRPL-TVLKLRGEKLELQLLEIAQREETD---E 113
            R G  +G+D G +R G+A S   GF   P+ TV + +G+   +  +  A+ +E     E
Sbjct: 1   MRAGVRIGIDPGDARIGVARSDPSGFLATPVETVRRGKGDLARIGRILAAEEDEGATVLE 60

Query: 114 FIIGLPKSWDGSETPQSNKVRSVAGRLAVRAAERGWRVYLLDEHRTSAEAVDRMINMGLS 173
            ++GLP+S  G E P + KVR  AGRLA R A     V L+DE  T+  A   + + G +
Sbjct: 61  VVVGLPRSLSGREGPAAAKVREFAGRLAARVAP--VPVRLVDERMTTVSAEAMLRDQGRT 118

Query: 174 KSARQTKTDAYAAVV 188
              R+   D  AAV+
Sbjct: 119 GGKRRAVVDQAAAVL 133

Could be a nuclease that resolves Holliday junction intermediates in genetic recombination.
Nocardioides sp. (strain BAA-499 / JS614) (taxid: 196162)
EC: 3EC: .EC: 1EC: .EC: -EC: .EC: -

>sp|Q2IQC1|RUVX_ANADE Putative Holliday junction resolvase OS=Anaeromyxobacter dehalogenans (strain 2CP-C) GN=Adeh_1232 PE=3 SV=1

 Score = 62.4 bits (150), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 47/127 (37%), Positives = 67/127 (52%), Gaps = 6/127 (4%)

Query: 65  SLGVDLGLSRTGLALSKGF--CVRPLTVLKLRGEKLELQLL-EIAQREETDEFIIGLPKS 121
           +LGVDLG  R GLA++       R +T +  RGE  +L  + E+A+  E    ++GLP +
Sbjct: 3   TLGVDLGRVRIGLAVADEILRTARAVTTVVRRGEAEDLAAIAEVARDYEVTRAVVGLPLN 62

Query: 122 WDGSETPQSNKVRSVAGRLAVRAAERGWRVYLLDEHRTSAEAVDRMINMGLSKSARQTKT 181
            DG+E P +   R  A RL    A  G  V L DE  +S EA  R+   G+S   ++ + 
Sbjct: 63  MDGTEGPSARLARGFAPRL---EAALGVPVELFDERLSSFEAESRLRARGVSARDQRGQV 119

Query: 182 DAYAAVV 188
           DA AA V
Sbjct: 120 DAEAAAV 126

Could be a nuclease that resolves Holliday junction intermediates in genetic recombination.

Anaeromyxobacter dehalogenans (strain 2CP-C) (taxid: 290397)

EC: 3

EC: .

EC: 1

EC: .

EC: -

EC: .

EC: -

>sp|B4UH04|RUVX_ANASK Putative Holliday junction resolvase OS=Anaeromyxobacter sp. (strain K) GN=AnaeK_2633 PE=3 SV=1

 Score = 60.5 bits (145), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 47/127 (37%), Positives = 66/127 (51%), Gaps = 6/127 (4%)

Query: 65  SLGVDLGLSRTGLALSKGF--CVRPLTVLKLRGEKLELQLL-EIAQREETDEFIIGLPKS 121
           +LGVDLG  R GLA++       R +T +  R E  +L  + E+A+  E    ++GLP +
Sbjct: 3   TLGVDLGRVRIGLAVADEILRTARAVTTVVRRTEAEDLSAIAEVARDYEVTRAVVGLPLN 62

Query: 122 WDGSETPQSNKVRSVAGRLAVRAAERGWRVYLLDEHRTSAEAVDRMINMGLSKSARQTKT 181
            DG+E P +   R  A RL    A  G  V L DE  +S EA  R+   GLS   ++ + 
Sbjct: 63  MDGTEGPSARLARGFAPRL---EAALGVPVELFDERLSSFEAESRLRARGLSAREQRGQV 119

Query: 182 DAYAAVV 188
           DA AA V
Sbjct: 120 DAEAAAV 126

Could be a nuclease that resolves Holliday junction intermediates in genetic recombination.

Anaeromyxobacter sp. (strain K) (taxid: 447217)

EC: 3

EC: .

EC: 1

EC: .

EC: -

EC: .

EC: -

>sp|B8JDZ9|RUVX_ANAD2 Putative Holliday junction resolvase OS=Anaeromyxobacter dehalogenans (strain 2CP-1 / ATCC BAA-258) GN=A2cp1_2727 PE=3 SV=1

 Score = 60.5 bits (145), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 47/127 (37%), Positives = 66/127 (51%), Gaps = 6/127 (4%)

Query: 65  SLGVDLGLSRTGLALSKGF--CVRPLTVLKLRGEKLELQLL-EIAQREETDEFIIGLPKS 121
           +LGVDLG  R GLA++       R +T +  R E  +L  + E+A+  E    ++GLP +
Sbjct: 3   TLGVDLGRVRIGLAVADEILRTARAVTTVVRRTEAEDLAAIAEVARDYEVTRAVVGLPLN 62

Query: 122 WDGSETPQSNKVRSVAGRLAVRAAERGWRVYLLDEHRTSAEAVDRMINMGLSKSARQTKT 181
            DG+E P +   R  A RL    A  G  V L DE  +S EA  R+   GLS   ++ + 
Sbjct: 63  MDGTEGPSARLARGFAPRL---EAALGVPVELFDERLSSFEAESRLRARGLSAREQRGQV 119

Query: 182 DAYAAVV 188
           DA AA V
Sbjct: 120 DAEAAAV 126

Could be a nuclease that resolves Holliday junction intermediates in genetic recombination.

Anaeromyxobacter dehalogenans (strain 2CP-1 / ATCC BAA-258) (taxid: 455488)

EC: 3

EC: .

EC: 1

EC: .

EC: -

EC: .

EC: -

>sp|A7HDE0|RUVX_ANADF Putative Holliday junction resolvase OS=Anaeromyxobacter sp. (strain Fw109-5) GN=Anae109_2535 PE=3 SV=1

 Score = 58.9 bits (141), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 47/126 (37%), Positives = 66/126 (52%), Gaps = 6/126 (4%)

Query: 66  LGVDLGLSRTGLALSKGF--CVRPLTVLKLRGEKLELQLLEIAQRE-ETDEFIIGLPKSW 122
           LG+DLG +R GLAL+       RPL+V++ R  + +L  +    RE E    ++GLP + 
Sbjct: 4   LGLDLGRARIGLALADDVLRTARPLSVVRHRTREADLASIAATLREWEVGTAVVGLPLNM 63

Query: 123 DGSETPQSNKVRSVAGRLAVRAAERGWRVYLLDEHRTSAEAVDRMINMGLSKSARQTKTD 182
           DGSE   +   R+ A  LA RA   G  V L DE  ++ EA  R+   G S    + + D
Sbjct: 64  DGSEGASARYARAFAEELA-RAT--GVPVELFDERLSTFEAESRLREQGFSARELRGRVD 120

Query: 183 AYAAVV 188
           A AA V
Sbjct: 121 AEAAAV 126

Could be a nuclease that resolves Holliday junction intermediates in genetic recombination.

Anaeromyxobacter sp. (strain Fw109-5) (taxid: 404589)

EC: 3

EC: .

EC: 1

EC: .

EC: -

EC: .

EC: -

>sp|Q2RHZ7|RUVX_MOOTA Putative Holliday junction resolvase OS=Moorella thermoacetica (strain ATCC 39073) GN=Moth_1640 PE=3 SV=1

 Score = 58.2 bits (139), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 41/124 (33%), Positives = 66/124 (53%), Gaps = 6/124 (4%)

Query: 66  LGVDLGLSRTGLALSK--GFCVRPLTVLKLRGEKLELQLL-EIAQREETDEFIIGLPKSW 122
           +G+D+G    G+ALS   G+  + LT ++ R    +L  L E+ +R   +E ++GLP++ 
Sbjct: 4   MGLDVGTKTIGVALSDPLGWTAQGLTTIRRRNLAADLAALKELVRRYGVEELVVGLPRNM 63

Query: 123 DGSETPQSNKVRSVAGRLAVRAAERGWRVYLLDEHRTSAEAVDRMINMGLSKSARQTKTD 182
           +GS  PQ+  VR+ A  L    AE G  V+  DE  T+  A   ++   LS+  R+   D
Sbjct: 64  NGSLGPQAEAVRAFARHL---QAEVGLPVHFFDERLTTVAAGRVLLEADLSRRRRRQVID 120

Query: 183 AYAA 186
             AA
Sbjct: 121 QVAA 124

Could be a nuclease that resolves Holliday junction intermediates in genetic recombination.

Moorella thermoacetica (strain ATCC 39073) (taxid: 264732)

EC: 3

EC: .

EC: 1

EC: .

EC: -

EC: .

EC: -

>sp|A7MJR8|RUVX_CROS8 Putative Holliday junction resolvase OS=Cronobacter sakazakii (strain ATCC BAA-894) GN=ESA_00393 PE=3 SV=1

 Score = 55.8 bits (133), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 42/133 (31%), Positives = 67/133 (50%), Gaps = 6/133 (4%)

Query: 63  GFSLGVDLGLSRTGLALSKGFCV--RPLTVLKLRGEKLELQLLEIAQRE-ETDEFIIGLP 119
           G  L  D G    G+A+ +      RPLT +K +    +  L+E   +E + D+ I+GLP
Sbjct: 3   GTLLAFDFGTKSIGVAIGQRVTATARPLTAIKAQNGNPDWTLIEKLLKEWQPDDVIVGLP 62

Query: 120 KSWDGSETPQSNKVRSVAGRLAVRAAERGWRVYLLDEHRTSAEAVDRMINMGLSKSARQT 179
            + DG+E P + + R+ A RL  R    G +V L DE  ++ EA   +   G  ++  + 
Sbjct: 63  LNMDGTEQPLTARARTFANRLHGRF---GIKVTLHDERLSTVEARAGLFERGGFRALNKG 119

Query: 180 KTDAYAAVVRQES 192
             D+ +AVV  ES
Sbjct: 120 SVDSASAVVILES 132

Could be a nuclease that resolves Holliday junction intermediates in genetic recombination.

Cronobacter sakazakii (strain ATCC BAA-894) (taxid: 290339)

EC: 3

EC: .

EC: 1

EC: .

EC: -

EC: .

EC: -

>sp|Q3SFS3|RUVX_THIDA Putative Holliday junction resolvase OS=Thiobacillus denitrificans (strain ATCC 25259) GN=Tbd_2580 PE=3 SV=1

 Score = 55.5 bits (132), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 47/128 (36%), Positives = 64/128 (50%), Gaps = 8/128 (6%)

Query: 63  GFSLGVDLGLSRTGLA---LSKGFCVRPLTVLKLRGEKLELQLLE-IAQREETDEFIIGL 118
           G  L  DLGL RTG+A   L+ G    PLTV++       +  +E +A   +   F++GL
Sbjct: 8   GTVLAFDLGLKRTGVASGELAIGIA-HPLTVIQAESTDARMAAIEKLAAEWQPALFVLGL 66

Query: 119 PKSWDGSETPQSNKVRSVAGRLAVRAAERGWRVYLLDEHRTSAEAVDRMINMGLSKSARQ 178
           P   DGSE   +   R+ A RL  R  ER   V+L+DE  TSA A   +   G+     +
Sbjct: 67  PTRADGSENEMTRVARNFARRLESR-FERP--VFLIDERLTSATAESELHARGIHGKKNK 123

Query: 179 TKTDAYAA 186
             TDA AA
Sbjct: 124 ALTDAVAA 131

Could be a nuclease that resolves Holliday junction intermediates in genetic recombination.

Thiobacillus denitrificans (strain ATCC 25259) (taxid: 292415)

EC: 3

EC: .

EC: 1

EC: .

EC: -

EC: .

EC: -

>sp|C6C125|RUVX_DESAD Putative Holliday junction resolvase OS=Desulfovibrio salexigens (strain ATCC 14822 / DSM 2638 / NCIB 8403 / VKM B-1763) GN=Desal_1125 PE=3 SV=1

 Score = 55.1 bits (131), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 41/130 (31%), Positives = 65/130 (50%), Gaps = 6/130 (4%)

Query: 66  LGVDLGLSRTGLALSKG--FCVRPLTVL-KLRGEKLELQLLEIAQREETDEFIIGLPKSW 122
           L +D G  R GLA+S        P  V+ +   + +  +LLEI + E+  + +IGLP S 
Sbjct: 4   LSIDFGTKRVGLAISDPDQIFAFPYKVMERTTRDAMFSELLEIIENEKVGDIVIGLPLSL 63

Query: 123 DGSETPQSNKVRSVAGRLAVRAAERGWRVYLLDEHRTSAEAVDRMINMGLSKSARQTKTD 182
           DG +T  + +VR+ A  L  R       ++L+DE  +S  A D +   GL    R+   D
Sbjct: 64  DGEDTLTTRQVRNFAASLERRV---DLPIHLVDERLSSIAAEDELKEAGLWDRKRKKNLD 120

Query: 183 AYAAVVRQES 192
           + AA +  E+
Sbjct: 121 SQAAKIILET 130

Could be a nuclease that resolves Holliday junction intermediates in genetic recombination.

Desulfovibrio salexigens (strain ATCC 14822 / DSM 2638 / NCIB 8403 / VKM B-1763) (taxid: 526222)

EC: 3

EC: .

EC: 1

EC: .

EC: -

EC: .

EC: -

>sp|B7NI12|RUVX_ECO7I Putative Holliday junction resolvase OS=Escherichia coli O7:K1 (strain IAI39 / ExPEC) GN=yqgF PE=3 SV=1

 Score = 54.7 bits (130), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 41/133 (30%), Positives = 65/133 (48%), Gaps = 6/133 (4%)

Query: 63  GFSLGVDLGLSRTGLALSKGFC--VRPLTVLKLRGEKLELQLLEIAQRE-ETDEFIIGLP 119
           G  L  D G    G+A+ +      RPL  +K +    +  L+E   +E + DE I+GLP
Sbjct: 3   GTLLAFDFGTKSIGVAVGQRITGTARPLPAIKAQDGTPDWNLIERLLKEWQPDEIIVGLP 62

Query: 120 KSWDGSETPQSNKVRSVAGRLAVRAAERGWRVYLLDEHRTSAEAVDRMINMGLSKSARQT 179
            + DG+E P + + R  A R+  R    G  V L DE  ++ EA   +   G  ++  + 
Sbjct: 63  LNMDGTEQPLTARARKFANRIHGRF---GIEVKLHDERLSTVEARSGLFEQGGYRALNKG 119

Query: 180 KTDAYAAVVRQES 192
           K D+ +AV+  ES
Sbjct: 120 KVDSASAVIILES 132

Could be a nuclease that resolves Holliday junction intermediates in genetic recombination.

Escherichia coli O7:K1 (strain IAI39 / ExPEC) (taxid: 585057)

EC: 3

EC: .

EC: 1

EC: .

EC: -

EC: .

EC: -

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	204
224129716	254	predicted protein [Populus trichocarpa]	0.921	0.740	0.664	2e-63
297734533	679	unnamed protein product [Vitis vinifera]	0.740	0.222	0.769	5e-58
356506432	226	PREDICTED: putative Holliday junction re	0.740	0.668	0.730	2e-57
359489199	229	PREDICTED: putative Holliday junction re	0.715	0.637	0.780	3e-57
449431960	235	PREDICTED: putative Holliday junction re	0.720	0.625	0.729	1e-54
297844086	238	DNA binding protein [Arabidopsis lyrata	0.882	0.756	0.611	2e-53
255573708	239	hydrolase, acting on ester bonds, putati	0.911	0.778	0.623	1e-51
79317769	254	putative holliday junction resolvase [Ar	0.745	0.598	0.717	2e-49
414867730	235	TPA: holliday junction resolvase [Zea ma	0.686	0.595	0.683	2e-46
226500782	235	holliday junction resolvase [Zea mays] g	0.686	0.595	0.683	2e-46

>gi|224129716|ref|XP_002328785.1| predicted protein [Populus trichocarpa] gi|222839083|gb|EEE77434.1| predicted protein [Populus trichocarpa]

 Score =  247 bits (631), Expect = 2e-63,   Method: Compositional matrix adjust.
 Identities = 127/191 (66%), Positives = 146/191 (76%), Gaps = 3/191 (1%)

Query: 15  LIFPKFNDNRKFHLNRTRNFGQRIGALSSVEEFLPNATRRKKDSLWRGGFSLGVDLGLSR 74
           L+FP F  +    L+  +   +R+ AL S+ E  PNA RRK D LWRGGFSLGVDLGLSR
Sbjct: 42  LLFPNFTTS-SLQLDSDKPCRRRLRALLSIHEIPPNALRRKNDPLWRGGFSLGVDLGLSR 100

Query: 75  TGLALSKGFCVRPLTVLKLRGEKLELQLLEIAQREETDEFIIGLPKSWDGSETPQSNKVR 134
           +G+ALSKGF VRPLTVL+LRG+KLEL+LLEIA+ EE DEFIIGLPKSWDG ETPQSNKVR
Sbjct: 101 SGVALSKGFTVRPLTVLELRGQKLELRLLEIAENEEVDEFIIGLPKSWDGKETPQSNKVR 160

Query: 135 SVAGRLAVRAAERGWRVYLLDEHRTSAEAVDRMINMGLSKSARQTKTDAYAAVVRQESI- 193
           SVAGR AV AA RGWRVYL DEH TS EA +RMI+MGL+KS RQ K DAYAAV+  E   
Sbjct: 161 SVAGRFAVLAAHRGWRVYLQDEHGTSTEATNRMIDMGLNKSTRQKKVDAYAAVMVLERYF 220

Query: 194 -TFGHLMNIIF 203
            TFG    ++ 
Sbjct: 221 STFGEGTELVL 231

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297734533|emb|CBI16584.3| unnamed protein product [Vitis vinifera]

 Score =  229 bits (584), Expect = 5e-58,   Method: Compositional matrix adjust.
 Identities = 117/152 (76%), Positives = 128/152 (84%), Gaps = 1/152 (0%)

Query: 37  RIGALSSVEEFLPNATRRKKDSLWRGGFSLGVDLGLSRTGLALSKGFCVRPLTVLKLRGE 96
           RI A+S + E LPNA RRK +  W GGFSLGVDLG+SRTGLALSKGF VRPL+VLKLRG+
Sbjct: 485 RIRAVS-LNEILPNALRRKHNPHWTGGFSLGVDLGMSRTGLALSKGFSVRPLSVLKLRGQ 543

Query: 97  KLELQLLEIAQREETDEFIIGLPKSWDGSETPQSNKVRSVAGRLAVRAAERGWRVYLLDE 156
           KLELQLLEIA REE DEFIIGLP S DG ETPQSNKVRSVAGRLA RAAERGWRVYL DE
Sbjct: 544 KLELQLLEIAGREEVDEFIIGLPVSDDGKETPQSNKVRSVAGRLAARAAERGWRVYLQDE 603

Query: 157 HRTSAEAVDRMINMGLSKSARQTKTDAYAAVV 188
           H TS EA+  MI+MG SKSARQ + DAYAA++
Sbjct: 604 HGTSEEALSLMIDMGHSKSARQNRIDAYAAMM 635

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356506432|ref|XP_003521987.1| PREDICTED: putative Holliday junction resolvase-like [Glycine max]

 Score =  227 bits (579), Expect = 2e-57,   Method: Compositional matrix adjust.
 Identities = 111/152 (73%), Positives = 132/152 (86%), Gaps = 1/152 (0%)

Query: 37  RIGALSSVEEFLPNATRRKKDSLWRGGFSLGVDLGLSRTGLALSKGFCVRPLTVLKLRGE 96
           R+ AL+ ++E  PNA R+K++  WRGGFSLG+DLGL+RTGLALSKGF +RPLTVL+LRG+
Sbjct: 34  RVKALT-LDELPPNALRKKREPQWRGGFSLGLDLGLARTGLALSKGFSIRPLTVLELRGQ 92

Query: 97  KLELQLLEIAQREETDEFIIGLPKSWDGSETPQSNKVRSVAGRLAVRAAERGWRVYLLDE 156
           KLE+Q++ IA+ EE DEFIIGLPKS DG ETPQSNKVRSVAGRLAVRAAERGWRVYL DE
Sbjct: 93  KLEVQIINIAEEEEVDEFIIGLPKSSDGKETPQSNKVRSVAGRLAVRAAERGWRVYLQDE 152

Query: 157 HRTSAEAVDRMINMGLSKSARQTKTDAYAAVV 188
           H T+ EA DRMINM LSKS++Q K DAYAA++
Sbjct: 153 HGTTEEAKDRMINMSLSKSSQQKKLDAYAAMM 184

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359489199|ref|XP_002275849.2| PREDICTED: putative Holliday junction resolvase [Vitis vinifera]

 Score =  226 bits (577), Expect = 3e-57,   Method: Compositional matrix adjust.
 Identities = 114/146 (78%), Positives = 124/146 (84%)

Query: 43  SVEEFLPNATRRKKDSLWRGGFSLGVDLGLSRTGLALSKGFCVRPLTVLKLRGEKLELQL 102
           S+ E LPNA RRK +  W GGFSLGVDLG+SRTGLALSKGF VRPL+VLKLRG+KLELQL
Sbjct: 40  SLNEILPNALRRKHNPHWTGGFSLGVDLGMSRTGLALSKGFSVRPLSVLKLRGQKLELQL 99

Query: 103 LEIAQREETDEFIIGLPKSWDGSETPQSNKVRSVAGRLAVRAAERGWRVYLLDEHRTSAE 162
           LEIA REE DEFIIGLP S DG ETPQSNKVRSVAGRLA RAAERGWRVYL DEH TS E
Sbjct: 100 LEIAGREEVDEFIIGLPVSDDGKETPQSNKVRSVAGRLAARAAERGWRVYLQDEHGTSEE 159

Query: 163 AVDRMINMGLSKSARQTKTDAYAAVV 188
           A+  MI+MG SKSARQ + DAYAA++
Sbjct: 160 ALSLMIDMGHSKSARQNRIDAYAAMM 185

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449431960|ref|XP_004133768.1| PREDICTED: putative Holliday junction resolvase-like [Cucumis sativus] gi|449522992|ref|XP_004168509.1| PREDICTED: putative Holliday junction resolvase-like [Cucumis sativus]

 Score =  218 bits (556), Expect = 1e-54,   Method: Compositional matrix adjust.
 Identities = 108/148 (72%), Positives = 124/148 (83%), Gaps = 1/148 (0%)

Query: 41  LSSVEEFLPNATRRKKDSLWRGGFSLGVDLGLSRTGLALSKGFCVRPLTVLKLRGEKLEL 100
           +SS+E   PNA RRK D  WRGGFSLGVDLG SRTGLALSKGF  RPLTVL+LRG+KLE 
Sbjct: 50  ISSIE-LPPNALRRKLDPHWRGGFSLGVDLGTSRTGLALSKGFSTRPLTVLELRGQKLEA 108

Query: 101 QLLEIAQREETDEFIIGLPKSWDGSETPQSNKVRSVAGRLAVRAAERGWRVYLLDEHRTS 160
           +L+EIA++EE DEFIIGLPKS DG ETPQSNK+RS+AGR+A RAAERGWRVYL DEH T+
Sbjct: 109 KLIEIAEQEEADEFIIGLPKSCDGKETPQSNKIRSIAGRVAARAAERGWRVYLYDEHGTT 168

Query: 161 AEAVDRMINMGLSKSARQTKTDAYAAVV 188
           AEA   MI+ GL+KS RQ K DAYAA++
Sbjct: 169 AEAESHMISRGLNKSTRQKKIDAYAAMM 196

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297844086|ref|XP_002889924.1| DNA binding protein [Arabidopsis lyrata subsp. lyrata] gi|297335766|gb|EFH66183.1| DNA binding protein [Arabidopsis lyrata subsp. lyrata]

 Score =  214 bits (545), Expect = 2e-53,   Method: Compositional matrix adjust.
 Identities = 121/198 (61%), Positives = 148/198 (74%), Gaps = 18/198 (9%)

Query: 1   MCSLQS----------QHFLNSPLLIFPKFNDNRKFHLNRTRNFGQRIGALSSVEEFLPN 50
           MCSL S          Q ++N+PL+  P+ +         +RN    + A +S++E  PN
Sbjct: 1   MCSLHSLSSVAISFRTQKYVNTPLV--PRLSSIG------SRNNPLPLRAATSIDEIPPN 52

Query: 51  ATRRKKDSLWRGGFSLGVDLGLSRTGLALSKGFCVRPLTVLKLRGEKLELQLLEIAQREE 110
           A RRK D  WRGGFSLGVDLGLSRTG+A+SKG+ V+PLTVLK RG+KLE +LLEIA+ EE
Sbjct: 53  AVRRKIDRDWRGGFSLGVDLGLSRTGVAISKGYTVKPLTVLKSRGQKLETRLLEIAEEEE 112

Query: 111 TDEFIIGLPKSWDGSETPQSNKVRSVAGRLAVRAAERGWRVYLLDEHRTSAEAVDRMINM 170
            DEFIIGLP+S DG ET QSNK+RSVAGRLAV+AAERGWRVY+ DEH T++EA DRMI M
Sbjct: 113 VDEFIIGLPRSSDGKETIQSNKIRSVAGRLAVQAAERGWRVYVFDEHGTTSEASDRMIVM 172

Query: 171 GLSKSARQTKTDAYAAVV 188
           GLSKS RQ ++DAYAAV+
Sbjct: 173 GLSKSERQNRSDAYAAVI 190

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255573708|ref|XP_002527775.1| hydrolase, acting on ester bonds, putative [Ricinus communis] gi|223532810|gb|EEF34585.1| hydrolase, acting on ester bonds, putative [Ricinus communis]

 Score =  207 bits (528), Expect = 1e-51,   Method: Compositional matrix adjust.
 Identities = 124/199 (62%), Positives = 142/199 (71%), Gaps = 13/199 (6%)

Query: 1   MCSLQSQHFLNS---PLLI--FPKFNDNRKF------HLNRTRNFGQRIGALSSVEEFLP 49
           MCSL+S    ++   PL I   PK  +   F       +    NF  R  A+ S EE  P
Sbjct: 3   MCSLKSFCIQSTQLFPLSINSLPKVINTSAFLRQSLPQICIHNNFKLR--AVLSTEEVPP 60

Query: 50  NATRRKKDSLWRGGFSLGVDLGLSRTGLALSKGFCVRPLTVLKLRGEKLELQLLEIAQRE 109
           NA RR+ D  WRGGFSLG+DLGLSRTGLA+SKGF  +PLTVL+LRG+KLE +LLEIA+ E
Sbjct: 61  NAARRRSDPQWRGGFSLGIDLGLSRTGLAISKGFSFKPLTVLELRGQKLETRLLEIAEDE 120

Query: 110 ETDEFIIGLPKSWDGSETPQSNKVRSVAGRLAVRAAERGWRVYLLDEHRTSAEAVDRMIN 169
           E DEFIIGLPKSWDG ET Q NKVRSVAGR+AVRAAERGWRVYL DEH TS +A   MIN
Sbjct: 121 EADEFIIGLPKSWDGKETSQCNKVRSVAGRIAVRAAERGWRVYLQDEHGTSTDATYWMIN 180

Query: 170 MGLSKSARQTKTDAYAAVV 188
           +GLSK ARQ   DAYAAV+
Sbjct: 181 VGLSKGARQKSIDAYAAVM 199

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|79317769|ref|NP_001031028.1| putative holliday junction resolvase [Arabidopsis thaliana] gi|332190735|gb|AEE28856.1| putative holliday junction resolvase [Arabidopsis thaliana]

 Score =  200 bits (509), Expect = 2e-49,   Method: Compositional matrix adjust.
 Identities = 109/152 (71%), Positives = 130/152 (85%)

Query: 40  ALSSVEEFLPNATRRKKDSLWRGGFSLGVDLGLSRTGLALSKGFCVRPLTVLKLRGEKLE 99
           A++S++E  PNA RRK D  WRGGFSLGVDLGLSRTG+A+SKG+ V+PLTVLK RG+KLE
Sbjct: 58  AVTSIDEIPPNAVRRKIDRNWRGGFSLGVDLGLSRTGIAISKGYTVKPLTVLKSRGQKLE 117

Query: 100 LQLLEIAQREETDEFIIGLPKSWDGSETPQSNKVRSVAGRLAVRAAERGWRVYLLDEHRT 159
            +LLEIA+ EE DEFIIGLP+S DG ET QSNK+RSVAGRLA++AAERGWRVY+ DEH T
Sbjct: 118 TRLLEIAEEEEADEFIIGLPRSSDGKETIQSNKIRSVAGRLAIQAAERGWRVYVFDEHGT 177

Query: 160 SAEAVDRMINMGLSKSARQTKTDAYAAVVRQE 191
           ++EA DRMI MGLSKS RQ ++DAYAAV+  E
Sbjct: 178 TSEASDRMIVMGLSKSERQNRSDAYAAVILLE 209

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|414867730|tpg|DAA46287.1| TPA: holliday junction resolvase [Zea mays]

 Score =  191 bits (485), Expect = 2e-46,   Method: Compositional matrix adjust.
 Identities = 97/142 (68%), Positives = 117/142 (82%), Gaps = 2/142 (1%)

Query: 49  PNATRRKKDSLWRGG-FSLGVDLGLSRTGLALSKGFCV-RPLTVLKLRGEKLELQLLEIA 106
           PNA RR +D LW GG FSLGVDLG +RTGLA+ +G    RPLTVL+LRG+KLEL LL++A
Sbjct: 57  PNARRRGRDPLWHGGGFSLGVDLGDARTGLAIGRGITFPRPLTVLRLRGQKLELALLDVA 116

Query: 107 QREETDEFIIGLPKSWDGSETPQSNKVRSVAGRLAVRAAERGWRVYLLDEHRTSAEAVDR 166
           +++E DE IIGLP S DGSETPQSNKVRSV GRLAV+AA+RG RVYL DE+ TS +A+D 
Sbjct: 117 RQQEADELIIGLPVSADGSETPQSNKVRSVVGRLAVQAAQRGLRVYLQDEYGTSTDALDY 176

Query: 167 MINMGLSKSARQTKTDAYAAVV 188
           MI+ G+ KSAR TK+DAYAAV+
Sbjct: 177 MISRGVKKSARDTKSDAYAAVM 198

Source: Zea mays

Species: Zea mays

Genus: Zea

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|226500782|ref|NP_001149481.1| holliday junction resolvase [Zea mays] gi|195627468|gb|ACG35564.1| holliday junction resolvase [Zea mays]

 Score =  191 bits (484), Expect = 2e-46,   Method: Compositional matrix adjust.
 Identities = 97/142 (68%), Positives = 117/142 (82%), Gaps = 2/142 (1%)

Query: 49  PNATRRKKDSLWRGG-FSLGVDLGLSRTGLALSKGFCV-RPLTVLKLRGEKLELQLLEIA 106
           PNA RR +D LW GG FSLGVDLG +RTGLA+ +G    RPLTVL+LRG+KLEL LL++A
Sbjct: 57  PNARRRGRDPLWHGGGFSLGVDLGDARTGLAIGRGITFPRPLTVLRLRGQKLELALLDVA 116

Query: 107 QREETDEFIIGLPKSWDGSETPQSNKVRSVAGRLAVRAAERGWRVYLLDEHRTSAEAVDR 166
           +++E DE IIGLP S DGSETPQSNKVRSV GRLAV+AA+RG RVYL DE+ TS +A+D 
Sbjct: 117 RQQEADELIIGLPVSADGSETPQSNKVRSVVGRLAVQAAQRGLRVYLQDEYGTSTDALDY 176

Query: 167 MINMGLSKSARQTKTDAYAAVV 188
           MI+ G+ KSAR TK+DAYAAV+
Sbjct: 177 MISRGVKKSARDTKSDAYAAVM 198

Source: Zea mays

Species: Zea mays

Genus: Zea

Family: Poaceae

Order: Poales

Class: Liliopsida

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	204
TAIR|locus:1009023117	254	AT1G12244 [Arabidopsis thalian	0.911	0.732	0.614	4.3e-54
UNIPROTKB|P0A8I1	138	yqgF [Escherichia coli K-12 (t	0.622	0.920	0.300	2.9e-09
UNIPROTKB|Q0BZU8	151	HNE_2300 "Putative Holliday ju	0.637	0.860	0.330	7.6e-09
UNIPROTKB|Q8EBZ8	141	SO_3347 "Putative Holliday jun	0.632	0.914	0.281	9.7e-09
TIGR_CMR|SO_3347	141	SO_3347 "conserved hypothetica	0.632	0.914	0.281	9.7e-09
UNIPROTKB|Q81LK2	137	BAS4282 "Putative Holliday jun	0.583	0.868	0.286	4e-07
TIGR_CMR|BA_4614	137	BA_4614 "conserved hypothetica	0.583	0.868	0.286	4e-07
UNIPROTKB|Q48P91	146	PSPPH_0475 "Putative Holliday	0.651	0.910	0.281	2e-06
UNIPROTKB|Q87VA1	146	PSPTO_5038 "Putative Holliday	0.651	0.910	0.281	2e-06
UNIPROTKB|Q3AEN4	138	CHY_0542 "Putative Holliday ju	0.588	0.869	0.277	4.5e-06

TAIR|locus:1009023117 AT1G12244 [Arabidopsis thaliana (taxid:3702)]

 Score = 559 (201.8 bits), Expect = 4.3e-54, P = 4.3e-54
 Identities = 121/197 (61%), Positives = 146/197 (74%)

Query:     1 MCSLQSQHFLNSPLLIF--PKFNDNRKFHLNRTRNFGQRI----GALSSVEEFLPNATRR 54
             MCSL   H  +S  + F   K+ +    H  R    G R      A++S++E  PNA RR
Sbjct:    18 MCSL---HSFSSVAISFRTQKYVNTSLVH--RLSPIGYRNYPLPWAVTSIDEIPPNAVRR 72

Query:    55 KKDSLWRGGFSLGVDLGLSRTGLALSKGFCVRPLTVLKLRGEKLELQLLEIAQREETDEF 114
             K D  WRGGFSLGVDLGLSRTG+A+SKG+ V+PLTVLK RG+KLE +LLEIA+ EE DEF
Sbjct:    73 KIDRNWRGGFSLGVDLGLSRTGIAISKGYTVKPLTVLKSRGQKLETRLLEIAEEEEADEF 132

Query:   115 IIGLPKSWDGSETPQSNKVRSVAGRLAVRAAERGWRVYLLDEHRTSAEAVDRMINMGLSK 174
             IIGLP+S DG ET QSNK+RSVAGRLA++AAERGWRVY+ DEH T++EA DRMI MGLSK
Sbjct:   133 IIGLPRSSDGKETIQSNKIRSVAGRLAIQAAERGWRVYVFDEHGTTSEASDRMIVMGLSK 192

Query:   175 SARQTKTDAYAAVVRQE 191
             S RQ ++DAYAAV+  E
Sbjct:   193 SERQNRSDAYAAVILLE 209

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0006139 "nucleobase-containing compound metabolic process" evidence=IEA

GO:0006281 "DNA repair" evidence=IEA

GO:0006310 "DNA recombination" evidence=IEA

GO:0006974 "response to DNA damage stimulus" evidence=IEA

GO:0009507 "chloroplast" evidence=ISM

GO:0016788 "hydrolase activity, acting on ester bonds" evidence=IEA

UNIPROTKB|P0A8I1 yqgF [Escherichia coli K-12 (taxid:83333)]

 Score = 136 (52.9 bits), Expect = 2.9e-09, P = 2.9e-09
 Identities = 40/133 (30%), Positives = 65/133 (48%)

Query:    63 GFSLGVDLGLSRTGLALSKGFC--VRPLTVLKLRGEKLELQLLEIAQRE-ETDEFIIGLP 119
             G  L  D G    G+A+ +      RPL  +K +    +  ++E   +E + DE I+GLP
Sbjct:     3 GTLLAFDFGTKSIGVAVGQRITGTARPLPAIKAQDGTPDWNIIERLLKEWQPDEIIVGLP 62

Query:   120 KSWDGSETPQSNKVRSVAGRLAVRAAERGWRVYLLDEHRTSAEAVDRMINMGLSKSARQT 179
              + DG+E P + + R  A R+  R    G  V L DE  ++ EA   +   G  ++  + 
Sbjct:    63 LNMDGTEQPLTARARKFANRIHGRF---GVEVKLHDERLSTVEARSGLFEQGGYRALNKG 119

Query:   180 KTDAYAAVVRQES 192
             K D+ +AV+  ES
Sbjct:   120 KVDSASAVIILES 132

GO:0003674 "molecular_function" evidence=ND

GO:0008150 "biological_process" evidence=ND

GO:0016788 "hydrolase activity, acting on ester bonds" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0090305 "nucleic acid phosphodiester bond hydrolysis" evidence=IEA

GO:0031564 "transcription antitermination" evidence=IGI;IMP

GO:0016787 "hydrolase activity" evidence=IEA

GO:0006974 "response to DNA damage stimulus" evidence=IEA

GO:0006281 "DNA repair" evidence=IEA

GO:0006139 "nucleobase-containing compound metabolic process" evidence=ISS

GO:0005737 "cytoplasm" evidence=IEA

GO:0004518 "nuclease activity" evidence=IEA;ISS

GO:0006310 "DNA recombination" evidence=IEA

UNIPROTKB|Q0BZU8 HNE_2300 "Putative Holliday junction resolvase" [Hyphomonas neptunium ATCC 15444 (taxid:228405)]

 Score = 132 (51.5 bits), Expect = 7.6e-09, P = 7.6e-09
 Identities = 46/139 (33%), Positives = 70/139 (50%)

Query:    61 RGGFSLGVDLGLSRTGLALSKGF--CVRPL-TVLKLR-GEKLELQLLEIAQREETDEFII 116
             R G  LG+D G +  G+A +        P+ T+LK +    LE +LL I         I+
Sbjct:    11 REGVLLGIDPGTATIGVAATDRIRMMASPVETILKKKLAPSLE-RLLHIYDERAAVGLIV 69

Query:   117 GLPKSWDGSETPQSNKVRSVAGRLAVRAAERGWRVYLLDEHRTSAEAVDRMINMGLSKSA 176
             GLP + DGS  P++  VR++   L      R   V   DE  +SAEA D M   G ++  
Sbjct:    70 GLPLNVDGSMGPRAQSVRTLVSSLL---KVRDLPVTFQDERYSSAEAGDIMRAAGATRRN 126

Query:   177 RQTKTDAYAA-VVRQESIT 194
             R+ + DA AA V+ Q++++
Sbjct:   127 REARIDASAAAVILQDALS 145

GO:0003674 "molecular_function" evidence=ND

GO:0005575 "cellular_component" evidence=ND

GO:0008150 "biological_process" evidence=ND

UNIPROTKB|Q8EBZ8 SO_3347 "Putative Holliday junction resolvase" [Shewanella oneidensis MR-1 (taxid:211586)]

 Score = 131 (51.2 bits), Expect = 9.7e-09, P = 9.7e-09
 Identities = 38/135 (28%), Positives = 68/135 (50%)

Query:    66 LGVDLGLSRTGLALSKGFCVR--PLTVLK-LRGEKLELQLLEIAQREETDEFIIGLPKSW 122
             LG D G    G+A+ +       PL  +K + G     ++ ++ Q  + D  ++GLP + 
Sbjct:     7 LGFDFGTKSIGVAVGQQITASATPLLSIKAVDGIPNWEEIAKLIQEWQPDLVVVGLPLNM 66

Query:   123 DGSETPQSNKVRSVAGRLAVRAAERGWRVYLLDEHRTSAEAVDRMINMGLSKSARQTKTD 182
             DG+E   +++ R  A RL    A+ G +++  DE  T+ +A  R+  +G  K+  + + D
Sbjct:    67 DGTEQEMTHRARKFANRLN---AKFGVKIFTQDERLTTTDAKARLFELGGYKALTKGQVD 123

Query:   183 AYAAVVRQESITFGH 197
             A +AV+  ES    H
Sbjct:   124 AVSAVLIIESYFENH 138

GO:0003674 "molecular_function" evidence=ND

GO:0005575 "cellular_component" evidence=ND

GO:0008150 "biological_process" evidence=ND

TIGR_CMR|SO_3347 SO_3347 "conserved hypothetical protein TIGR00250" [Shewanella oneidensis MR-1 (taxid:211586)]

 Score = 131 (51.2 bits), Expect = 9.7e-09, P = 9.7e-09
 Identities = 38/135 (28%), Positives = 68/135 (50%)

Query:    66 LGVDLGLSRTGLALSKGFCVR--PLTVLK-LRGEKLELQLLEIAQREETDEFIIGLPKSW 122
             LG D G    G+A+ +       PL  +K + G     ++ ++ Q  + D  ++GLP + 
Sbjct:     7 LGFDFGTKSIGVAVGQQITASATPLLSIKAVDGIPNWEEIAKLIQEWQPDLVVVGLPLNM 66

Query:   123 DGSETPQSNKVRSVAGRLAVRAAERGWRVYLLDEHRTSAEAVDRMINMGLSKSARQTKTD 182
             DG+E   +++ R  A RL    A+ G +++  DE  T+ +A  R+  +G  K+  + + D
Sbjct:    67 DGTEQEMTHRARKFANRLN---AKFGVKIFTQDERLTTTDAKARLFELGGYKALTKGQVD 123

Query:   183 AYAAVVRQESITFGH 197
             A +AV+  ES    H
Sbjct:   124 AVSAVLIIESYFENH 138

GO:0008150 "biological_process" evidence=ND

GO:0003674 "molecular_function" evidence=ND

GO:0005575 "cellular_component" evidence=ND

UNIPROTKB|Q81LK2 BAS4282 "Putative Holliday junction resolvase" [Bacillus anthracis (taxid:1392)]

 Score = 117 (46.2 bits), Expect = 4.0e-07, P = 4.0e-07
 Identities = 37/129 (28%), Positives = 69/129 (53%)

Query:    66 LGVDLGLSRTGLALSK--GFCVRPLTVLKLRGEKLEL---QLLEIAQREETDEFIIGLPK 120
             LG+D+G    G+A+S   G+  + L  +K+  E+ +    ++ E+ ++ + D+ ++GLPK
Sbjct:     4 LGLDVGTKTVGVAISDEMGWTAQGLETIKINEERGQFGFDRISELVKQYDVDKIVVGLPK 63

Query:   121 SWDGSETPQSNKVRSVAGRLAVRAAERGWRVYLLDEHRTSAEAVDRM-INMGLSKSARQT 179
             + +G+  P+    +  A  L  R   +   V + DE R S  A +R+ I+  +S+  R+ 
Sbjct:    64 NMNGTIGPRGEACQQFAENL--RELLQ-LDVVMWDE-RLSTMAAERLLISADVSRKKRKQ 119

Query:   180 KTDAYAAVV 188
               D  AAVV
Sbjct:   120 VIDKMAAVV 128

GO:0003674 "molecular_function" evidence=ND

GO:0005575 "cellular_component" evidence=ND

GO:0008150 "biological_process" evidence=ND

TIGR_CMR|BA_4614 BA_4614 "conserved hypothetical protein TIGR00250" [Bacillus anthracis str. Ames (taxid:198094)]

 Score = 117 (46.2 bits), Expect = 4.0e-07, P = 4.0e-07
 Identities = 37/129 (28%), Positives = 69/129 (53%)

Query:    66 LGVDLGLSRTGLALSK--GFCVRPLTVLKLRGEKLEL---QLLEIAQREETDEFIIGLPK 120
             LG+D+G    G+A+S   G+  + L  +K+  E+ +    ++ E+ ++ + D+ ++GLPK
Sbjct:     4 LGLDVGTKTVGVAISDEMGWTAQGLETIKINEERGQFGFDRISELVKQYDVDKIVVGLPK 63

Query:   121 SWDGSETPQSNKVRSVAGRLAVRAAERGWRVYLLDEHRTSAEAVDRM-INMGLSKSARQT 179
             + +G+  P+    +  A  L  R   +   V + DE R S  A +R+ I+  +S+  R+ 
Sbjct:    64 NMNGTIGPRGEACQQFAENL--RELLQ-LDVVMWDE-RLSTMAAERLLISADVSRKKRKQ 119

Query:   180 KTDAYAAVV 188
               D  AAVV
Sbjct:   120 VIDKMAAVV 128

GO:0003674 "molecular_function" evidence=ND

GO:0005575 "cellular_component" evidence=ND

GO:0008150 "biological_process" evidence=ND

UNIPROTKB|Q48P91 PSPPH_0475 "Putative Holliday junction resolvase" [Pseudomonas syringae pv. phaseolicola 1448A (taxid:264730)]

 Score = 111 (44.1 bits), Expect = 2.0e-06, P = 2.0e-06
 Identities = 40/142 (28%), Positives = 64/142 (45%)

Query:    66 LGVDLGLSRTGLALSKGFC--VRPLTVLKLRGEKLELQLLEIAQRE-ETDEFIIGLPKSW 122
             LG+D G  + G+A+ +      R L  LK +    +   ++    E + D  ++GLP + 
Sbjct:     8 LGIDYGTKQIGVAVGQAITGQARELCTLKAQNGVPDWDKVQALINEWKPDAIVVGLPLNM 67

Query:   123 DGSETPQSNKVRSVAGRLAVRAAERGWRVYLLDEHRTSAEAV-DRMINMGLSKSARQTKT 181
             DG+ +  S +    + +L  R    G  VY  DE  T+ EA  +RM   G   S R    
Sbjct:    68 DGTPSDMSARAEKFSRKLNGRF---GVTVYTHDERLTTFEAKGERMARGGQKGSYRNNPV 124

Query:   182 DAYAAVVRQESITFGH--LMNI 201
             DA AA +  +     H  L+N+
Sbjct:   125 DAIAAALLLQGWLDEHPELLNV 146

GO:0003674 "molecular_function" evidence=ND

GO:0005575 "cellular_component" evidence=ND

GO:0008150 "biological_process" evidence=ND

UNIPROTKB|Q87VA1 PSPTO_5038 "Putative Holliday junction resolvase" [Pseudomonas syringae pv. tomato str. DC3000 (taxid:223283)]

 Score = 111 (44.1 bits), Expect = 2.0e-06, P = 2.0e-06
 Identities = 40/142 (28%), Positives = 64/142 (45%)

Query:    66 LGVDLGLSRTGLALSKGFC--VRPLTVLKLRGEKLELQLLEIAQRE-ETDEFIIGLPKSW 122
             LG+D G  + G+A+ +      R L  LK +    +   ++    E + D  ++GLP + 
Sbjct:     8 LGIDYGTKQIGVAVGQAITGQARELCTLKAQNGVPDWDKVQALINEWKPDAIVVGLPLNM 67

Query:   123 DGSETPQSNKVRSVAGRLAVRAAERGWRVYLLDEHRTSAEAV-DRMINMGLSKSARQTKT 181
             DG+ +  S +    + +L  R    G  VY  DE  T+ EA  +RM   G   S R    
Sbjct:    68 DGTPSEMSARAEKFSRKLNGRF---GVTVYTHDERLTTFEAKGERMARGGQKGSYRDNPV 124

Query:   182 DAYAAVVRQESITFGH--LMNI 201
             DA AA +  +     H  L+N+
Sbjct:   125 DAIAAALLLQGWLDEHPELLNV 146

GO:0003674 "molecular_function" evidence=ND

GO:0005575 "cellular_component" evidence=ND

GO:0008150 "biological_process" evidence=ND

UNIPROTKB|Q3AEN4 CHY_0542 "Putative Holliday junction resolvase" [Carboxydothermus hydrogenoformans Z-2901 (taxid:246194)]

 Score = 108 (43.1 bits), Expect = 4.5e-06, P = 4.5e-06
 Identities = 35/126 (27%), Positives = 62/126 (49%)

Query:    66 LGVDLGLSRTGLALSK--GFCVRPLTVLKLRGEKLELQ-LLEIAQREETDEFIIGLPKSW 122
             LG+D+G  + G+ALS   G   + LTV+     K +L+ + +I       E +IG P++ 
Sbjct:     4 LGLDVGDKKIGVALSDELGLTAQGLTVIYRTSLKKDLEEIKKIIDLHHVTEVVIGYPRNM 63

Query:   123 DGSETPQSNKVRSVAGRLAVRAAERGWRVYLLDEHRTSAEAVDRMINMGLSKSARQTKTD 182
             +G+  P++  V+  A  L       G +    DE  ++ EA   +I+  +S+  R+   D
Sbjct:    64 NGTAGPRAELVKRFARELYKFT---GIKPVFWDERLSTVEAEKLLISGDISRRKRKKVID 120

Query:   183 AYAAVV 188
               AA +
Sbjct:   121 KLAATL 126

GO:0003674 "molecular_function" evidence=ND

GO:0005575 "cellular_component" evidence=ND

GO:0008150 "biological_process" evidence=ND

---

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	204
pfam03652	134	pfam03652, UPF0081, Uncharacterized protein family	2e-25
PRK00109	138	PRK00109, PRK00109, Holliday junction resolvase-li	4e-18
COG0816	141	COG0816, COG0816, Predicted endonuclease involved	1e-17
TIGR00250	130	TIGR00250, RNAse_H_YqgF, RNAse H-fold protein YqgF	3e-12
smart00732	99	smart00732, YqgFc, Likely ribonuclease with RNase	6e-11

>gnl|CDD|217659 pfam03652, UPF0081, Uncharacterized protein family (UPF0081)

 Score = 95.6 bits (239), Expect = 2e-25
 Identities = 43/126 (34%), Positives = 67/126 (53%), Gaps = 6/126 (4%)

Query: 66  LGVDLGLSRTGLALSKGFC--VRPLTVLKLRGEKLEL-QLLEIAQREETDEFIIGLPKSW 122
           LG+D+G  R G+A+S        PL  ++ +    +L +L E+ +  + D  ++GLP + 
Sbjct: 4   LGLDVGTKRIGVAISDPLGILASPLETIRRKNGNPDLEELAELIKEWQPDGIVVGLPLNM 63

Query: 123 DGSETPQSNKVRSVAGRLAVRAAERGWRVYLLDEHRTSAEAVDRMINMGLSKSARQTKTD 182
           DGSE   + +VR  A RL  R    G  V L+DE  T+ EA   +   GLS+  R+   D
Sbjct: 64  DGSEGEMTKRVRKFARRLKKR---FGLPVELVDERLTTVEAERILREAGLSRKKRKEVVD 120

Query: 183 AYAAVV 188
           + AAV+
Sbjct: 121 SIAAVI 126

Length = 134

>gnl|CDD|234639 PRK00109, PRK00109, Holliday junction resolvase-like protein; Reviewed

 Score = 76.7 bits (190), Expect = 4e-18
 Identities = 40/126 (31%), Positives = 68/126 (53%), Gaps = 6/126 (4%)

Query: 66  LGVDLGLSRTGLALS--KGFCVRPLTVLKLRGEKLEL-QLLEIAQREETDEFIIGLPKSW 122
           LG+D+G  R G+A+S   G   +PL  +K      +  +L ++ +  + D  ++GLP + 
Sbjct: 7   LGLDVGTKRIGVAVSDPLGGTAQPLETIKRNNGTPDWDRLEKLIKEWQPDGLVVGLPLNM 66

Query: 123 DGSETPQSNKVRSVAGRLAVRAAERGWRVYLLDEHRTSAEAVDRMINMGLSKSARQTKTD 182
           DG+E P++ + R  A RL  R    G  V L+DE  ++ EA   + ++G  K  R+   D
Sbjct: 67  DGTEGPRTERARKFANRLEGR---FGLPVVLVDERLSTVEAERALADVGSRKKLRKGVID 123

Query: 183 AYAAVV 188
           + AAV+
Sbjct: 124 SLAAVI 129

Length = 138

>gnl|CDD|223886 COG0816, COG0816, Predicted endonuclease involved in recombination (possible Holliday junction resolvase in Mycoplasmas and B

 Score = 75.3 bits (186), Expect = 1e-17
 Identities = 41/128 (32%), Positives = 64/128 (50%), Gaps = 9/128 (7%)

Query: 66  LGVDLGLSRTGLALS--KGFCVRPLTVLKLRGEKLEL---QLLEIAQREETDEFIIGLPK 120
           L +D+G  R G+A+S   G    PL  +K R          LL++ +  + D  ++GLP 
Sbjct: 5   LALDVGTKRIGVAVSDILGSLASPLETIK-RKNGKPQDFNALLKLVKEYQVDTVVVGLPL 63

Query: 121 SWDGSETPQSNKVRSVAGRLAVRAAERGWRVYLLDEHRTSAEAVDRMINMGLSKSARQTK 180
           + DG+E P++   R  A RL  R       V L DE  ++ EA   +I  G+S+  R+  
Sbjct: 64  NMDGTEGPRAELARKFAERLKKRF---NLPVVLWDERLSTVEAERMLIEAGVSRKKRKGV 120

Query: 181 TDAYAAVV 188
            D+ AAV+
Sbjct: 121 IDSLAAVL 128

subtilis) [DNA replication, recombination, and repair]. Length = 141

>gnl|CDD|129352 TIGR00250, RNAse_H_YqgF, RNAse H-fold protein YqgF

 Score = 61.0 bits (148), Expect = 3e-12
 Identities = 38/130 (29%), Positives = 65/130 (50%), Gaps = 6/130 (4%)

Query: 66  LGVDLGLSRTGLALSK--GFCVRPLTVLKLR-GEKLELQLLEIAQREETDEFIIGLPKSW 122
           LG+D G    G+A     G+  + +  +K + GE    ++ E+ +    D+ ++GLP + 
Sbjct: 1   LGLDFGTKSIGVAGQDITGWTAQGIPTIKAQDGEPDWSRIEELLKEWTPDKIVVGLPLNM 60

Query: 123 DGSETPQSNKVRSVAGRLAVRAAERGWRVYLLDEHRTSAEAVDRMINMGLSKSARQTKTD 182
           DG+E P + + +  A RL  R    G  V L DE  ++ EA   +   G  ++ R+ K D
Sbjct: 61  DGTEGPLTERAQKFANRLEGRF---GVPVVLWDERLSTVEAESGLFARGGFRALRKGKID 117

Query: 183 AYAAVVRQES 192
             AAV+  +S
Sbjct: 118 KAAAVIILQS 127

This protein family, which exhibits an RNAse H fold in crystal structure, has been proposed as a putative Holliday junction resolvase, an alternate to RuvC [Unknown function, General]. Length = 130

>gnl|CDD|128971 smart00732, YqgFc, Likely ribonuclease with RNase H fold

 Score = 56.8 bits (138), Expect = 6e-11
 Identities = 26/101 (25%), Positives = 46/101 (45%), Gaps = 8/101 (7%)

Query: 66  LGVDLGLSRTGLALS--KGFCVRPLTVLKL-RGEKLELQLLEIAQREETDEFIIGLPKSW 122
           LG+D G    G+A+    G    PL V+     E    +L ++ ++ + D  +IGLP + 
Sbjct: 4   LGLDPGRKGIGVAVVDETGKLADPLEVIPRTNKEADAARLKKLIKKYQPDLIVIGLPLNM 63

Query: 123 DGSETPQSNKVRSVAGRLAVRAAERGWRVYLLDEHRTSAEA 163
           +G+ + ++    + A  L  R       V L+DE   +  A
Sbjct: 64  NGTASRETE--EAFAELLKER---FNLPVVLVDERLATVYA 99

YqgF proteins are likely to function as an alternative to RuvC in most bacteria, and could be the principal holliday junction resolvases in low-GC Gram-positive bacteria. In Spt6p orthologues, the catalytic residues are substituted indicating that they lack enzymatic functions. Length = 99

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	204
PRK00109	138	Holliday junction resolvase-like protein; Reviewed	100.0
PF03652	135	UPF0081: Uncharacterised protein family (UPF0081);	100.0
COG0816	141	Predicted endonuclease involved in recombination (	100.0
TIGR00250	130	RNAse_H_YqgF RNAse H-fold protein YqgF. This prote	100.0
smart00732	99	YqgFc Likely ribonuclease with RNase H fold. YqgF	99.54
PRK00039	164	ruvC Holliday junction resolvase; Reviewed	97.71
PF02075	149	RuvC: Crossover junction endodeoxyribonuclease Ruv	97.53
cd00529	154	RuvC_resolvase Holliday junction resolvases (HJRs)	97.43
TIGR00228	156	ruvC crossover junction endodeoxyribonuclease RuvC	97.2
PF04312	138	DUF460: Protein of unknown function (DUF460); Inte	97.09
COG2183	780	Tex Transcriptional accessory protein [Transcripti	96.8
COG2433	652	Uncharacterized conserved protein [Function unknow	96.29
COG1548	330	Predicted transcriptional regulator/sugar kinase [	96.28
PF14639	150	YqgF: Holliday-junction resolvase-like of SPT6 ; P	96.15
COG0817	160	RuvC Holliday junction resolvasome, endonuclease s	95.97
TIGR01766	82	tspaseT_teng_C transposase, IS605 OrfB family, cen	93.77
PRK09557	301	fructokinase; Reviewed	92.14
COG1940	314	NagC Transcriptional regulator/sugar kinase [Trans	91.49
PRK05082	291	N-acetylmannosamine kinase; Provisional	91.13
TIGR00744	318	ROK_glcA_fam ROK family protein (putative glucokin	89.68
PF01548	144	DEDD_Tnp_IS110: Transposase; InterPro: IPR002525 T	89.11
PRK13310	303	N-acetyl-D-glucosamine kinase; Provisional	88.61
PRK13321	256	pantothenate kinase; Reviewed	86.07
PRK09698	302	D-allose kinase; Provisional	85.54
PF04848	143	Pox_A22: Poxvirus A22 protein; InterPro: IPR006932	85.39
PRK13311	256	N-acetyl-D-glucosamine kinase; Provisional	84.84
PF14239	176	RRXRR: RRXRR protein	84.25
PF07318	343	DUF1464: Protein of unknown function (DUF1464); In	83.82
PF07282	69	OrfB_Zn_ribbon: Putative transposase DNA-binding d	82.85
PRK00292	316	glk glucokinase; Provisional	82.34
COG4012	342	Uncharacterized protein conserved in archaea [Func	81.64
PHA02942	383	putative transposase; Provisional	80.23

>PRK00109 Holliday junction resolvase-like protein; Reviewed

Probab=100.00  E-value=5.4e-40  Score=263.80  Aligned_cols=130  Identities=32%  Similarity=0.469  Sum_probs=121.1

Q ss_pred             CceEEEEecCCCeEEEEEecC--CeeeeeeeEEccc-hhHHHHHHHHHHHcCCCEEEEeecCCCCCCCChhHHHHHHHHH
Q 028759           62 GGFSLGVDLGLSRTGLALSKG--FCVRPLTVLKLRG-EKLELQLLEIAQREETDEFIIGLPKSWDGSETPQSNKVRSVAG  138 (204)
Q Consensus        62 ~g~iLalD~G~kRIGVAvsD~--~~A~Pl~~i~~~~-~~~~~~L~~li~e~~i~~IVVGlPl~~dGt~~~~~~~v~~Fa~  138 (204)
                      .+++||||||+||||||+||.  .+|+|+.++.+++ ...+..|.+++++|++++||||+|++|||+++++++.+++|++
T Consensus         3 ~~~iLalD~G~kriGvAv~d~~~~~a~pl~~i~~~~~~~~~~~l~~~i~~~~i~~iVvGlP~~~~G~~~~~~~~v~~f~~   82 (138)
T PRK00109          3 SGRILGLDVGTKRIGVAVSDPLGGTAQPLETIKRNNGTPDWDRLEKLIKEWQPDGLVVGLPLNMDGTEGPRTERARKFAN   82 (138)
T ss_pred             CCcEEEEEeCCCEEEEEEecCCCCEEcCEEEEEcCCCchHHHHHHHHHHHhCCCEEEEeccCCCCCCcCHHHHHHHHHHH
Confidence            478999999999999999995  5899999998754 3467899999999999999999999999999999999999999


Q ss_pred             HHHHhhccCCCcEEEEcCCCcHHHHHHHHHHcCCCccccCCCCcHHHHHHHhcc-cc
Q 028759          139 RLAVRAAERGWRVYLLDEHRTSAEAVDRMINMGLSKSARQTKTDAYAAVVRQES-IT  194 (204)
Q Consensus       139 ~L~~~~~~~~lpV~lvDER~TT~eA~~~L~e~G~~rkkrK~~vD~~AA~iILq~-l~  194 (204)
                      +|++++   ++||++|||||||.+|+++|++.|.+++++|+.+|++||++|||+ |+
T Consensus        83 ~L~~~~---~~~v~~~DEr~TT~~A~~~l~~~~~~~~~~k~~vD~~AA~iILq~yL~  136 (138)
T PRK00109         83 RLEGRF---GLPVVLVDERLSTVEAERALADVGSRKKLRKGVIDSLAAVIILQSYLD  136 (138)
T ss_pred             HHHHHh---CCCEEEEcCCcCHHHHHHHHHHcCCChhhcccchhHHHHHHHHHHHHh
Confidence            999885   899999999999999999999999888888899999999999999 65

>PF03652 UPF0081: Uncharacterised protein family (UPF0081); InterPro: IPR005227 Holliday junction resolvases (HJRs) are key enzymes of DNA recombination

Probab=100.00  E-value=2e-41  Score=271.19  Aligned_cols=130  Identities=35%  Similarity=0.492  Sum_probs=119.3

Q ss_pred             ceEEEEecCCCeEEEEEecC--CeeeeeeeEEccc-hhHHHHHHHHHHHcCCCEEEEeecCCCCCCCChhHHHHHHHHHH
Q 028759           63 GFSLGVDLGLSRTGLALSKG--FCVRPLTVLKLRG-EKLELQLLEIAQREETDEFIIGLPKSWDGSETPQSNKVRSVAGR  139 (204)
Q Consensus        63 g~iLalD~G~kRIGVAvsD~--~~A~Pl~~i~~~~-~~~~~~L~~li~e~~i~~IVVGlPl~~dGt~~~~~~~v~~Fa~~  139 (204)
                      +++||||||+||||||+||.  .+|+|++++.+.+ ..+++.|.+++++|+|+.||||+|++|||+++++++.+++|+++
T Consensus         1 mriL~lD~G~kriGiAvsd~~~~~a~pl~~i~~~~~~~~~~~l~~li~~~~i~~iVvGlP~~~~G~~~~~~~~v~~f~~~   80 (135)
T PF03652_consen    1 MRILGLDYGTKRIGIAVSDPLGIIASPLETIPRRNREKDIEELKKLIEEYQIDGIVVGLPLNMDGSESEQARRVRKFAEE   80 (135)
T ss_dssp             -EEEEEEECSSEEEEEEEETTTSSEEEEEEEEECCCCCCHHHHHHHHHHCCECEEEEEEEBBCTSSC-CCHHHHHHHHHH
T ss_pred             CeEEEEEeCCCeEEEEEecCCCCeEeeeEEEECCCCchHHHHHHHHHHHhCCCEEEEeCCcccCCCccHHHHHHHHHHHH
Confidence            57999999999999999996  4899999999653 46889999999999999999999999999999999999999999


Q ss_pred             HHHhhccCCCcEEEEcCCCcHHHHHHHHHHcCCCccccCCCCcHHHHHHHhcc-cc
Q 028759          140 LAVRAAERGWRVYLLDEHRTSAEAVDRMINMGLSKSARQTKTDAYAAVVRQES-IT  194 (204)
Q Consensus       140 L~~~~~~~~lpV~lvDER~TT~eA~~~L~e~G~~rkkrK~~vD~~AA~iILq~-l~  194 (204)
                      |+++++  ++||++|||||||.+|++.|++.|++++++|+.+|++||++|||+ |+
T Consensus        81 L~~~~~--~ipV~~~DEr~TT~~A~~~l~~~g~~~~k~k~~iD~~AA~iILq~yLd  134 (135)
T PF03652_consen   81 LKKRFP--GIPVILVDERLTTKEAERRLRESGLSRKKRKKKIDSIAAAIILQSYLD  134 (135)
T ss_dssp             HHHHH---TSEEEEEECSCSHHCCHCCHHHTT-SHHHHCHHHCCCHHHHHHHHHHC
T ss_pred             HHHhcC--CCcEEEECCChhHHHHHHHHHHcCCChhhcCccccHHHHHHHHHHHHh
Confidence            999863  999999999999999999999999999999999999999999998 54

The principal HJRs are now known or confidently predicted for all bacteria and archaea whose genomes have been completely sequenced, with many species encoding multiple potential HJRs. Structural and evolutionary relationships of HJRs and related nucleases suggests that the HJR function has evolved independently from at least four distinct structural folds, namely RNase H, endonuclease, endonuclease VII-colicin E and RusA (IPR008822 from INTERPRO): The endonuclease fold, whose structural prototypes are the phage exonuclease, the very short patch repair nuclease (Vsr) and type II restriction enzymes, is shown to encompass by far a greater diversity of nucleases than previously suspected. This fold unifies archaeal HJRs (IPR002732 from INTERPRO), repair nucleases such as RecB (IPR004586 from INTERPRO) and Vsr (IPR004603 from INTERPRO), restriction enzymes and a variety of predicted nucleases whose specific activities remain to be determined. The RNase H fold characterises the RuvC family (IPR002176 from INTERPRO), which is nearly ubiquitous in bacteria, and in addition the YqgF family (IPR005227 from INTERPRO). The proteins of this family, typified by Escherichia coli YqgF, are likely to function as an alternative to RuvC in most bacteria, but could be the principal HJRs in low-GC Gram-positive bacteria and Aquifex. Endonuclease VII of phage T4 (IPR004211 from INTERPRO) is shown to serve as a structural template for many nucleases, including McrA and other type II restriction enzymes. Together with colicin E7, endonuclease VII defines a distinct metal-dependent nuclease fold. Horizontal gene transfer, lineage-specific gene loss and gene family expansion, and non-orthologous gene displacement seem to have been major forces in the evolution of HJRs and related nucleases. A remarkable case of displacement is seen in the Lyme disease spirochete Borrelia burgdorferi, which does not possess any of the typical HJRs, but instead encodes, in its chromosome and each of the linear plasmids, members of the exonuclease family predicted to function as HJRs. The diversity of HJRs and related nucleases in bacteria and archaea contrasts with their near absence in eukaryotes. The few detected eukaryotic representatives of the endonuclease fold and the RNase H fold have probably been acquired from bacteria via horizontal gene transfer. The identity of the principal HJR(s) involved in recombination in eukaryotes remains uncertain; this function could be performed by topoisomerase IB or by a novel, so far undetected, class of enzymes. Likely HJRs and related nucleases were identified in the genomes of numerous bacterial and eukaryotic DNA viruses. Gene flow between viral and cellular genomes has probably played a major role in the evolution of this class of enzymes. This family represents the YqgF family of putative Holliday junction resolvases. With the exception of the spirochetes, the YqgF family is represented in all bacterial lineages, including the mycoplasmas with their highly degenerate genomes. The RuvC resolvases are conspicuously absent in the low-GC Gram-positive bacterial lineage, with the exception of Ureaplasma parvum (Ureaplasma urealyticum biotype 1) (Q9PQY7 from SWISSPROT, []). Furthermore, loss of function ruvC mutants of E. coli show a residual HJR activity that cannot be ascribed to the prophage-encoded RusA resolvase []. This suggests that the YqgF family proteins could be alternative HJRs whose function partially overlaps with that of RuvC [].; GO: 0016788 hydrolase activity, acting on ester bonds, 0006281 DNA repair, 0006310 DNA recombination, 0006974 response to DNA damage stimulus, 0005737 cytoplasm; PDB: 1NU0_A 1OVQ_A 1NMN_B 1VHX_B 1IV0_A.

>COG0816 Predicted endonuclease involved in recombination (possible Holliday junction resolvase in Mycoplasmas and B

Probab=100.00  E-value=2.6e-40  Score=267.30  Aligned_cols=130  Identities=32%  Similarity=0.422  Sum_probs=122.7

Q ss_pred             ceEEEEecCCCeEEEEEecC--CeeeeeeeEEccch--hHHHHHHHHHHHcCCCEEEEeecCCCCCCCChhHHHHHHHHH
Q 028759           63 GFSLGVDLGLSRTGLALSKG--FCVRPLTVLKLRGE--KLELQLLEIAQREETDEFIIGLPKSWDGSETPQSNKVRSVAG  138 (204)
Q Consensus        63 g~iLalD~G~kRIGVAvsD~--~~A~Pl~~i~~~~~--~~~~~L~~li~e~~i~~IVVGlPl~~dGt~~~~~~~v~~Fa~  138 (204)
                      +++||||||+||||||+||.  .+|+|++++.+.+.  ..+..|.+++++|+++.||||+|++|+|+++++++.+++|++
T Consensus         2 ~~ilalD~G~KrIGvA~sd~~~~~A~pl~~i~~~~~~~~~~~~l~~li~~~~~~~vVVGlP~~m~g~~~~~~~~~~~f~~   81 (141)
T COG0816           2 MRILALDVGTKRIGVAVSDILGSLASPLETIKRKNGKPQDFNALLKLVKEYQVDTVVVGLPLNMDGTEGPRAELARKFAE   81 (141)
T ss_pred             ceEEEEecCCceEEEEEecCCCccccchhhheeccccHhhHHHHHHHHHHhCCCEEEEecCcCCCCCcchhHHHHHHHHH
Confidence            68999999999999999995  49999999997665  378999999999999999999999999999999999999999


Q ss_pred             HHHHhhccCCCcEEEEcCCCcHHHHHHHHHHcCCCccccCCCCcHHHHHHHhcc-ccc
Q 028759          139 RLAVRAAERGWRVYLLDEHRTSAEAVDRMINMGLSKSARQTKTDAYAAVVRQES-ITF  195 (204)
Q Consensus       139 ~L~~~~~~~~lpV~lvDER~TT~eA~~~L~e~G~~rkkrK~~vD~~AA~iILq~-l~~  195 (204)
                      +|++++   ++||++||||+||++|++.|++.|++++++|+.+|++||++|||+ |+.
T Consensus        82 ~L~~r~---~lpv~l~DERltTv~A~~~L~~~~~~~~~rk~~iD~~AA~~ILq~~ld~  136 (141)
T COG0816          82 RLKKRF---NLPVVLWDERLSTVEAERMLIEAGVSRKKRKGVIDSLAAVLILESYLDR  136 (141)
T ss_pred             HHHHhc---CCCEEEEcCccCHHHHHHHHHHcCCchhhhcchhHHHHHHHHHHHHHHh
Confidence            999985   899999999999999999999999999999999999999999999 653

subtilis) [DNA replication, recombination, and repair]

>TIGR00250 RNAse_H_YqgF RNAse H-fold protein YqgF

Probab=100.00  E-value=8.1e-40  Score=260.44  Aligned_cols=124  Identities=29%  Similarity=0.406  Sum_probs=117.2

Q ss_pred             EEEecCCCeEEEEEecC--CeeeeeeeEEccc-hhHHHHHHHHHHHcCCCEEEEeecCCCCCCCChhHHHHHHHHHHHHH
Q 028759           66 LGVDLGLSRTGLALSKG--FCVRPLTVLKLRG-EKLELQLLEIAQREETDEFIIGLPKSWDGSETPQSNKVRSVAGRLAV  142 (204)
Q Consensus        66 LalD~G~kRIGVAvsD~--~~A~Pl~~i~~~~-~~~~~~L~~li~e~~i~~IVVGlPl~~dGt~~~~~~~v~~Fa~~L~~  142 (204)
                      ||||||+||||||+||.  .+|+|++++..++ ...+..|.+++++|+++.||||+|++|||+++++++.+++|+++|++
T Consensus         1 laiD~G~kriGvA~~d~~~~~a~pl~~i~~~~~~~~~~~l~~~i~~~~~~~iVvGlP~~~dG~~~~~a~~v~~f~~~L~~   80 (130)
T TIGR00250         1 LGLDFGTKSIGVAGQDITGWTAQGIPTIKAQDGEPDWSRIEELLKEWTPDKIVVGLPLNMDGTEGPLTERAQKFANRLEG   80 (130)
T ss_pred             CeEccCCCeEEEEEECCCCCEEeceEEEEecCCcHHHHHHHHHHHHcCCCEEEEeccCCCCcCcCHHHHHHHHHHHHHHH
Confidence            69999999999999995  5899999998743 46789999999999999999999999999999999999999999998


Q ss_pred             hhccCCCcEEEEcCCCcHHHHHHHHHHcCCCccccCCCCcHHHHHHHhcc
Q 028759          143 RAAERGWRVYLLDEHRTSAEAVDRMINMGLSKSARQTKTDAYAAVVRQES  192 (204)
Q Consensus       143 ~~~~~~lpV~lvDER~TT~eA~~~L~e~G~~rkkrK~~vD~~AA~iILq~  192 (204)
                      ++   ++||++||||+||.+|+++|++.|++++++|..+|++||++|||+
T Consensus        81 ~~---~~~v~~~DEr~TT~~A~~~l~~~g~~~~~~k~~vD~~AA~iILq~  127 (130)
T TIGR00250        81 RF---GVPVVLWDERLSTVEAESGLFARGGFRALRKGKIDKAAAVIILQS  127 (130)
T ss_pred             Hh---CCCEEEEcCCcCHHHHHHHHHHcCCChhhccccHhHHHHHHHHHH
Confidence            85   899999999999999999999999999999999999999999998

This protein family, which exhibits an RNAse H fold in crystal structure, has been proposed as a putative Holliday junction resolvase, an alternate to RuvC.

>smart00732 YqgFc Likely ribonuclease with RNase H fold

Probab=99.54  E-value=8.6e-14  Score=102.80  Aligned_cols=95  Identities=26%  Similarity=0.364  Sum_probs=78.5

Q ss_pred             eEEEEecCCCeEEEEEecC--CeeeeeeeEEc-cchhHHHHHHHHHHHcCCCEEEEeecCCCCCCCChhHHHHHHHHHHH
Q 028759           64 FSLGVDLGLSRTGLALSKG--FCVRPLTVLKL-RGEKLELQLLEIAQREETDEFIIGLPKSWDGSETPQSNKVRSVAGRL  140 (204)
Q Consensus        64 ~iLalD~G~kRIGVAvsD~--~~A~Pl~~i~~-~~~~~~~~L~~li~e~~i~~IVVGlPl~~dGt~~~~~~~v~~Fa~~L  140 (204)
                      ++||||+|..+||+|+.|.  ....+..+... +.....+.|.+++++++++.|+||.|-.++|.......  ..|.+.|
T Consensus         2 ~ilgiD~Ggt~i~~a~~d~~g~~~~~~~~~~~~~~~~~~~~l~~~i~~~~~~~i~Ig~pg~v~g~~~~~~~--~~l~~~l   79 (99)
T smart00732        2 RVLGLDPGRKGIGVAVVDETGKLADPLEVIPRTNKEADAARLKKLIKKYQPDLIVIGLPLNMNGTASRETE--EAFAELL   79 (99)
T ss_pred             cEEEEccCCCeEEEEEECCCCCEecCEEEEEecCcchHHHHHHHHHHHhCCCEEEEeCCcCCCCCcCHHHH--HHHHHHH
Confidence            5899999999999999983  45555554432 22456789999999999999999999999998776554  8899999


Q ss_pred             HHhhccCCCcEEEEcCCCcHHHH
Q 028759          141 AVRAAERGWRVYLLDEHRTSAEA  163 (204)
Q Consensus       141 ~~~~~~~~lpV~lvDER~TT~eA  163 (204)
                      ++++   ++||+++||.+||.+|
T Consensus        80 ~~~~---~~pv~~~nDa~st~~a   99 (99)
T smart00732       80 KERF---NLPVVLVDERLATVYA   99 (99)
T ss_pred             HHhh---CCcEEEEeCCcccccC
Confidence            8875   8999999999999875

YqgF proteins are likely to function as an alternative to RuvC in most bacteria, and could be the principal holliday junction resolvases in low-GC Gram-positive bacteria. In Spt6p orthologues, the catalytic residues are substituted indicating that they lack enzymatic functions.

>PRK00039 ruvC Holliday junction resolvase; Reviewed

Probab=97.71  E-value=0.00049  Score=57.01  Aligned_cols=98  Identities=22%  Similarity=0.167  Sum_probs=60.9

Q ss_pred             ceEEEEecCCCeEEEEEecC--Cee--eeeeeEEccc--------hhHHHHHHHHHHHcCCCEEEEeecCCCC-CCCChh
Q 028759           63 GFSLGVDLGLSRTGLALSKG--FCV--RPLTVLKLRG--------EKLELQLLEIAQREETDEFIIGLPKSWD-GSETPQ  129 (204)
Q Consensus        63 g~iLalD~G~kRIGVAvsD~--~~A--~Pl~~i~~~~--------~~~~~~L~~li~e~~i~~IVVGlPl~~d-Gt~~~~  129 (204)
                      +++||||+|..++|+|+.+.  ...  --.+++..+.        ....+.|.+++++|+|+.++|=-|+-.. ....-.
T Consensus         2 m~iLGIDPgl~~tG~avi~~~~~~~~~~~~G~i~t~~~~~~~~Rl~~I~~~l~~~i~~~~Pd~vaiE~~f~~~n~~sa~~   81 (164)
T PRK00039          2 MRILGIDPGLRRTGYGVIEVEGRRLSYVASGVIRTPSDLDLPERLKQIYDGLSELIDEYQPDEVAIEEVFFNKNPQSALK   81 (164)
T ss_pred             CEEEEEccccCceeEEEEEecCCeEEEEEeeEEECCCCCCHHHHHHHHHHHHHHHHHHhCCCEEEEehhhhccChHHHHH
Confidence            58999999999999999873  222  2233554321        1345789999999999999999887432 222211


Q ss_pred             HHHHHHHHHHHHHhhccCCCcEEEEcCCCcHHHHHHHH
Q 028759          130 SNKVRSVAGRLAVRAAERGWRVYLLDEHRTSAEAVDRM  167 (204)
Q Consensus       130 ~~~v~~Fa~~L~~~~~~~~lpV~lvDER~TT~eA~~~L  167 (204)
                      .-+++--+.....+   .++||+.+    |..+.+...
T Consensus        82 l~~arGvi~la~~~---~~ipv~ey----~P~~VKk~v  112 (164)
T PRK00039         82 LGQARGVAILAAAQ---RGLPVAEY----TPLQVKKAV  112 (164)
T ss_pred             HHHHHHHHHHHHHH---cCCCEEEE----CHHHhhhhh
Confidence            12233333333322   59999865    555555443

>PF02075 RuvC: Crossover junction endodeoxyribonuclease RuvC; InterPro: IPR002176 The Escherichia coli ruvC gene is involved in DNA repair and in the late step of RecE and RecF pathway recombination []

Probab=97.53  E-value=0.0012  Score=53.69  Aligned_cols=96  Identities=24%  Similarity=0.229  Sum_probs=50.6

Q ss_pred             EEEEecCCCeEEEEEecC--C--eeeeeeeEEccch--------hHHHHHHHHHHHcCCCEEEEeecCCCCCCCC-hhHH
Q 028759           65 SLGVDLGLSRTGLALSKG--F--CVRPLTVLKLRGE--------KLELQLLEIAQREETDEFIIGLPKSWDGSET-PQSN  131 (204)
Q Consensus        65 iLalD~G~kRIGVAvsD~--~--~A~Pl~~i~~~~~--------~~~~~L~~li~e~~i~~IVVGlPl~~dGt~~-~~~~  131 (204)
                      |||||+|..++|.|+-+.  .  ..--..++..+..        ...+.|.+++++|+|+.++|=-|.......+ -..-
T Consensus         1 ILGIDPgl~~tG~avi~~~~~~~~~i~~G~I~t~~~~~~~~Rl~~I~~~l~~li~~~~P~~vaiE~~f~~~n~~s~~~l~   80 (149)
T PF02075_consen    1 ILGIDPGLSNTGYAVIEEDGGKLRLIDYGTIKTSSKDSLPERLKEIYEELEELIEEYNPDEVAIEEIFFGKNPKSALKLG   80 (149)
T ss_dssp             EEEEE--SSEEEEEEEEEETTEEEEEEEEEEE---S--HHHHHHHHHHHHHHHHHHH--SEEEEEE-S----HHHHHHHH
T ss_pred             CEEECCCCCCeeEEEEEeeCCEEEEEEeCeEECCCCCCHHHHHHHHHHHHHHHHHhhCCCEEEeehhhhccCHHHHHHHH
Confidence            799999999999999983  2  2233345553221        2357899999999999999998874322111 1111


Q ss_pred             HHHHHHHHHHHhhccCCCcEEEEcCCCcHHHHHHHH
Q 028759          132 KVRSVAGRLAVRAAERGWRVYLLDEHRTSAEAVDRM  167 (204)
Q Consensus       132 ~v~~Fa~~L~~~~~~~~lpV~lvDER~TT~eA~~~L  167 (204)
                      +++-.+.....   ..++||..    +|..+.++.+
T Consensus        81 ~arGvi~l~~~---~~~i~v~~----y~P~~vKk~v  109 (149)
T PF02075_consen   81 QARGVILLAAA---QRGIPVFE----YTPSEVKKAV  109 (149)
T ss_dssp             HHHHHHHHHHH---TTT--EEE----EEHHHHHHHH
T ss_pred             HHHHHHHHHHH---HcCCeEEE----ECHHHHHHHh
Confidence            22233222222   25889875    4666666654

RuvC protein (3.1.22.4 from EC) cleaves cruciform junctions, which are formed by the extrusion of inverted repeat sequences from a super-coiled plasmid and which are structurally analogous to Holliday junctions, by introducing nicks into strands with the same polarity. The nicks leave a 5'terminal phosphate and a 3'terminal hydroxyl group which are ligated by E. coli or Bacteriophage T4 DNA ligases. Analysis of the cleavage sites suggests that DNA topology rather than a particular sequence determines the cleavage site. RuvC protein also cleaves Holliday junctions that are formed between gapped circular and linear duplex DNA by the function of RecA protein. The active form of RuvC protein is a dimer. This is mechanistically suited for an endonuclease involved in swapping DNA strands at the crossover junctions. It is inferred that RuvC protein is an endonuclease that resolves Holliday structures in vivo []. RucC is a small protein of about 20 kD. It requires and binds a magnesium ion. The structure of E. coli ruvC is a 3-layer alpha-beta sandwich containing a 5-stranded beta-sheet sandwiched between 5 alpha-helices [].; GO: 0004520 endodeoxyribonuclease activity, 0006281 DNA repair, 0006310 DNA recombination; PDB: 1HJR_A.

>cd00529 RuvC_resolvase Holliday junction resolvases (HJRs) are endonucleases that specifically resolve Holliday junction DNA intermediates during homologous recombination

Probab=97.43  E-value=0.0025  Score=51.78  Aligned_cols=92  Identities=18%  Similarity=0.162  Sum_probs=55.7

Q ss_pred             eEEEEecCCCeEEEEEecC--Cee--eeeeeEEccc--------hhHHHHHHHHHHHcCCCEEEEeecCCCCCCCChhHH
Q 028759           64 FSLGVDLGLSRTGLALSKG--FCV--RPLTVLKLRG--------EKLELQLLEIAQREETDEFIIGLPKSWDGSETPQSN  131 (204)
Q Consensus        64 ~iLalD~G~kRIGVAvsD~--~~A--~Pl~~i~~~~--------~~~~~~L~~li~e~~i~~IVVGlPl~~dGt~~~~~~  131 (204)
                      ++||||+|..++|+|+.+.  ...  .-..++..+.        ....+.|.+++.+|+|+.++|=-+.--.+.  +.+.
T Consensus         1 rILGIDPGl~~~G~av~~~~~~~~~~~~~g~i~t~~~~~~~~rl~~I~~~l~~~i~~~~Pd~vaiE~~~~~~n~--~s~~   78 (154)
T cd00529           1 RILGIDPGSRNTGYGVIEQEGRKLIYLASGVIRTSSDAPLPSRLKTIYDGLNEVIDQFQPDVVAIERVFFAKNP--DSAL   78 (154)
T ss_pred             CEEEEccCcCceEEEEEEeeCCeEEEEEeeEEECCCCCCHHHHHHHHHHHHHHHHHHhCCCEEEEEEhhcccCh--HHHH
Confidence            5899999999999999873  222  2234555331        134578999999999999999876632222  2222


Q ss_pred             HHHHHHHHHHHhhccCCCcEEEEcCC
Q 028759          132 KVRSVAGRLAVRAAERGWRVYLLDEH  157 (204)
Q Consensus       132 ~v~~Fa~~L~~~~~~~~lpV~lvDER  157 (204)
                      .+-.+-..+-..+...++||+.++-.
T Consensus        79 ~l~~~~Gvi~~~~~~~~i~v~e~~P~  104 (154)
T cd00529          79 KLGQARGALILALANRNLPVFEYTPN  104 (154)
T ss_pred             HHHHHHHHHHHHHHHcCCCEEEEccC
Confidence            22111111111122258898887644

HJR's occur in archaea, bacteria, and in the mitochondria of certain fungi, however this CD includes only the bacterial and mitochondrial HJR's. These are referred to as the RuvC family of Holliday junction resolvases, RuvC being the E.coli HJR. RuvC and its orthologs are homodimers and are structurely similar to RNase H and Hsp70.

>TIGR00228 ruvC crossover junction endodeoxyribonuclease RuvC

Probab=97.20  E-value=0.0024  Score=52.81  Aligned_cols=95  Identities=18%  Similarity=0.158  Sum_probs=58.5

Q ss_pred             EEEEecCCCeEEEEEecC--Ce--eeeeeeEEccch-------hHHHHHHHHHHHcCCCEEEEeecCCC-CCCCChhHHH
Q 028759           65 SLGVDLGLSRTGLALSKG--FC--VRPLTVLKLRGE-------KLELQLLEIAQREETDEFIIGLPKSW-DGSETPQSNK  132 (204)
Q Consensus        65 iLalD~G~kRIGVAvsD~--~~--A~Pl~~i~~~~~-------~~~~~L~~li~e~~i~~IVVGlPl~~-dGt~~~~~~~  132 (204)
                      +||||+|..++|.||-+.  ..  .--..++..+..       ...+.|.+++++|+|+.+.|=-++-. |....-..-+
T Consensus         1 ILGIDPGl~~tG~gvi~~~~~~~~~v~~G~I~t~~~~~~~RL~~I~~~l~~~i~~y~P~~~aiE~~F~~~N~~sa~~lg~   80 (156)
T TIGR00228         1 ILGIDPGSRVTGYGVIRQVGRQLSYLGSGCIRTKVDDLPSRLKLIYAGVTEIITQFQPNYFAIEQVFMAKNADSALKLGQ   80 (156)
T ss_pred             CEeECcccccccEEEEEecCCeEEEEEeeEEECCCCCHHHHHHHHHHHHHHHHHHhCCCEEEEeHHhhccCHHHHHHHHH
Confidence            599999999999999883  22  233345543221       23578999999999999999887743 2222222223


Q ss_pred             HHHHHHHHHHhhccCCCcEEEEcCCCcHHHHHHH
Q 028759          133 VRSVAGRLAVRAAERGWRVYLLDEHRTSAEAVDR  166 (204)
Q Consensus       133 v~~Fa~~L~~~~~~~~lpV~lvDER~TT~eA~~~  166 (204)
                      ++-.+-....   ..++||+   | ||..+.++.
T Consensus        81 arGvilla~~---~~~ipv~---E-y~P~~vKka  107 (156)
T TIGR00228        81 ARGVAIVAAV---NQELPVF---E-YAARQVKQT  107 (156)
T ss_pred             HHHHHHHHHH---HcCCCEE---E-ECHHHHHHH
Confidence            3333322222   2599998   3 666655443

Endonuclease that resolves Holliday junction intermediates in genetic recombination. The active form of the protein is a dimer. Structure studies reveals that the catalytic center, comprised of four acidic residues, lies at the bottom of a cleft that fits a DNA duplex. The model hits a single Synechocystis PCC6803 protein at a score of 30, below the trusted cutoff, that appears orthologous and may act as authentic RuvC.

>PF04312 DUF460: Protein of unknown function (DUF460); InterPro: IPR007408 This is an archaeal protein of unknown function

Probab=97.09  E-value=0.0097  Score=48.45  Aligned_cols=108  Identities=17%  Similarity=0.124  Sum_probs=68.1

Q ss_pred             CceEEEEecCCCeEEEEEecCCeeeeeeeEEccchhHHHHHHHHHHHcCCCEEEEeecCCCCCCCChhHHHHHHHHHHHH
Q 028759           62 GGFSLGVDLGLSRTGLALSKGFCVRPLTVLKLRGEKLELQLLEIAQREETDEFIIGLPKSWDGSETPQSNKVRSVAGRLA  141 (204)
Q Consensus        62 ~g~iLalD~G~kRIGVAvsD~~~A~Pl~~i~~~~~~~~~~L~~li~e~~i~~IVVGlPl~~dGt~~~~~~~v~~Fa~~L~  141 (204)
                      ...|.|||+|+ .+|+|+-|-. ..++.+...++ -....+.++|.+++-=.||-=     |=+.-  -.    ++++|+
T Consensus        31 ~~lIVGiDPG~-ttgiAildL~-G~~l~l~S~R~-~~~~evi~~I~~~G~PviVAt-----DV~p~--P~----~V~Kia   96 (138)
T PF04312_consen   31 RYLIVGIDPGT-TTGIAILDLD-GELLDLKSSRN-MSRSEVIEWISEYGKPVIVAT-----DVSPP--PE----TVKKIA   96 (138)
T ss_pred             CCEEEEECCCc-eeEEEEEecC-CcEEEEEeecC-CCHHHHHHHHHHcCCEEEEEe-----cCCCC--cH----HHHHHH
Confidence            47899999998 6899999832 24455444333 234577777877766555543     43333  33    444555


Q ss_pred             HhhccCCCcEEEEcCCCcHHHHHHHHHHcCCCccccCCCCcHHHHH
Q 028759          142 VRAAERGWRVYLLDEHRTSAEAVDRMINMGLSKSARQTKTDAYAAV  187 (204)
Q Consensus       142 ~~~~~~~lpV~lvDER~TT~eA~~~L~e~G~~rkkrK~~vD~~AA~  187 (204)
                      ..|   +-.++.=++.+|..|=.+...+.+.+-.. ---=|++||+
T Consensus        97 ~~f---~A~ly~P~~dlsveeK~~l~~~~~~~~~n-~HeRDALAAA  138 (138)
T PF04312_consen   97 RSF---NAVLYTPERDLSVEEKQELAREYSERYEN-DHERDALAAA  138 (138)
T ss_pred             HHh---CCcccCCCCcCCHHHHHHHHHhhCCCCCC-chHHhHhhcC
Confidence            543   55677778999999888888876641111 1223888885

>COG2183 Tex Transcriptional accessory protein [Transcription]

Probab=96.80  E-value=0.011  Score=59.43  Aligned_cols=89  Identities=15%  Similarity=0.233  Sum_probs=59.6

Q ss_pred             CceEEEEecCCCe-EEEEEecCC--eeeeeeeEEcc----chhHHHHHHHHHHHcCCCEEEEeecCCCCCCCChhHHHHH
Q 028759           62 GGFSLGVDLGLSR-TGLALSKGF--CVRPLTVLKLR----GEKLELQLLEIAQREETDEFIIGLPKSWDGSETPQSNKVR  134 (204)
Q Consensus        62 ~g~iLalD~G~kR-IGVAvsD~~--~A~Pl~~i~~~----~~~~~~~L~~li~e~~i~~IVVGlPl~~dGt~~~~~~~v~  134 (204)
                      +..+||||+|... |=+||.|+.  ...--.+++..    .....+.|..++..|+|+.|.||     +||.+..   +.
T Consensus       329 ~~~~lglDPg~rtG~k~Avvd~tGk~l~~~~Iyp~~p~~~~~~~~~~l~~l~~~~~Ve~iaIG-----ngTaSre---te  400 (780)
T COG2183         329 PKATLGLDPGFRTGCKVAVVDDTGKLLDTATIYPHPPVNQSDKAEATLKDLIRKYKVELIAIG-----NGTASRE---TE  400 (780)
T ss_pred             CcceeecCCccccccEEEEEcCCCceeceeEEEcCCCccchHHHHHHHHHHHHHhCceEEEEe-----cCCcchh---HH
Confidence            3479999999655 567888843  11111122221    13455788999999999999999     8998754   45


Q ss_pred             HHHHHHHHhhccCCCcEEEEcCCC
Q 028759          135 SVAGRLAVRAAERGWRVYLLDEHR  158 (204)
Q Consensus       135 ~Fa~~L~~~~~~~~lpV~lvDER~  158 (204)
                      +|+..+-+..+..++..+.|.|..
T Consensus       401 ~fv~~vl~~~~~~~~~~viVsEag  424 (780)
T COG2183         401 KFVADVLKELPKEKVLKVIVSEAG  424 (780)
T ss_pred             HHHHHHHHhccCCCCcEEEEcccc
Confidence            566666655433477888888764

>COG2433 Uncharacterized conserved protein [Function unknown]

Probab=96.29  E-value=0.053  Score=53.41  Aligned_cols=121  Identities=21%  Similarity=0.274  Sum_probs=81.9

Q ss_pred             hhhhcccccccccCCCCCCceEEEEecCCCeEEEEEecCCeeeeeeeEEccchhHHHHHHHHHHHcCCCEEEEeecCCCC
Q 028759           44 VEEFLPNATRRKKDSLWRGGFSLGVDLGLSRTGLALSKGFCVRPLTVLKLRGEKLELQLLEIAQREETDEFIIGLPKSWD  123 (204)
Q Consensus        44 ~~~~~~~~~~~~~~~~~~~g~iLalD~G~kRIGVAvsD~~~A~Pl~~i~~~~~~~~~~L~~li~e~~i~~IVVGlPl~~d  123 (204)
                      .=+|.|.+.++.       ..|.|||||+ .+|+|+-|-. -.++.+...++ -....+.++|.+++-=.||--     |
T Consensus       232 rief~pl~~~r~-------~lIVGIDPGi-TtgiAvldld-Gevl~~~S~r~-~~~~eVve~I~~lG~PvvVAt-----D  296 (652)
T COG2433         232 RIEFVPLRPERR-------SLIVGIDPGI-TTGIAVLDLD-GEVLDLESRRG-IDRSEVVEFISELGKPVVVAT-----D  296 (652)
T ss_pred             ccccccCccccc-------ceEEEeCCCc-eeeEEEEecC-CcEEeeecccc-CCHHHHHHHHHHcCCceEEEc-----c
Confidence            335667766643       5799999998 6899999832 12333333322 234688889998876666654     5


Q ss_pred             CCCChhHHHHHHHHHHHHHhhccCCCcEEEEcCCCcHHHHHHHHHHcCCCccccCCCCcHHHHHHH
Q 028759          124 GSETPQSNKVRSVAGRLAVRAAERGWRVYLLDEHRTSAEAVDRMINMGLSKSARQTKTDAYAAVVR  189 (204)
Q Consensus       124 Gt~~~~~~~v~~Fa~~L~~~~~~~~lpV~lvDER~TT~eA~~~L~e~G~~rkkrK~~vD~~AA~iI  189 (204)
                      =+.-|      .|+++|+..|   +-+.+.=|+++|+.|=.+.++..+++-... -.=|++||++-
T Consensus       297 Vtp~P------~~V~KiAasf---~A~ly~P~~dLsveEK~~~~r~~~~~~~dd-H~RDALAAA~k  352 (652)
T COG2433         297 VTPAP------ETVKKIAASF---NAVLYTPDRDLSVEEKQEALRTLKISVSDD-HERDALAAAYK  352 (652)
T ss_pred             CCCCh------HHHHHHHHHc---CCcccCCcccCCHHHHHHHHhhcCCCCCCc-hHHHHHHHHHH
Confidence            55554      5667777764   777888899999999988777766654432 22489999863

>COG1548 Predicted transcriptional regulator/sugar kinase [Transcription / Carbohydrate transport and metabolism]

Probab=96.28  E-value=0.018  Score=51.95  Aligned_cols=104  Identities=21%  Similarity=0.239  Sum_probs=68.0

Q ss_pred             ceEEEEecCCCeEEEEEecCCe-eeeeeeEEc--cchhHHHHHHHHHHHcCCCEEEEeecCCCCCCCChhHHHHHHHHHH
Q 028759           63 GFSLGVDLGLSRTGLALSKGFC-VRPLTVLKL--RGEKLELQLLEIAQREETDEFIIGLPKSWDGSETPQSNKVRSVAGR  139 (204)
Q Consensus        63 g~iLalD~G~kRIGVAvsD~~~-A~Pl~~i~~--~~~~~~~~L~~li~e~~i~~IVVGlPl~~dGt~~~~~~~v~~Fa~~  139 (204)
                      ..+||||+|...+-+|.+||.. ..-+-.+++  +...+...|++++.+++++.+=|=+--..-.-....++-|+..++.
T Consensus         3 ~kilGiDIGGAntk~a~~DG~~~~~d~~YlPMWk~k~rL~~~Lkei~~k~~~~~vgvvMTaELaD~f~tk~eGVe~Ii~~   82 (330)
T COG1548           3 MKILGIDIGGANTKIASSDGDNYKIDHIYLPMWKKKDRLEETLKEIVHKDNVDYVGVVMTAELADAFKTKAEGVEDIIDT   82 (330)
T ss_pred             ceEEEeeccCccchhhhccCCeeeeeEEEeccccchhHHHHHHHHHhccCCcceeEEEeeHHHHHHhhhHHhHHHHHHHH
Confidence            6799999999999999999853 223333443  2235667888988778888554433222222223355667777888


Q ss_pred             HHHhhccCCCcEEEEcCC--CcHHHHHHHHHH
Q 028759          140 LAVRAAERGWRVYLLDEH--RTSAEAVDRMIN  169 (204)
Q Consensus       140 L~~~~~~~~lpV~lvDER--~TT~eA~~~L~e  169 (204)
                      .++.|   +.||+++|=.  +-|.||.+.+.+
T Consensus        83 v~~Af---~~pv~~v~~~G~~~ssEa~~~~~~  111 (330)
T COG1548          83 VEKAF---NCPVYVVDVNGNFLSSEALKNPRE  111 (330)
T ss_pred             HHHhc---CCceEEEeccCcCcChhHhcCHHH
Confidence            88775   8999999843  334477765544

>PF14639 YqgF: Holliday-junction resolvase-like of SPT6 ; PDB: 3PSI_A 3PSF_A

Probab=96.15  E-value=0.091  Score=42.98  Aligned_cols=92  Identities=16%  Similarity=0.124  Sum_probs=41.5

Q ss_pred             CceEEEEecCCCe----EEEEEecCC-eeeeeeeE-Ec-----cchhHHHHHHHHHHHcCCCEEEEeecCCCCCCCChhH
Q 028759           62 GGFSLGVDLGLSR----TGLALSKGF-CVRPLTVL-KL-----RGEKLELQLLEIAQREETDEFIIGLPKSWDGSETPQS  130 (204)
Q Consensus        62 ~g~iLalD~G~kR----IGVAvsD~~-~A~Pl~~i-~~-----~~~~~~~~L~~li~e~~i~~IVVGlPl~~dGt~~~~~  130 (204)
                      +-++|||-+|.-+    +-.|+-|.. -..-...+ ..     ...++.+.|.+++.+++|+.|+||      |. +..+
T Consensus         4 ~~rVla~~~g~g~~~~~~~~v~ld~~G~v~d~~~~~~~~~~~~~~~~~~~~l~~~i~~~kP~vI~v~------g~-~~~s   76 (150)
T PF14639_consen    4 GPRVLALSWGSGDGDDAVFCVVLDENGEVLDHLKLVYNERDRERKEEDMERLKKFIEKHKPDVIAVG------GN-SRES   76 (150)
T ss_dssp             ---EEEEE-TT--TTS-EEEEEE-TTS-EEEEEEE-S-TT-SS-SHHHHHHHHHHHHHH--SEEEE--------S-STHH
T ss_pred             CCEEEEEEcCCCCCCCCEEEEEECCCCcEEEEEEEcCCccchHHHHHHHHHHHHHHHHcCCeEEEEc------CC-ChhH
Confidence            4679999999666    334454521 11111111 11     113456789999999999999997      42 3445


Q ss_pred             HHHHHHHHHHHHhhc----cCCCcEEEEcCCCcH
Q 028759          131 NKVRSVAGRLAVRAA----ERGWRVYLLDEHRTS  160 (204)
Q Consensus       131 ~~v~~Fa~~L~~~~~----~~~lpV~lvDER~TT  160 (204)
                      ++..++.+.+-+...    ...++|+++||...+
T Consensus        77 ~~l~~~v~~~v~~~~~~~~~~~i~V~~v~~~~A~  110 (150)
T PF14639_consen   77 RKLYDDVRDIVEELDEDEQMPPIPVVIVDDEVAR  110 (150)
T ss_dssp             HHHHHHHHHHHHHTTB-TTS-B--EEE---TTHH
T ss_pred             HHHHHHHHHHHHHhhhcccCCCceEEEECcHHHH
Confidence            554444444433221    136899999997643

>COG0817 RuvC Holliday junction resolvasome, endonuclease subunit [DNA replication, recombination, and repair]

Probab=95.97  E-value=0.013  Score=48.69  Aligned_cols=95  Identities=25%  Similarity=0.272  Sum_probs=57.8

Q ss_pred             EEEecCCCeEEEEEecC--Ceeeee--eeEEccch--------hHHHHHHHHHHHcCCCEEEEeecCC-CCCCCChhHHH
Q 028759           66 LGVDLGLSRTGLALSKG--FCVRPL--TVLKLRGE--------KLELQLLEIAQREETDEFIIGLPKS-WDGSETPQSNK  132 (204)
Q Consensus        66 LalD~G~kRIGVAvsD~--~~A~Pl--~~i~~~~~--------~~~~~L~~li~e~~i~~IVVGlPl~-~dGt~~~~~~~  132 (204)
                      ||||||..+||.+|-+.  ....++  .+|.....        .+.+.|.+++.+|+|+.+.|=-.+- -|-+..-..-+
T Consensus         1 lGIDPGl~~~G~gvI~~~~~~l~~v~~G~I~t~~~~~l~~RL~~l~~~l~~vl~~~~P~~~AIE~~F~~kN~~s~lklgQ   80 (160)
T COG0817           1 LGIDPGLRRTGYGVIEVEGRQLSYLASGVIRTSSDAPLAERLKQLYDGLSEVLDEYQPDEVAIEQVFVNKNADSALKLGQ   80 (160)
T ss_pred             CCcCCCccccceEEEEccCCeEEEEeeeEEecCCCccHHHHHHHHHHHHHHHHHHhCCCeeehhHHHHhcChHHHHHHHH
Confidence            68999999999999993  344444  45543311        2457888999999999999987763 22222222222


Q ss_pred             HHHHHHHHHHhhccCCCcEEEEcCCCcHHHHHHHH
Q 028759          133 VRSVAGRLAVRAAERGWRVYLLDEHRTSAEAVDRM  167 (204)
Q Consensus       133 v~~Fa~~L~~~~~~~~lpV~lvDER~TT~eA~~~L  167 (204)
                      ++-.+-....   +.++||..    ||..+.+.-.
T Consensus        81 ARGv~~la~~---~~~l~v~e----Y~p~~VKkav  108 (160)
T COG0817          81 ARGVALLAAA---RRGLPVFE----YTPNQVKKAV  108 (160)
T ss_pred             HHHHHHHHHH---HcCCChhh----ccHHHHHHHh
Confidence            2222222222   24888874    5666665554

>TIGR01766 tspaseT_teng_C transposase, IS605 OrfB family, central region

Probab=93.77  E-value=0.29  Score=35.02  Aligned_cols=61  Identities=20%  Similarity=0.225  Sum_probs=37.5

Q ss_pred             HHHHHHHHHHcCCCEEEEeecCCCCCCC---Ch-hHHH-----HHHHHHHHHHhhccCCCcEEEEcCCCcH
Q 028759           99 ELQLLEIAQREETDEFIIGLPKSWDGSE---TP-QSNK-----VRSVAGRLAVRAAERGWRVYLLDEHRTS  160 (204)
Q Consensus        99 ~~~L~~li~e~~i~~IVVGlPl~~dGt~---~~-~~~~-----v~~Fa~~L~~~~~~~~lpV~lvDER~TT  160 (204)
                      ...|.+...+ .++.||||...+..+..   +. ..+.     -..|.+.|+-...++|++|..|||.+||
T Consensus        13 a~~iv~~~~~-~~~~Ivie~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~yka~~~Gi~v~~v~~~yTS   82 (82)
T TIGR01766        13 VKQIVEYAKE-NNGTIVLEDLKNIKEMVDKKSKYLRRKLHQWSFRKLISKIKYKAEEYGIEVIEVNPAYTS   82 (82)
T ss_pred             HHHHHHHHHH-cCCEEEECCccchhhhcchhhHHHHHHHHhhhHHHHHHHHHHHHHHcCCeEEEeCccccc
Confidence            3456666666 77999999865333321   11 1111     2334555554444579999999999997

This model represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by pfam model pfam01385, and other proteins.

>PRK09557 fructokinase; Reviewed

Probab=92.14  E-value=1.2  Score=39.18  Aligned_cols=98  Identities=15%  Similarity=0.165  Sum_probs=57.8

Q ss_pred             eEEEEecCCCeEEEEEecC--C-eeeeeeeEEcc---chhHHHHHHHHHHHc-----CCCEEEEeecCCC---CCCCC--
Q 028759           64 FSLGVDLGLSRTGLALSKG--F-CVRPLTVLKLR---GEKLELQLLEIAQRE-----ETDEFIIGLPKSW---DGSET--  127 (204)
Q Consensus        64 ~iLalD~G~kRIGVAvsD~--~-~A~Pl~~i~~~---~~~~~~~L~~li~e~-----~i~~IVVGlPl~~---dGt~~--  127 (204)
                      ++||+|+|..++-+++.|.  . ..+  ..++..   .....+.+.+++++.     .+.+|.||.|=..   +|...  
T Consensus         1 ~~lgidig~t~~~~~l~d~~g~i~~~--~~~~~~~~~~~~~~~~i~~~i~~~~~~~~~~~gIgi~~pG~vd~~~g~i~~~   78 (301)
T PRK09557          1 MRIGIDLGGTKIEVIALDDAGEELFR--KRLPTPRDDYQQTIEAIATLVDMAEQATGQRGTVGVGIPGSISPYTGLVKNA   78 (301)
T ss_pred             CEEEEEECCCcEEEEEECCCCCEEEE--EEecCCCCCHHHHHHHHHHHHHHHHhhcCCceEEEecCcccCcCCCCeEEec
Confidence            4799999999999999993  2 211  222221   123445555555443     3567999998433   23111  


Q ss_pred             hhHH-HHHHHHHHHHHhhccCCCcEEEEcCCCcHHHHHHH
Q 028759          128 PQSN-KVRSVAGRLAVRAAERGWRVYLLDEHRTSAEAVDR  166 (204)
Q Consensus       128 ~~~~-~v~~Fa~~L~~~~~~~~lpV~lvDER~TT~eA~~~  166 (204)
                      +..- .--.+.+.|++++   ++||++.+.-.....|+.+
T Consensus        79 ~~~~~~~~~l~~~l~~~~---~~pv~~~NDa~aaA~aE~~  115 (301)
T PRK09557         79 NSTWLNGQPLDKDLSARL---NREVRLANDANCLAVSEAV  115 (301)
T ss_pred             CCccccCCCHHHHHHHHH---CCCEEEccchhHHHHHHHH
Confidence            0000 1124566777775   8999998887776666644

>COG1940 NagC Transcriptional regulator/sugar kinase [Transcription / Carbohydrate transport and metabolism]

Probab=91.49  E-value=1.3  Score=38.97  Aligned_cols=103  Identities=18%  Similarity=0.157  Sum_probs=61.3

Q ss_pred             CceEEEEecCCCeEEEEEecCC---eeeeeeeEEccch--h----HHHHHHHHHHHc----CCCEEEEeecCCCCCCC--
Q 028759           62 GGFSLGVDLGLSRTGLALSKGF---CVRPLTVLKLRGE--K----LELQLLEIAQRE----ETDEFIIGLPKSWDGSE--  126 (204)
Q Consensus        62 ~g~iLalD~G~kRIGVAvsD~~---~A~Pl~~i~~~~~--~----~~~~L~~li~e~----~i~~IVVGlPl~~dGt~--  126 (204)
                      ...++|||+|..+|=+|+.|..   ........+....  .    ..+.+++++.++    .+.+|.++.|-..+...  
T Consensus         5 ~~~~lgidIggt~i~~~l~d~~g~~l~~~~~~~~~~~~~~~~~~~i~~~i~~~~~~~~~~~~~iGIgi~~pg~~~~~~~~   84 (314)
T COG1940           5 AMTVLGIDIGGTKIKVALVDLDGEILLRERIPTPTPDPEEAILEAILALVAELLKQAQGRVAIIGIGIPGPGDVDNGTVI   84 (314)
T ss_pred             CcEEEEEEecCCEEEEEEECCCCcEEEEEEEecCCCCchhHHHHHHHHHHHHHHHhcCCcCceEEEEeccceeccCCcEE
Confidence            5789999999999999999942   2222222221111  2    234455555543    35566666665444321  


Q ss_pred             --ChhHHHH--HHHHHHHHHhhccCCCcEEEEcCCCcHHHHHHHH
Q 028759          127 --TPQSNKV--RSVAGRLAVRAAERGWRVYLLDEHRTSAEAVDRM  167 (204)
Q Consensus       127 --~~~~~~v--~~Fa~~L~~~~~~~~lpV~lvDER~TT~eA~~~L  167 (204)
                        .+...-.  -.|++.|++.+   ++||...++-..-.-|+..+
T Consensus        85 ~~~~~~~~~~~~~l~~~L~~~~---~~Pv~veNDan~aalaE~~~  126 (314)
T COG1940          85 VPAPNLGWWNGVDLAEELEARL---GLPVFVENDANAAALAEAWF  126 (314)
T ss_pred             eecCCCCccccccHHHHHHHHH---CCCEEEecHHHHHHHHHHHh
Confidence              1111111  34788899886   89999999877777666554

>PRK05082 N-acetylmannosamine kinase; Provisional

Probab=91.13  E-value=3.8  Score=35.69  Aligned_cols=97  Identities=15%  Similarity=0.101  Sum_probs=59.4

Q ss_pred             eEEEEecCCCeEEEEEecC--C-eeeeeeeEEcc---c-hhHHHHHHHHHHHc--CCCEEEEeecCCCC-CCC---Ch-h
Q 028759           64 FSLGVDLGLSRTGLALSKG--F-CVRPLTVLKLR---G-EKLELQLLEIAQRE--ETDEFIIGLPKSWD-GSE---TP-Q  129 (204)
Q Consensus        64 ~iLalD~G~kRIGVAvsD~--~-~A~Pl~~i~~~---~-~~~~~~L~~li~e~--~i~~IVVGlPl~~d-Gt~---~~-~  129 (204)
                      .++|+|+|..++-+++.|-  . .+  ...++..   . ....+.+.+++.+.  ++.+|.||.|=..| |..   .+ .
T Consensus         2 ~~lgvdig~~~i~~~l~dl~g~i~~--~~~~~~~~~~~~~~~~~~i~~~i~~~~~~~~~igi~~pG~vd~~~~~~~~~~~   79 (291)
T PRK05082          2 TTLAIDIGGTKIAAALVGEDGQIRQ--RRQIPTPASQTPEALRQALSALVSPLQAQADRVAVASTGIINDGILTALNPHN   79 (291)
T ss_pred             cEEEEEECCCEEEEEEEcCCCcEEE--EEEecCCCCCCHHHHHHHHHHHHHHhhhcCcEEEEeCcccccCCeeEEecCCC
Confidence            4899999999999999993  2 22  1122211   1 23456666666653  67899999984332 211   10 0


Q ss_pred             H--HHHHHHHHHHHHhhccCCCcEEEEcCCCcHHHHHH
Q 028759          130 S--NKVRSVAGRLAVRAAERGWRVYLLDEHRTSAEAVD  165 (204)
Q Consensus       130 ~--~~v~~Fa~~L~~~~~~~~lpV~lvDER~TT~eA~~  165 (204)
                      .  -.-..+.+.|++++   ++||++.++-.+..-|+.
T Consensus        80 ~~~w~~~~l~~~l~~~~---~~pv~v~NDa~a~a~aE~  114 (291)
T PRK05082         80 LGGLLHFPLVQTLEQLT---DLPTIALNDAQAAAWAEY  114 (291)
T ss_pred             CccccCCChHHHHHHHh---CCCEEEECcHHHHHHHHH
Confidence            0  01124666777775   899999888777666654

>TIGR00744 ROK_glcA_fam ROK family protein (putative glucokinase)

Probab=89.68  E-value=1.4  Score=38.61  Aligned_cols=98  Identities=15%  Similarity=0.166  Sum_probs=56.6

Q ss_pred             EEEecCCCeEEEEEecCC-eeeeeeeEEc--cchhHHHHHH----HHHHH-----cCCCEEEEeecCCCCCCCChh----
Q 028759           66 LGVDLGLSRTGLALSKGF-CVRPLTVLKL--RGEKLELQLL----EIAQR-----EETDEFIIGLPKSWDGSETPQ----  129 (204)
Q Consensus        66 LalD~G~kRIGVAvsD~~-~A~Pl~~i~~--~~~~~~~~L~----~li~e-----~~i~~IVVGlPl~~dGt~~~~----  129 (204)
                      +|+|+|..++-+++.|.. ........+.  ......+.|.    +++++     .++.+|-||.|=..|...+..    
T Consensus         1 lgidig~t~~~~~l~d~~g~i~~~~~~~~~~~~~~~~~~l~~~i~~~~~~~~~~~~~i~gIgva~pG~vd~~~g~~~~~~   80 (318)
T TIGR00744         1 IGVDIGGTTIKLGVVDEEGNILSKWKVPTDTTPETIVDAIASAVDSFIQHIAKVGHEIVAIGIGAPGPVNRQRGTVYFAV   80 (318)
T ss_pred             CEEEeCCCEEEEEEECCCCCEEEEEEeCCCCCHHHHHHHHHHHHHHHHHhcCCCccceEEEEEeccccccCCCCEEEecC
Confidence            589999999999999931 1111111211  1223334444    44433     257789999984443222110    


Q ss_pred             ---HHHHHHHHHHHHHhhccCCCcEEEEcCCCcHHHHHHHH
Q 028759          130 ---SNKVRSVAGRLAVRAAERGWRVYLLDEHRTSAEAVDRM  167 (204)
Q Consensus       130 ---~~~v~~Fa~~L~~~~~~~~lpV~lvDER~TT~eA~~~L  167 (204)
                         -.. ..+.+.|++++   ++||++.+.-....-|+..+
T Consensus        81 ~~~w~~-~~l~~~l~~~~---~~pv~v~NDa~~~alaE~~~  117 (318)
T TIGR00744        81 NLDWKQ-EPLKEKVEARV---GLPVVVENDANAAALGEYKK  117 (318)
T ss_pred             CCCCCC-CCHHHHHHHHH---CCCEEEechHHHHHHHHHHh
Confidence               011 13667787775   89999998877766666543

This alignment models one branch of the ROK superfamily of proteins. The three members of the seed alignment for this model all have experimental evidence for activity as glucokinase, but the set of related proteins is crowded with paralogs of different or unknown function. Proteins scoring above the trusted_cutoff will show strong similarity to at least one known glucokinase and may be designated as putative glucokinases. However, definitive identification of glucokinases should be done only with extreme caution.

>PF01548 DEDD_Tnp_IS110: Transposase; InterPro: IPR002525 Transposase proteins are necessary for efficient DNA transposition

Probab=89.11  E-value=1.8  Score=33.68  Aligned_cols=107  Identities=15%  Similarity=0.079  Sum_probs=62.9

Q ss_pred             EEEEecCCCeEEEEEecCCe-eeeeeeEEccchhHHHHHHHHHHHcCCCEEEEeecCCCCCCCChhHHHHHHHHHHHHHh
Q 028759           65 SLGVDLGLSRTGLALSKGFC-VRPLTVLKLRGEKLELQLLEIAQREETDEFIIGLPKSWDGSETPQSNKVRSVAGRLAVR  143 (204)
Q Consensus        65 iLalD~G~kRIGVAvsD~~~-A~Pl~~i~~~~~~~~~~L~~li~e~~i~~IVVGlPl~~dGt~~~~~~~v~~Fa~~L~~~  143 (204)
                      ++|||+|....=+++.|... ......+.+ +...+..+.+.+.++.  .++||+  ..-|..+      ..++..|.. 
T Consensus         1 ~vGiDv~k~~~~v~v~~~~~~~~~~~~~~~-~~~~~~~l~~~l~~~~--~~~v~~--E~tg~y~------~~l~~~L~~-   68 (144)
T PF01548_consen    1 FVGIDVSKDTHDVCVIDPNGEKLRRFKFEN-DPAGLEKLLDWLASLG--PVLVVM--EATGGYW------RPLADFLQD-   68 (144)
T ss_pred             eEEEEcccCeEEEEEEcCCCcEEEEEEEec-cccchhHHhhhhcccc--cccccc--ccccccc------hhhhhheec-
Confidence            58999999999999999643 344444543 3344577777777775  555653  2223333      234444554 


Q ss_pred             hccCCCcEEEEcCCCcHHHHHHHHHHcCCCccccCCCCcHHHHHHHhcc
Q 028759          144 AAERGWRVYLLDEHRTSAEAVDRMINMGLSKSARQTKTDAYAAVVRQES  192 (204)
Q Consensus       144 ~~~~~lpV~lvDER~TT~eA~~~L~e~G~~rkkrK~~vD~~AA~iILq~  192 (204)
                         .+.+|++++=+.....++..    +  ++.+-.+.|+..-+.++..
T Consensus        69 ---~g~~v~~vnp~~~~~~~~~~----~--~~~KtD~~DA~~ia~~~~~  108 (144)
T PF01548_consen   69 ---AGIEVVVVNPLQVKRFRKSL----G--RRAKTDKIDARAIARLLRR  108 (144)
T ss_pred             ---cccccccccccccccccccc----c--ccccccccchHHHHHHHhc
Confidence               38999999765554433211    1  2223456676665555544

This entry represents the N-terminal region of the pilin gene inverting protein (PIVML) and members of the IS111A/IS1328/IS1533 family of 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

>PRK13310 N-acetyl-D-glucosamine kinase; Provisional

Probab=88.61  E-value=2.7  Score=36.84  Aligned_cols=100  Identities=15%  Similarity=0.118  Sum_probs=57.6

Q ss_pred             eEEEEecCCCeEEEEEecC--C-eeeeeeeEE-ccchhHHHHHHHHHHHc----C-CCEEEEeecCCCCCCCCh--hHH-
Q 028759           64 FSLGVDLGLSRTGLALSKG--F-CVRPLTVLK-LRGEKLELQLLEIAQRE----E-TDEFIIGLPKSWDGSETP--QSN-  131 (204)
Q Consensus        64 ~iLalD~G~kRIGVAvsD~--~-~A~Pl~~i~-~~~~~~~~~L~~li~e~----~-i~~IVVGlPl~~dGt~~~--~~~-  131 (204)
                      +++|||+|..+|-+++.|.  . ..+-....+ .......+.+.+++++.    . +..|-||.|=..|-..+.  ... 
T Consensus         1 ~~lgidig~t~i~~~l~d~~g~i~~~~~~~~~~~~~~~~~~~i~~~i~~~~~~~~~~~~igia~pG~vd~~~g~~~~~~~   80 (303)
T PRK13310          1 MYYGFDIGGTKIELGVFNEKLELQWEERVPTPRDSYDAFLDAVCELVAEADQRFGCKGSVGIGIPGMPETEDGTLYAANV   80 (303)
T ss_pred             CeEEEEeCCCcEEEEEECCCCcEEEEEEecCCCcCHHHHHHHHHHHHHHHHhhcCCcceEEEeCCCcccCCCCEEeccCc
Confidence            4799999999999999993  2 221111111 11223445566555442    2 347889988544321110  000 


Q ss_pred             ---HHHHHHHHHHHhhccCCCcEEEEcCCCcHHHHHHH
Q 028759          132 ---KVRSVAGRLAVRAAERGWRVYLLDEHRTSAEAVDR  166 (204)
Q Consensus       132 ---~v~~Fa~~L~~~~~~~~lpV~lvDER~TT~eA~~~  166 (204)
                         .--.+.+.|++++   ++||++.+.-..-..|+..
T Consensus        81 ~~w~~~~l~~~l~~~~---~~pV~ieNDa~aaalaE~~  115 (303)
T PRK13310         81 PAASGKPLRADLSARL---GRDVRLDNDANCFALSEAW  115 (303)
T ss_pred             ccccCCcHHHHHHHHH---CCCeEEeccHhHHHHHHhh
Confidence               0124667788775   8999998887666656543

>PRK13321 pantothenate kinase; Reviewed

Probab=86.07  E-value=13  Score=32.22  Aligned_cols=55  Identities=18%  Similarity=0.219  Sum_probs=36.5

Q ss_pred             eEEEEecCCCeEEEEEecCCeeeeeeeEEcc---c-hhHHHHHHHHHHHc-----CCCEEEEee
Q 028759           64 FSLGVDLGLSRTGLALSKGFCVRPLTVLKLR---G-EKLELQLLEIAQRE-----ETDEFIIGL  118 (204)
Q Consensus        64 ~iLalD~G~kRIGVAvsD~~~A~Pl~~i~~~---~-~~~~~~L~~li~e~-----~i~~IVVGl  118 (204)
                      ++|+||.|..+|=+|+.|+........++..   . ......+.++++++     +++.++|+-
T Consensus         1 MiL~IDIGnT~ik~gl~~~~~i~~~~~~~T~~~~~~~~~~~~l~~l~~~~~~~~~~i~~i~vss   64 (256)
T PRK13321          1 MLLLIDVGNTNIKLGVFDGDRLLRSFRLPTDKSRTSDELGILLLSLFRHAGLDPEDIRAVVISS   64 (256)
T ss_pred             CEEEEEECCCeEEEEEEECCEEEEEEEEecCCCCCHHHHHHHHHHHHHHcCCChhhCCeEEEEe
Confidence            4799999999999999985311111122211   1 23456788888776     489999994

>PRK09698 D-allose kinase; Provisional

Probab=85.54  E-value=7.9  Score=33.79  Aligned_cols=97  Identities=14%  Similarity=0.151  Sum_probs=56.8

Q ss_pred             ceEEEEecCCCeEEEEEecC--C-eee---eeeeEEccc---hhHHHHHHHHHHHc--CCCEEEEeecCCCCCCCC----
Q 028759           63 GFSLGVDLGLSRTGLALSKG--F-CVR---PLTVLKLRG---EKLELQLLEIAQRE--ETDEFIIGLPKSWDGSET----  127 (204)
Q Consensus        63 g~iLalD~G~kRIGVAvsD~--~-~A~---Pl~~i~~~~---~~~~~~L~~li~e~--~i~~IVVGlPl~~dGt~~----  127 (204)
                      ..++|+|+|..++-+++.|.  . .++   |..... ..   ..+.+.+.+++++.  ++.+|-||.|=..|...+    
T Consensus         4 ~~~lgidig~t~i~~~l~d~~g~i~~~~~~~~~~~~-~~~~~~~l~~~i~~~~~~~~~~i~gigia~pG~vd~~~g~i~~   82 (302)
T PRK09698          4 NVVLGIDMGGTHIRFCLVDAEGEILHCEKKRTAEVI-APDLVSGLGEMIDEYLRRFNARCHGIVMGFPALVSKDRRTVIS   82 (302)
T ss_pred             cEEEEEEcCCcEEEEEEEcCCCCEEEEEEeCCcccc-chHHHHHHHHHHHHHHHHcCCCeeEEEEeCCcceeCCCCEEEe
Confidence            57999999999999999992  2 222   221110 11   12234455666653  678999999844332111    


Q ss_pred             -hhH----HHHHHHHHHHHHhhccCCCcEEEEcCCCcHHHH
Q 028759          128 -PQS----NKVRSVAGRLAVRAAERGWRVYLLDEHRTSAEA  163 (204)
Q Consensus       128 -~~~----~~v~~Fa~~L~~~~~~~~lpV~lvDER~TT~eA  163 (204)
                       +..    -.-..+.+.|++++   ++||++.+.-.....|
T Consensus        83 ~~~~~~~~~~~~~l~~~l~~~~---~~pv~v~NDa~aaa~~  120 (302)
T PRK09698         83 TPNLPLTALDLYDLADKLENTL---NCPVFFSRDVNLQLLW  120 (302)
T ss_pred             cCCCCccccccCCHHHHHHHHh---CCCEEEcchHhHHHHH
Confidence             100    11124667787775   8999988875554434

>PF04848 Pox_A22: Poxvirus A22 protein; InterPro: IPR006932 This family, representing the Poxvirus A22 protein, is a Holliday junction resolvase, it specifically cleaves and resolves four-way DNA Holliday junctions into linear duplex products

Probab=85.39  E-value=19  Score=29.47  Aligned_cols=115  Identities=13%  Similarity=0.175  Sum_probs=65.2

Q ss_pred             eEEEEecCCCeEEEEEecCCeeeeeeeEEccc---hh--HHHHHHHHHHHcCCCEEEEeecCCCCCCCChhHHHHHHHHH
Q 028759           64 FSLGVDLGLSRTGLALSKGFCVRPLTVLKLRG---EK--LELQLLEIAQREETDEFIIGLPKSWDGSETPQSNKVRSVAG  138 (204)
Q Consensus        64 ~iLalD~G~kRIGVAvsD~~~A~Pl~~i~~~~---~~--~~~~L~~li~e~~i~~IVVGlPl~~dGt~~~~~~~v~~Fa~  138 (204)
                      .++|||+|.+..|..+-+..... +..+..+.   +.  ....+.++++ ++++.|+|=-    +...++.. ++..|.+
T Consensus         2 ii~sIDiGikNlA~~iie~~~~~-i~~~~i~~~~~~~~~~~~~~~dl~~-~~~d~VlIEr----Q~~r~~~~-~i~~fI~   74 (143)
T PF04848_consen    2 IILSIDIGIKNLAYCIIEFEGNK-IRVIDISKVDWSRDWEYRILKDLLK-YEADTVLIER----QPPRNPNV-KIVHFIH   74 (143)
T ss_pred             eEEEEecCCCceeEEEEEcCCCe-EEEEEeccCCcccchHHHHHHHHhh-ccCCEEEEec----CCCCCcch-hHHHHHH
Confidence            58999999999999999942111 33332211   11  1233444544 9999999984    34444433 4455654


Q ss_pred             HHHHhhccCCCcEEEEcCCC-----------cHHHHHHHHHHcCCCccccC-CCCcHHHHHH
Q 028759          139 RLAVRAAERGWRVYLLDEHR-----------TSAEAVDRMINMGLSKSARQ-TKTDAYAAVV  188 (204)
Q Consensus       139 ~L~~~~~~~~lpV~lvDER~-----------TT~eA~~~L~e~G~~rkkrK-~~vD~~AA~i  188 (204)
                      ..-.   ..+..|..+|=.+           |-.-++..+.+.|...--.+ +++|++|=++
T Consensus        75 ~~f~---~~~~kv~~v~p~~~~~~Y~~RKk~SVe~~~~~~~~~~~~~~i~~~kK~DDlADa~  133 (143)
T PF04848_consen   75 GYFY---IKNTKVICVSPKMKGWSYRERKKRSVEVFKNWIKEFGIDDFIPKSKKKDDLADAF  133 (143)
T ss_pred             HHhc---cCCceEEEECcccccCCHHHHHHHHHHHHHHHHHhCCchhhchhhccchHHHHHH
Confidence            4432   2367888888553           33444555555443321122 4668887665

; GO: 0000287 magnesium ion binding, 0000400 four-way junction DNA binding, 0016788 hydrolase activity, acting on ester bonds, 0006281 DNA repair, 0006310 DNA recombination

>PRK13311 N-acetyl-D-glucosamine kinase; Provisional

Probab=84.84  E-value=8.9  Score=32.93  Aligned_cols=99  Identities=14%  Similarity=0.098  Sum_probs=59.3

Q ss_pred             eEEEEecCCCeEEEEEecCC-eeeeeeeEEc---cchhHHHHHHHHHHHc-----CCCEEEEeecCCCC---CCC----C
Q 028759           64 FSLGVDLGLSRTGLALSKGF-CVRPLTVLKL---RGEKLELQLLEIAQRE-----ETDEFIIGLPKSWD---GSE----T  127 (204)
Q Consensus        64 ~iLalD~G~kRIGVAvsD~~-~A~Pl~~i~~---~~~~~~~~L~~li~e~-----~i~~IVVGlPl~~d---Gt~----~  127 (204)
                      +++|+|+|..++-+++.|.. .......++.   +..+..+.+.+++++.     .+.+|-||.|=-.|   |..    .
T Consensus         1 ~~lgidiggt~i~~~l~d~~g~i~~~~~~~~~~~~~~~~~~~i~~~i~~~~~~~~~~~gIgv~~pG~vd~~~g~i~~~~~   80 (256)
T PRK13311          1 MYYGFDMGGTKIELGVFDENLQRIWHKRVPTPREDYPQLLQILRDLTEEADTYCGVQGSVGIGIPGLPNADDGTVFTANV   80 (256)
T ss_pred             CEEEEEECCCcEEEEEECCCCCEEEEEEecCCCcCHHHHHHHHHHHHHHHHhhcCCCceEEEEecCcEECCCCEEEccCC
Confidence            47999999999999999931 1111111211   1123455666666543     23578888884222   211    0


Q ss_pred             hhHHHHHHHHHHHHHhhccCCCcEEEEcCCCcHHHHHHH
Q 028759          128 PQSNKVRSVAGRLAVRAAERGWRVYLLDEHRTSAEAVDR  166 (204)
Q Consensus       128 ~~~~~v~~Fa~~L~~~~~~~~lpV~lvDER~TT~eA~~~  166 (204)
                      +.-.. ..+++.|++++   ++||.+-++-.....|+.+
T Consensus        81 ~~w~~-~~l~~~l~~~~---~~pV~leNDanaaAlaE~~  115 (256)
T PRK13311         81 PSAMG-QPLQADLSRLI---QREVRIDNDANCFALSEAW  115 (256)
T ss_pred             CcccC-CChHHHHHHHH---CCCEEEEchhhHHHHHHHH
Confidence            11111 36777888775   8999999987777767654

>PF14239 RRXRR: RRXRR protein

Probab=84.25  E-value=2.6  Score=35.71  Aligned_cols=22  Identities=32%  Similarity=0.453  Sum_probs=19.4

Q ss_pred             CceEEEEecCCCeEEEEEecCC
Q 028759           62 GGFSLGVDLGLSRTGLALSKGF   83 (204)
Q Consensus        62 ~g~iLalD~G~kRIGVAvsD~~   83 (204)
                      ....|+||+|.|.+|+|+.+..
T Consensus        50 qpi~lgiDpGsk~tGiav~~~~   71 (176)
T PF14239_consen   50 QPIRLGIDPGSKTTGIAVVSEK   71 (176)
T ss_pred             cCEEEEECCCCCeEEEEEEeCC
Confidence            3578999999999999999864

>PF07318 DUF1464: Protein of unknown function (DUF1464); InterPro: IPR009927 This family consists of several hypothetical archaeal proteins of around 350 residues in length

Probab=83.82  E-value=5.4  Score=37.10  Aligned_cols=96  Identities=18%  Similarity=0.115  Sum_probs=54.7

Q ss_pred             EEecCCCeEEEEEecC-CeeeeeeeEEccc-hhHHHHHHHHHHHc-CCCEEEE----eecCCCCCCCCh-----------
Q 028759           67 GVDLGLSRTGLALSKG-FCVRPLTVLKLRG-EKLELQLLEIAQRE-ETDEFII----GLPKSWDGSETP-----------  128 (204)
Q Consensus        67 alD~G~kRIGVAvsD~-~~A~Pl~~i~~~~-~~~~~~L~~li~e~-~i~~IVV----GlPl~~dGt~~~-----------  128 (204)
                      |+|+||+-+-++..|. --..-...+++.. .+....+.+.++++ ++|.|+.    |+|+..-...++           
T Consensus         1 GIDpGT~s~dv~~~dd~g~v~~~~~ipt~~v~~~p~~iv~~l~~~~~~dlIa~psGyG~pl~~~~ei~d~e~~l~tl~~~   80 (343)
T PF07318_consen    1 GIDPGTKSFDVCGLDDDGKVIFYFSIPTEEVAKNPSIIVEELEEFGDIDLIAGPSGYGLPLKRIREITDREIFLLTLIEE   80 (343)
T ss_pred             CCCCCCCcEEEEEEccCCcEEEEeeccHHHhhhCHHHHHHHHHhccCCCEEEeCCcCCcccccccccchhhhhceEeecc
Confidence            6899999999999986 2222222233211 12334577777777 9998886    667543222211           


Q ss_pred             -hHH----HHHHHHHHHHHhhccCCCcEEEEc--CCCcHHHHHHH
Q 028759          129 -QSN----KVRSVAGRLAVRAAERGWRVYLLD--EHRTSAEAVDR  166 (204)
Q Consensus       129 -~~~----~v~~Fa~~L~~~~~~~~lpV~lvD--ER~TT~eA~~~  166 (204)
                       ...    -.+++...+++.    ++|+++.-  =.+.|+-+.+.
T Consensus        81 ~~~g~~~~Glr~~~~~l~~~----~l~~~~iPgVi~LptVP~~RK  121 (343)
T PF07318_consen   81 SEVGRRIGGLRKLVRELAES----NLPAYFIPGVIHLPTVPAWRK  121 (343)
T ss_pred             cccccccccHHHHHHHHHhC----CCCEEEeCceeccCCCchHhh
Confidence             001    145566666443    67777664  35666665444

The function of this family is unknown.

>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins

Probab=82.85  E-value=1.2  Score=31.02  Aligned_cols=54  Identities=28%  Similarity=0.247  Sum_probs=32.7

Q ss_pred             HHHHHHHHhhccCCCcEEEEcCCCcHHHHHHHHHHcCCCccc----c---------CCCCcHHHHHHHhcc
Q 028759          135 SVAGRLAVRAAERGWRVYLLDEHRTSAEAVDRMINMGLSKSA----R---------QTKTDAYAAVVRQES  192 (204)
Q Consensus       135 ~Fa~~L~~~~~~~~lpV~lvDER~TT~eA~~~L~e~G~~rkk----r---------K~~vD~~AA~iILq~  192 (204)
                      +|.+.|+....+.|++|+.+||.+||..--.    -|...+.    +         ...-|-.||.-|+++
T Consensus         3 ~~~~~L~yka~~~G~~v~~v~~~~TSq~C~~----CG~~~~~~~~~r~~~C~~Cg~~~~rD~naA~NI~~r   69 (69)
T PF07282_consen    3 QFRQRLEYKAEEYGIQVVEVDEAYTSQTCPR----CGHRNKKRRSGRVFTCPNCGFEMDRDVNAARNILRR   69 (69)
T ss_pred             HHHHHHHHHHHHhCCEEEEECCCCCccCccC----cccccccccccceEEcCCCCCEECcHHHHHHHHhcC
Confidence            3444555444346999999999999885421    1111111    0         134589999988863

More information about these proteins can be found at Protein of the Month: Transposase [].

>PRK00292 glk glucokinase; Provisional

Probab=82.34  E-value=8.9  Score=33.94  Aligned_cols=98  Identities=15%  Similarity=0.166  Sum_probs=56.4

Q ss_pred             eEEEEecCCCeEEEEEec-CC-eeeeeeeEEccc-hhHHHHHHHHHHH---cCCCEEEEeecCCCCCCCChhHHH-HHHH
Q 028759           64 FSLGVDLGLSRTGLALSK-GF-CVRPLTVLKLRG-EKLELQLLEIAQR---EETDEFIIGLPKSWDGSETPQSNK-VRSV  136 (204)
Q Consensus        64 ~iLalD~G~kRIGVAvsD-~~-~A~Pl~~i~~~~-~~~~~~L~~li~e---~~i~~IVVGlPl~~dGt~~~~~~~-v~~F  136 (204)
                      .+||+|+|..+|=+++.| .. .......++.+. ....+.+.+++++   .++..|.||.|=..|...-..+.. -...
T Consensus         3 ~~lgiDIGgT~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~gigIg~pG~vd~~~i~~~n~~w~~~   82 (316)
T PRK00292          3 PALVGDIGGTNARFALCDWANGEIEQIKTYATADYPSLEDAIRAYLADEHGVQVRSACFAIAGPVDGDEVRMTNHHWAFS   82 (316)
T ss_pred             eEEEEEcCccceEEEEEecCCCceeeeEEEecCCCCCHHHHHHHHHHhccCCCCceEEEEEeCcccCCEEEecCCCcccC
Confidence            589999999999999997 22 111122333221 2355667777764   357899999985433211000000 0112


Q ss_pred             HHHHHHhhccCCCc-EEEEcCCCcHHHHH
Q 028759          137 AGRLAVRAAERGWR-VYLLDEHRTSAEAV  164 (204)
Q Consensus       137 a~~L~~~~~~~~lp-V~lvDER~TT~eA~  164 (204)
                      .+.|++++   ++| |++.+.-..-.-|+
T Consensus        83 ~~~l~~~~---~~p~v~l~ND~~aaalgE  108 (316)
T PRK00292         83 IAAMKQEL---GLDHLLLINDFTAQALAI  108 (316)
T ss_pred             HHHHHHHh---CCCeEEEEecHHHHHccc
Confidence            46677765   886 99888754444443

>COG4012 Uncharacterized protein conserved in archaea [Function unknown]

Probab=81.64  E-value=11  Score=34.40  Aligned_cols=96  Identities=26%  Similarity=0.331  Sum_probs=64.5

Q ss_pred             eEEEEecCCCeEEEEEecCC-eeeeeeeEEccchhHHHHHHHHHHHcCCCEEEEeecCCCCCCCChhHHHHHHHHHHHHH
Q 028759           64 FSLGVDLGLSRTGLALSKGF-CVRPLTVLKLRGEKLELQLLEIAQREETDEFIIGLPKSWDGSETPQSNKVRSVAGRLAV  142 (204)
Q Consensus        64 ~iLalD~G~kRIGVAvsD~~-~A~Pl~~i~~~~~~~~~~L~~li~e~~i~~IVVGlPl~~dGt~~~~~~~v~~Fa~~L~~  142 (204)
                      .+|++|+|.-..-|-.-|+. --++.-+.+........+|..+.+ +.+..+++|-|  |.|..+.     ++|-+.|++
T Consensus         2 kila~DvG~GTqDi~~~d~~~EnSl~mVmPspt~~~A~R~R~~~~-~g~~l~l~G~~--MGGGp~t-----ravrrhlk~   73 (342)
T COG4012           2 KILAIDVGVGTQDIVAYDGDPENSLRMVMPSPTSTLAQRLRFMLR-EGPYLALIGVP--MGGGPTT-----RAVRRHLKK   73 (342)
T ss_pred             ceEEEEecCCceeEEEecCCcccceeEeecCchHHHHHHHHHHhc-cCCcEEEEeee--cCCChhh-----HHHHHHHhc
Confidence            58999999999988888864 456666666544455667777665 56699999977  4565443     445555653


Q ss_pred             hhccCCCcEEEE-cCCCcHHHHHHHHHHcCC
Q 028759          143 RAAERGWRVYLL-DEHRTSAEAVDRMINMGL  172 (204)
Q Consensus       143 ~~~~~~lpV~lv-DER~TT~eA~~~L~e~G~  172 (204)
                           +.+|+-- |--+|-..--+++.++|+
T Consensus        74 -----G~rVyatedAAlT~hddleRv~emgi   99 (342)
T COG4012          74 -----GTRVYATEDAALTLHDDLERVEEMGI   99 (342)
T ss_pred             -----CCeeEechhhhhhhhcCHHHHHhhCe
Confidence                 6777654 334555555677778775

>PHA02942 putative transposase; Provisional

Probab=80.23  E-value=3.4  Score=38.57  Aligned_cols=81  Identities=12%  Similarity=0.076  Sum_probs=47.1

Q ss_pred             HcCCCEEEEeecCCCCCCCChhHHHHH---------HHHHHHHHhhccCCCcEEEEcCCCcHHHHHHHHHHcCCCccc--
Q 028759          108 REETDEFIIGLPKSWDGSETPQSNKVR---------SVAGRLAVRAAERGWRVYLLDEHRTSAEAVDRMINMGLSKSA--  176 (204)
Q Consensus       108 e~~i~~IVVGlPl~~dGt~~~~~~~v~---------~Fa~~L~~~~~~~~lpV~lvDER~TT~eA~~~L~e~G~~rkk--  176 (204)
                      +++.+.|||+...+|........+.+.         .|...|+-.....|++|+.+|+++||..--    ..|...+.  
T Consensus       264 ~~~~~~IviEdL~gm~k~~~~l~k~~~~~~~~~~~~~l~~~LeYKA~~~G~~Vv~V~p~yTSq~Cs----~CG~~~~~l~  339 (383)
T PHA02942        264 DLGANVIKLEDLKNLIKDVNKLPAEFRDKLYLMQYHRIQYWIEWQAKKHGMIVEFVNPSYSSVSCP----KCGHKMVEIA  339 (383)
T ss_pred             hCCCCEEEEccHHHHHhcccccchHHHHHhhhhhHHHHHHHHHHHHHHhCCEEEEECCCCCCccCC----CCCCccCcCC
Confidence            556789999988766543222222222         222344433233699999999999986432    12321111  


Q ss_pred             -c---------CCCCcHHHHHHHhcc
Q 028759          177 -R---------QTKTDAYAAVVRQES  192 (204)
Q Consensus       177 -r---------K~~vD~~AA~iILq~  192 (204)
                       +         ...-|-.||.-|+..
T Consensus       340 ~r~f~C~~CG~~~drD~nAA~NI~~r  365 (383)
T PHA02942        340 HRYFHCPSCGYENDRDVIAIMNLNGR  365 (383)
T ss_pred             CCEEECCCCCCEeCcHHHHHHHHHHH
Confidence             1         134688999999876

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	204
1nmn_A	138	Structure Of Yqgf From Escherichia Coli, A Hypothet		6e-08
1ovq_A	138	Solution Structure Of The Hypothetical Protein Yqgf		6e-08
1nu0_A	138	Structure Of The Double Mutant (L6m; F134m, Semet F		1e-07

>pdb|1NMN|A Chain A, Structure Of Yqgf From Escherichia Coli, A Hypothetical Protein Length = 138

Iteration: 1
 Score = 53.9 bits (128), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 40/133 (30%), Positives = 65/133 (48%), Gaps = 6/133 (4%)
Query: 63  GFSLGVDLGLSRTGLALSKGFC--VRPLTVLKLRGEKLELQLLEIAQRE-ETDEFIIGLP 119
           G  L  D G    G+A+ +      RPL  +K +    +  ++E   +E + DE I+GLP
Sbjct: 3   GTLLAFDFGTKSIGVAVGQRITGTARPLPAIKAQDGTPDWNIIERLLKEWQPDEIIVGLP 62
Query: 120 KSWDGSETPQSNKVRSVAGRLAVRAAERGWRVYLLDEHRTSAEAVDRMINMGLSKSARQT 179
            + DG+E P + + R  A R+  R    G  V L DE  ++ EA   +   G  ++  + 
Sbjct: 63  LNMDGTEQPLTARARKFANRIHGRF---GVEVKLHDERLSTVEARSGLFEQGGYRALNKG 119
Query: 180 KTDAYAAVVRQES 192
           K D+ +AV+  ES
Sbjct: 120 KVDSASAVIILES 132

>pdb|1OVQ|A Chain A, Solution Structure Of The Hypothetical Protein Yqgf From Escherichia Coli Length = 138

Iteration: 1
 Score = 53.9 bits (128), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 40/133 (30%), Positives = 65/133 (48%), Gaps = 6/133 (4%)
Query: 63  GFSLGVDLGLSRTGLALSKGFC--VRPLTVLKLRGEKLELQLLEIAQRE-ETDEFIIGLP 119
           G  L  D G    G+A+ +      RPL  +K +    +  ++E   +E + DE I+GLP
Sbjct: 3   GTLLAFDFGTKSIGVAVGQRITGTARPLPAIKAQDGTPDWNIIERLLKEWQPDEIIVGLP 62
Query: 120 KSWDGSETPQSNKVRSVAGRLAVRAAERGWRVYLLDEHRTSAEAVDRMINMGLSKSARQT 179
            + DG+E P + + R  A R+  R    G  V L DE  ++ EA   +   G  ++  + 
Sbjct: 63  LNMDGTEQPLTARARKFANRIHGRF---GVEVKLHDERLSTVEARSGLFEQGGYRALNKG 119
Query: 180 KTDAYAAVVRQES 192
           K D+ +AV+  ES
Sbjct: 120 KVDSASAVIILES 132

>pdb|1NU0|A Chain A, Structure Of The Double Mutant (L6m; F134m, Semet Form) Of Yqgf From Escherichia Coli, A Hypothetical Protein Length = 138

Iteration: 1
 Score = 53.1 bits (126), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 42/132 (31%), Positives = 66/132 (50%), Gaps = 11/132 (8%)
Query: 62  GGFSLGVDLGLSRTGLALSKGFCVRPLTVLKLRGEKLELQLLEIAQRE-ETDEFIIGLPK 120
           G  S+GV +G   TG A       RPL  +K +    +  ++E   +E + DE I+GLP 
Sbjct: 11  GTKSIGVAVGQRITGTA-------RPLPAIKAQDGTPDWNIIERLLKEWQPDEIIVGLPL 63
Query: 121 SWDGSETPQSNKVRSVAGRLAVRAAERGWRVYLLDEHRTSAEAVDRMINMGLSKSARQTK 180
           + DG+E P + + R  A R+  R    G  V L DE  ++ EA   +   G  ++  + K
Sbjct: 64  NXDGTEQPLTARARKFANRIHGRF---GVEVKLHDERLSTVEARSGLFEQGGYRALNKGK 120
Query: 181 TDAYAAVVRQES 192
            D+ +AV+  ES
Sbjct: 121 VDSASAVIILES 132

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	204
1nu0_A	138	Hypothetical protein YQGF; structural genomics, st	9e-24
1vhx_A	150	Putative holliday junction resolvase; structural g	1e-23
1iv0_A	98	Hypothetical protein; rnaseh-like, YQGF, structura	4e-17

>1nu0_A Hypothetical protein YQGF; structural genomics, structure 2 function project, S2F, unknown function; 1.60A {Escherichia coli} SCOP: c.55.3.8 PDB: 1nmn_A 1ovq_A Length = 138

 Score = 90.7 bits (226), Expect = 9e-24
 Identities = 34/126 (26%), Positives = 59/126 (46%), Gaps = 6/126 (4%)

Query: 66  LGVDLGLSRTGLALS--KGFCVRPLTVLKLRGEKLEL-QLLEIAQREETDEFIIGLPKSW 122
           +  D G    G+A+        RPL  +K +    +   +  + +  + DE I+GLP + 
Sbjct: 6   MAFDFGTKSIGVAVGQRITGTARPLPAIKAQDGTPDWNIIERLLKEWQPDEIIVGLPLNM 65

Query: 123 DGSETPQSNKVRSVAGRLAVRAAERGWRVYLLDEHRTSAEAVDRMINMGLSKSARQTKTD 182
           DG+E P + + R  A R+  R    G  V L DE  ++ EA   +   G  ++  + K D
Sbjct: 66  DGTEQPLTARARKFANRIHGR---FGVEVKLHDERLSTVEARSGLFEQGGYRALNKGKVD 122

Query: 183 AYAAVV 188
           + +AV+
Sbjct: 123 SASAVI 128

>1vhx_A Putative holliday junction resolvase; structural genomics, hydrolase; 1.96A {Bacillus subtilis} SCOP: c.55.3.8 Length = 150

 Score = 90.8 bits (226), Expect = 1e-23
 Identities = 34/128 (26%), Positives = 60/128 (46%), Gaps = 8/128 (6%)

Query: 66  LGVDLGLSRTGLALS--KGFCVRPLTVL---KLRGEKLELQLLEIAQREETDEFIIGLPK 120
           LG+DLG    G+ALS   G+  + +  +   +  G+    +L E+ +    D+ ++G PK
Sbjct: 6   LGLDLGTKTLGVALSDEMGWTAQGIETIKINEAEGDYGLSRLSELIKDYTIDKIVLGFPK 65

Query: 121 SWDGSETPQSNKVRSVAGRLAVRAAERGWRVYLLDEHRTSAEAVDRMINMGLSKSARQTK 180
           + +G+  P+    ++ A  L          V L DE  T+  A   +I   +S+  R+  
Sbjct: 66  NMNGTVGPRGEASQTFAKVLETT---YNVPVVLWDERLTTMAAEKMLIAADVSRQKRKKV 122

Query: 181 TDAYAAVV 188
            D  AAV+
Sbjct: 123 IDKMAAVM 130

>1iv0_A Hypothetical protein; rnaseh-like, YQGF, structural genomics, riken structural genomics/proteomics initiative, RSGI, unknown function; NMR {Thermus thermophilus} SCOP: c.55.3.8 Length = 98

 Score = 72.2 bits (178), Expect = 4e-17
 Identities = 27/98 (27%), Positives = 44/98 (44%), Gaps = 7/98 (7%)

Query: 66  LGVDLGLSRTGLALS--KGFCVRPLTVLKLRGEKLEL-QLLEIAQREETDEFIIGLPKSW 122
             +D+G +R GLA+             L  +  + ++  LL+  +RE   + ++GLP   
Sbjct: 4   GALDVGEARIGLAVGEEGVPLASGRGYLVRKTLEEDVEALLDFVRREGLGKLVVGLPLRT 63

Query: 123 DGSETPQSNKVRSVAGRLAVRAAERGWRVYLLDEHRTS 160
           D  E+ Q+ KV  +   L      RG  V L DE  T+
Sbjct: 64  DLKESAQAGKVLPLVEAL----RARGVEVELWDERFTT 97

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

No hit with probability above 80.00

---

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	204
d1vhxa_	140	c.55.3.8 (A:) Hypothetical protein YrrK (RuvX) {Ba	5e-17
d1nu0a_	138	c.55.3.8 (A:) Hypothetical protein YqgF (RuvX) {Es	3e-15
d1iv0a_	98	c.55.3.8 (A:) Hypothetical protein, YqgF homologue	2e-12

>d1vhxa_ c.55.3.8 (A:) Hypothetical protein YrrK (RuvX) {Bacillus subtilis [TaxId: 1423]} Length = 140

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Ribonuclease H-like
family: Putative Holliday junction resolvase RuvX
domain: Hypothetical protein YrrK (RuvX)
species: Bacillus subtilis [TaxId: 1423]

 Score = 72.1 bits (176), Expect = 5e-17
 Identities = 35/128 (27%), Positives = 61/128 (47%), Gaps = 8/128 (6%)

Query: 66  LGVDLGLSRTGLALS--KGFCVRPLTVLKLR---GEKLELQLLEIAQREETDEFIIGLPK 120
           LG+DLG    G+ALS   G+  + +  +K+    G+    +L E+ +    D+ ++G PK
Sbjct: 5   LGLDLGTKTLGVALSDEMGWTAQGIETIKINEAEGDYGLSRLSELIKDYTIDKIVLGFPK 64

Query: 121 SWDGSETPQSNKVRSVAGRLAVRAAERGWRVYLLDEHRTSAEAVDRMINMGLSKSARQTK 180
           + +G+  P+    ++ A  L          V L DE  T+  A   +I   +S+  R+  
Sbjct: 65  NMNGTVGPRGEASQTFAKVLETT---YNVPVVLWDERLTTMAAEKMLIAADVSRQKRKKV 121

Query: 181 TDAYAAVV 188
            D  AAV+
Sbjct: 122 IDKMAAVM 129

>d1nu0a_ c.55.3.8 (A:) Hypothetical protein YqgF (RuvX) {Escherichia coli [TaxId: 562]} Length = 138

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Ribonuclease H-like
family: Putative Holliday junction resolvase RuvX
domain: Hypothetical protein YqgF (RuvX)
species: Escherichia coli [TaxId: 562]

 Score = 67.4 bits (164), Expect = 3e-15
 Identities = 35/126 (27%), Positives = 61/126 (48%), Gaps = 6/126 (4%)

Query: 66  LGVDLGLSRTGLALS--KGFCVRPLTVLKLRGEKLELQLLE-IAQREETDEFIIGLPKSW 122
           +  D G    G+A+        RPL  +K +    +  ++E + +  + DE I+GLP + 
Sbjct: 6   MAFDFGTKSIGVAVGQRITGTARPLPAIKAQDGTPDWNIIERLLKEWQPDEIIVGLPLNM 65

Query: 123 DGSETPQSNKVRSVAGRLAVRAAERGWRVYLLDEHRTSAEAVDRMINMGLSKSARQTKTD 182
           DG+E P + + R  A R+  R    G  V L DE  ++ EA   +   G  ++  + K D
Sbjct: 66  DGTEQPLTARARKFANRIHGR---FGVEVKLHDERLSTVEARSGLFEQGGYRALNKGKVD 122

Query: 183 AYAAVV 188
           + +AV+
Sbjct: 123 SASAVI 128

>d1iv0a_ c.55.3.8 (A:) Hypothetical protein, YqgF homologue {Thermus thermophilus [TaxId: 274]} Length = 98

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Ribonuclease H-like
family: Putative Holliday junction resolvase RuvX
domain: Hypothetical protein, YqgF homologue
species: Thermus thermophilus [TaxId: 274]

 Score = 58.8 bits (142), Expect = 2e-12
 Identities = 27/98 (27%), Positives = 45/98 (45%), Gaps = 7/98 (7%)

Query: 66  LGVDLGLSRTGLALS--KGFCVRPLTVLKLRGEKLELQ-LLEIAQREETDEFIIGLPKSW 122
             +D+G +R GLA+             L  +  + +++ LL+  +RE   + ++GLP   
Sbjct: 4   GALDVGEARIGLAVGEEGVPLASGRGYLVRKTLEEDVEALLDFVRREGLGKLVVGLPLRT 63

Query: 123 DGSETPQSNKVRSVAGRLAVRAAERGWRVYLLDEHRTS 160
           D  E+ Q+ KV  +   L      RG  V L DE  T+
Sbjct: 64  DLKESAQAGKVLPLVEAL----RARGVEVELWDERFTT 97

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	204
d1nu0a_	138	Hypothetical protein YqgF (RuvX) {Escherichia coli	100.0
d1vhxa_	140	Hypothetical protein YrrK (RuvX) {Bacillus subtili	100.0
d1iv0a_	98	Hypothetical protein, YqgF homologue {Thermus ther	99.96
d3bzka5	149	Transcriptional accessory factor Tex {Pseudomonas	98.83
d1hjra_	158	RuvC resolvase {Escherichia coli [TaxId: 562]}	97.92
d1xc3a1	118	Putative fructokinase YhdR {Bacillus subtilis [Tax	96.18
d2ap1a2	117	Putative regulator protein YcfX {Salmonella typhim	95.51
d1z05a3	128	Transcriptional regulator VC2007 {Vibrio cholerae	94.82
d2hoea3	128	N-acetylglucosamine kinase {Thermotoga maritima [T	94.77
d1z6ra2	129	Mlc protein {Escherichia coli [TaxId: 562]}	94.15
d2aa4a1	119	N-acetylmannosamine kinase NanK {Escherichia coli	92.19
d2gupa1	114	Hypothetical protein SP2142 {Streptococcus pneumon	91.71
d1woqa1	129	Inorganic polyphosphate/ATP-glucomannokinase PPGMK	90.33
d1bupa1	185	Heat shock protein 70kDa, ATPase fragment {Cow (Bo	86.65
d1okja1	106	Hypothetical protein YeaZ {Escherichia coli [TaxId	85.2
d1dkgd1	183	Heat shock protein 70kDa, ATPase fragment {Escheri	84.47

>d1nu0a_ c.55.3.8 (A:) Hypothetical protein YqgF (RuvX) {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Ribonuclease H-like
family: Putative Holliday junction resolvase RuvX
domain: Hypothetical protein YqgF (RuvX)
species: Escherichia coli [TaxId: 562]

Probab=100.00  E-value=4.1e-40  Score=245.07  Aligned_cols=132  Identities=29%  Similarity=0.409  Sum_probs=123.7

Q ss_pred             CCEEEEEECCCCEEEEEEECC--CEEEEEEEEECCC-HHHHHHHHHHHHHCCCCEEEEEECCCCCCCCCHHHHHHHHHHH
Q ss_conf             952999935998199998529--7234405677256-2589999999987399989994147999999845799999999
Q 028759           62 GGFSLGVDLGLSRTGLALSKG--FCVRPLTVLKLRG-EKLELQLLEIAQREETDEFIIGLPKSWDGSETPQSNKVRSVAG  138 (204)
Q Consensus        62 ~~~iLglD~G~krIGiAisD~--~~A~Pl~vi~~~~-~~~~~~L~~li~e~~v~~iVIGlP~~~dGt~s~~~~~i~~Fa~  138 (204)
                      .||+||||||+||||+|+||.  .+|+|++++.+++ ..++..|.+++.+|+++.+|||+|++|+|+++++++.+++|++
T Consensus         2 ~griLgiD~G~kriGvAvsd~~~~~a~pl~~i~~~~~~~~~~~l~~i~~e~~~~~iVvG~P~~~~g~~~~~~~~v~~f~~   81 (138)
T d1nu0a_           2 SGTLMAFDFGTKSIGVAVGQRITGTARPLPAIKAQDGTPDWNIIERLLKEWQPDEIIVGLPLNMDGTEQPLTARARKFAN   81 (138)
T ss_dssp             CCEEEEEECCSSEEEEEEEETTTTEEEEEEEEEEETTEECHHHHHHHHHHHCCSEEEEEEEECTTSCBCHHHHHHHHHHH
T ss_pred             CCCEEEEEECCCEEEEEEECCCCCCCCCCEEEECCCCHHHHHHHHHHHHCCCCCEEEEECCCCCCCCHHHHHHHHHHHHH
T ss_conf             97489999389989999937987742542555503640569999987540476389961432235555799999999999


Q ss_pred             HHHHHHCCCCCCEEEECCCCCHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHCC-CCCC
Q ss_conf             998863328972899718772899999999749996645888939999998323-3359
Q 028759          139 RLAVRAAERGWRVYLLDEHRTSAEAVDRMINMGLSKSARQTKTDAYAAVVRQES-ITFG  196 (204)
Q Consensus       139 ~L~~~~~~~~lpV~l~DER~ST~~A~~~L~e~g~sr~krk~~iD~~AA~iILQ~-~~~g  196 (204)
                      +|+.++   ++||++||||+||.+|++.+++.|.+++++|+.+|++||++|||+ |+.+
T Consensus        82 ~L~~~~---~i~V~~~DEr~TS~eA~~~l~~~~~~~~~~k~~iD~~AA~lILq~~L~~~  137 (138)
T d1nu0a_          82 RIHGRF---GVEVKLHDERLSTVEARSGLFEQGGYRALNKGKVDSASAVIILESYMEQG  137 (138)
T ss_dssp             HHHHHH---CCCEEEEEEECCCCCC-------CCCCCCCHHHHTTHHHHHHHHHHHHTT
T ss_pred             HHHHCC---CCCEEEEECCCCHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHCC
T ss_conf             985454---98769971532499999999973563210465465999999999999736

>d1vhxa_ c.55.3.8 (A:) Hypothetical protein YrrK (RuvX) {Bacillus subtilis [TaxId: 1423]}

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Ribonuclease H-like
family: Putative Holliday junction resolvase RuvX
domain: Hypothetical protein YrrK (RuvX)
species: Bacillus subtilis [TaxId: 1423]

Probab=100.00  E-value=7.9e-39  Score=237.78  Aligned_cols=129  Identities=26%  Similarity=0.356  Sum_probs=119.7

Q ss_pred             CEEEEEECCCCEEEEEEECC--CEEEEEEEEECCCH---HHHHHHHHHHHHCCCCEEEEEECCCCCCCCCHHHHHHHHHH
Q ss_conf             52999935998199998529--72344056772562---58999999998739998999414799999984579999999
Q 028759           63 GFSLGVDLGLSRTGLALSKG--FCVRPLTVLKLRGE---KLELQLLEIAQREETDEFIIGLPKSWDGSETPQSNKVRSVA  137 (204)
Q Consensus        63 ~~iLglD~G~krIGiAisD~--~~A~Pl~vi~~~~~---~~~~~L~~li~e~~v~~iVIGlP~~~dGt~s~~~~~i~~Fa  137 (204)
                      .|+||||||+||||+|+||.  .+|+|+.++.++..   ..+..|.+++++|+|+.+|||+|++|||+++++++.++.|+
T Consensus         2 mriLgiD~G~kriGvAisd~~~~~a~pl~~i~~~~~~~~~~~~~l~~ii~e~~i~~iViGlP~~~dg~~~~~~~~~~~f~   81 (140)
T d1vhxa_           2 LRILGLDLGTKTLGVALSDEMGWTAQGIETIKINEAEGDYGLSRLSELIKDYTIDKIVLGFPKNMNGTVGPRGEASQTFA   81 (140)
T ss_dssp             EEEEEEEECSSEEEEEEECTTSSSEEEEEEEECBGGGTBCCHHHHHHHHTTSEEEEEEEECCCCBTTBCCHHHHHHHHHH
T ss_pred             CEEEEEEECCCEEEEEEECCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHCCCEEEEECCCCCCCCCHHHHHHHHHHH
T ss_conf             51999982799899999459988225516686125664168999999998516565998355224786136778889999


Q ss_pred             HHHHHHHCCCCCCEEEECCCCCHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHCC-CC
Q ss_conf             9998863328972899718772899999999749996645888939999998323-33
Q 028759          138 GRLAVRAAERGWRVYLLDEHRTSAEAVDRMINMGLSKSARQTKTDAYAAVVRQES-IT  194 (204)
Q Consensus       138 ~~L~~~~~~~~lpV~l~DER~ST~~A~~~L~e~g~sr~krk~~iD~~AA~iILQ~-~~  194 (204)
                      +.|...+   ++||++|||||||.+|++++++.|.+++++|+.+|++||++|||+ ++
T Consensus        82 ~~l~~~~---~i~V~~~DEr~TS~~A~~~l~~~~~~~~~~k~~iD~~AA~iILe~~L~  136 (140)
T d1vhxa_          82 KVLETTY---NVPVVLWDERLTTMAAEKMLIAADVSRQKRKKVIDKMAAVMILQGYLD  136 (140)
T ss_dssp             HHHHHHH---CSCEEEECCSSCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHCCCC---CCCEEEEECCCCHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHH
T ss_conf             9834677---855798414437999999999769970003414779999999999999

>d1iv0a_ c.55.3.8 (A:) Hypothetical protein, YqgF homologue {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Ribonuclease H-like
family: Putative Holliday junction resolvase RuvX
domain: Hypothetical protein, YqgF homologue
species: Thermus thermophilus [TaxId: 274]

Probab=99.96  E-value=2.4e-29  Score=183.93  Aligned_cols=95  Identities=29%  Similarity=0.318  Sum_probs=87.4

Q ss_pred             CEEEEEECCCCEEEEEEECC--CEEEEEEEEECCC-HHHHHHHHHHHHHCCCCEEEEEECCCCCCCCCHHHHHHHHHHHH
Q ss_conf             52999935998199998529--7234405677256-25899999999873999899941479999998457999999999
Q 028759           63 GFSLGVDLGLSRTGLALSKG--FCVRPLTVLKLRG-EKLELQLLEIAQREETDEFIIGLPKSWDGSETPQSNKVRSVAGR  139 (204)
Q Consensus        63 ~~iLglD~G~krIGiAisD~--~~A~Pl~vi~~~~-~~~~~~L~~li~e~~v~~iVIGlP~~~dGt~s~~~~~i~~Fa~~  139 (204)
                      .|+||||||+||||+|+||.  .+|+|+.++.+++ ..++..|.+++++|+++.+|||+|++|||+++++++.+++|+++
T Consensus         1 MriLglD~G~kriGiAisd~~~~~a~pl~~i~~~~~~~~~~~l~~ii~e~~i~~iVvGlP~~~dG~~~~~~~~v~~f~~~   80 (98)
T d1iv0a_           1 MRVGALDVGEARIGLAVGEEGVPLASGRGYLVRKTLEEDVEALLDFVRREGLGKLVVGLPLRTDLKESAQAGKVLPLVEA   80 (98)
T ss_dssp             CCEEEEEESSSEEEEEEECSCCSSCCCEEEEECCCHHHHHHHHHHHHHHHTCCEEEEECCCCCCSSSCCCSSTTHHHHHH
T ss_pred             CCEEEEECCCCEEEEEEECCCCCEECCEEEEECCCCHHHHHHHHHHHHHHCCCEEECCCCCCCCCCCCHHHHHHHHHHHH
T ss_conf             94999980899899999149998494568898778467899999999863301057166322379837889999999999


Q ss_pred             HHHHHCCCCCCEEEECCCCCHH
Q ss_conf             9886332897289971877289
Q 028759          140 LAVRAAERGWRVYLLDEHRTSA  161 (204)
Q Consensus       140 L~~~~~~~~lpV~l~DER~ST~  161 (204)
                      |++.    ++||++|||||||+
T Consensus        81 L~~~----~lpv~~~DErlTSk   98 (98)
T d1iv0a_          81 LRAR----GVEVELWDERFTTK   98 (98)
T ss_dssp             HHHT----TCEEEEECCSCCCC
T ss_pred             HHHC----CCCEEEECCCCCCC
T ss_conf             9647----99999986898888

>d3bzka5 c.55.3.13 (A:325-473) Transcriptional accessory factor Tex {Pseudomonas aeruginosa [TaxId: 287]}

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Ribonuclease H-like
family: Tex RuvX-like domain-like
domain: Transcriptional accessory factor Tex
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=98.83  E-value=4.9e-08  Score=62.92  Aligned_cols=95  Identities=16%  Similarity=0.193  Sum_probs=70.9

Q ss_pred             CCCEEEEEECC-CCEEEEEEECCC-EEEEEEEEEC----C-CHHHHHHHHHHHHHCCCCEEEEEECCCCCCCCCHHHHHH
Q ss_conf             89529999359-981999985297-2344056772----5-625899999999873999899941479999998457999
Q 028759           61 RGGFSLGVDLG-LSRTGLALSKGF-CVRPLTVLKL----R-GEKLELQLLEIAQREETDEFIIGLPKSWDGSETPQSNKV  133 (204)
Q Consensus        61 ~~~~iLglD~G-~krIGiAisD~~-~A~Pl~vi~~----~-~~~~~~~L~~li~e~~v~~iVIGlP~~~dGt~s~~~~~i  133 (204)
                      ++.++||+|+| +.-|++|+.|.. ...-..++..    + .+...+.|.+++++++++.|+||     ||+.   ++.+
T Consensus         3 ~~~~vlg~DPg~r~gck~AvlD~~G~vld~~viyp~~~~~~~~~a~~~l~~li~k~~p~vIaIG-----NgTa---sre~   74 (149)
T d3bzka5           3 GPRATLGLDPGLRTGVKVAVVDATGKLLDTATVYPHAPKNQWDQTLAVLAALCAKHQVELIAIG-----NGTA---SRET   74 (149)
T ss_dssp             CSCCEEEEECCSTTCEEEEEECTTSCEEEEEEECCSTTTCCHHHHHHHHHHHHHHTTCCEEEEE-----SSTT---HHHH
T ss_pred             CCCEEEEECCCCCCCCEEEEECCCCCEEEEEEEECCCCHHHHHHHHHHHHHHHHHCCCEEEEEC-----CCCC---HHHH
T ss_conf             8855888788865661899997999989999984379677999999999999998398699977-----9852---7899


Q ss_pred             HHHHHHHHHHHCCCCCCEEEECCCCCHHHH
Q ss_conf             999999988633289728997187728999
Q 028759          134 RSVAGRLAVRAAERGWRVYLLDEHRTSAEA  163 (204)
Q Consensus       134 ~~Fa~~L~~~~~~~~lpV~l~DER~ST~~A  163 (204)
                      +.|...|.+.....+++++++||...|.=.
T Consensus        75 ~~~v~~l~~~~~~~~i~~~iV~e~gAsvYs  104 (149)
T d3bzka5          75 DKLAGELIKKYPGMKLTKIMVSEAGASVYS  104 (149)
T ss_dssp             HHHHHHHHHHCGGGCCEEEEECCTTHHHHH
T ss_pred             HHHHHHHHHHCCCCCCEEEEEECCCHHHHH
T ss_conf             999999998577888689998265125431

>d1hjra_ c.55.3.6 (A:) RuvC resolvase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Ribonuclease H-like
family: RuvC resolvase
domain: RuvC resolvase
species: Escherichia coli [TaxId: 562]

Probab=97.92  E-value=0.0002  Score=42.36  Aligned_cols=96  Identities=19%  Similarity=0.175  Sum_probs=62.0

Q ss_pred             EEEEEECCCCEEEEEEEC--CCE--EEEEEEEECCCH-------HHHHHHHHHHHHCCCCEEEEEECCCCCCC-CCHHHH
Q ss_conf             299993599819999852--972--344056772562-------58999999998739998999414799999-984579
Q 028759           64 FSLGVDLGLSRTGLALSK--GFC--VRPLTVLKLRGE-------KLELQLLEIAQREETDEFIIGLPKSWDGS-ETPQSN  131 (204)
Q Consensus        64 ~iLglD~G~krIGiAisD--~~~--A~Pl~vi~~~~~-------~~~~~L~~li~e~~v~~iVIGlP~~~dGt-~s~~~~  131 (204)
                      .|||||+|..++|+|+-|  +..  .--.+++..+..       ...+.|.+++++++++.+++=-|+...+. ..-..-
T Consensus         2 iILGIDPGl~~~G~avid~~~~~~~~v~~g~i~t~~~~~~~Rl~~i~~~l~~li~~~~Pd~vaiE~~f~~~n~~sa~~l~   81 (158)
T d1hjra_           2 IILGIDPGSRVTGYGVIRQVGRQLSYLGSGCIRTKVDDLPSRLKLIYAGVTEIITQFQPDYFAIEQVFMAKNADSALKLG   81 (158)
T ss_dssp             EEEEEECCSSEEEEEEEEEETTEEEEEEEEEEECCCSCHHHHHHHHHHHHHHHHHHHCCSEEEEEECCCCCCTTTHHHHH
T ss_pred             EEEEECCCCCCEEEEEEEEECCEEEEEEEEEEECCCCCHHHHHHHHHHHHHHHHHCCCCCEEEEEEEHHCCCHHHHHHHH
T ss_conf             89998367786589999964987899995279679987699999999999999853499878987400024889999999


Q ss_pred             HHHHHHHHHHHHHCCCCCCEEEECCCCCHHHHHHH
Q ss_conf             99999999988633289728997187728999999
Q 028759          132 KVRSVAGRLAVRAAERGWRVYLLDEHRTSAEAVDR  166 (204)
Q Consensus       132 ~i~~Fa~~L~~~~~~~~lpV~l~DER~ST~~A~~~  166 (204)
                      +++.-+.....   +.++|+..+    |-.+.+..
T Consensus        82 ~arG~i~l~a~---~~~ipi~e~----~P~~vKk~  109 (158)
T d1hjra_          82 QARGVAIVAAV---NQELPVFEY----AARQVKQT  109 (158)
T ss_dssp             HHHHHHHHHHH---TTTCCEEEE----EHHHHHHH
T ss_pred             HHHHHHHHHHH---HCCCCEEEC----CHHHHHEE
T ss_conf             99999999999---808650124----41422201

>d1xc3a1 c.55.1.10 (A:1-118) Putative fructokinase YhdR {Bacillus subtilis [TaxId: 1423]}

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Actin-like ATPase domain
family: ROK
domain: Putative fructokinase YhdR
species: Bacillus subtilis [TaxId: 1423]

Probab=96.18  E-value=0.018  Score=31.37  Aligned_cols=100  Identities=9%  Similarity=-0.033  Sum_probs=66.7

Q ss_pred             EEEEEECCCCEEEEEEECCC-EEEEEEEEECCC-HHHHHHHHHHHHHCCCCEEEEEECCCCCCCC----------C--HH
Q ss_conf             29999359981999985297-234405677256-2589999999987399989994147999999----------8--45
Q 028759           64 FSLGVDLGLSRTGLALSKGF-CVRPLTVLKLRG-EKLELQLLEIAQREETDEFIIGLPKSWDGSE----------T--PQ  129 (204)
Q Consensus        64 ~iLglD~G~krIGiAisD~~-~A~Pl~vi~~~~-~~~~~~L~~li~e~~v~~iVIGlP~~~dGt~----------s--~~  129 (204)
                      .++|+|+|-.++-+++.|.. ...-...++... ....+.+.+.+.++++..+-||.|=..+...          +  ..
T Consensus         1 l~~giDiGgT~i~~~l~d~~g~i~~~~~~~t~~~~~~~~~i~~~~~~~~~~~igi~~~G~v~~~~~~~~~g~v~~~~~~~   80 (118)
T d1xc3a1           1 MLGGIEAGGTKFVCAVGREDGTIIDRIEFPTKMPDETIEKVIQYFSQFSLQAIGIGSFGPVDNDKTSQTYGTITATPKAG   80 (118)
T ss_dssp             CEEEEEECSSEEEEEEECTTSCEEEEEEEECCCHHHHHHHHHHHHTTSCCSEEEEEECSSBCCCTTSTTTTSBCCCSSTT
T ss_pred             CEEEEEECCCEEEEEEECCCCCEEEEEEECCCCHHHHHHHHHHHHHHCCCEECCEEEEEEEECCCCCCCEEEEECCCCCC
T ss_conf             99999966478999999599989999996589979999999999752144034466773234578820112997578655


Q ss_pred             HHHHHHHHHHHHHHHCCCCCCEEEECCCCCHHHHHHHH
Q ss_conf             79999999999886332897289971877289999999
Q 028759          130 SNKVRSVAGRLAVRAAERGWRVYLLDEHRTSAEAVDRM  167 (204)
Q Consensus       130 ~~~i~~Fa~~L~~~~~~~~lpV~l~DER~ST~~A~~~L  167 (204)
                      .+ --.+++.|++++   ++||++.+.-..-.-|+.++
T Consensus        81 w~-~~~l~~~l~~~~---~~pv~i~NDana~algE~~~  114 (118)
T d1xc3a1          81 WR-HYPFLQTVKNEM---KIPVGFSTDVNAAALGEFLF  114 (118)
T ss_dssp             TB-TCCHHHHHHHHH---CSCEEEEEHHHHHHHHHHHH
T ss_pred             CC-CCCHHHHHHHHH---CCCEEEEEHHHHHHHHHHHH
T ss_conf             45-867899999977---89989962698999999861

>d2ap1a2 c.55.1.10 (A:1-117) Putative regulator protein YcfX {Salmonella typhimurium [TaxId: 90371]}

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Actin-like ATPase domain
family: ROK
domain: Putative regulator protein YcfX
species: Salmonella typhimurium [TaxId: 90371]

Probab=95.51  E-value=0.047  Score=28.92  Aligned_cols=96  Identities=16%  Similarity=0.141  Sum_probs=56.5

Q ss_pred             EEEEEECCCCEEEEEEECC--C-EEEEEEEEEC--CC-HHHHHHHHHHH----HHC-CCCEEEEEECCCCCCCCCHH---
Q ss_conf             2999935998199998529--7-2344056772--56-25899999999----873-99989994147999999845---
Q 028759           64 FSLGVDLGLSRTGLALSKG--F-CVRPLTVLKL--RG-EKLELQLLEIA----QRE-ETDEFIIGLPKSWDGSETPQ---  129 (204)
Q Consensus        64 ~iLglD~G~krIGiAisD~--~-~A~Pl~vi~~--~~-~~~~~~L~~li----~e~-~v~~iVIGlP~~~dGt~s~~---  129 (204)
                      ++||+|+|-.+|=+|+.|.  . ..+  ..++.  .. ......+.+++    .+. .+..+-||.|=..|-..+..   
T Consensus         1 MyiGiDiGgT~i~~~l~d~~g~i~~~--~~~~t~~~~~~~~~~~i~~~i~~~~~~~~~~~~igi~~pG~vd~~~g~i~~~   78 (117)
T d2ap1a2           1 MYYGFDIGGTKIALGVFDSTRRLQWE--KRVPTPHTSYSAFLDAVCELVEEADQRFGVKGSVGIGIPGMPETEDGTLYAA   78 (117)
T ss_dssp             EEEEEEECSSEEEEEEEETTCCEEEE--EEEECCCSCHHHHHHHHHHHHHHHHHHHTSCCEEEEEESSBSCCTTSCCBCT
T ss_pred             CEEEEEECCCEEEEEEEECCCCEEEE--EEEEECCCCHHHHHHHHHHHHHHHHHHCCCCEEEEEECCCCCCCCCCEEECC
T ss_conf             99999978010999999699999999--8774024578999999999999988626741269872377543456666046


Q ss_pred             ---HHHHHHHHHHHHHHHCCCCCCEEEECCCCCHHHHH
Q ss_conf             ---79999999999886332897289971877289999
Q 028759          130 ---SNKVRSVAGRLAVRAAERGWRVYLLDEHRTSAEAV  164 (204)
Q Consensus       130 ---~~~i~~Fa~~L~~~~~~~~lpV~l~DER~ST~~A~  164 (204)
                         .-.-..+.+.|++++   ++||++-+.-....-|+
T Consensus        79 ~~~~w~~~~l~~~l~~~~---~~pv~l~NDan~aalaE  113 (117)
T d2ap1a2          79 NVPAASGKPLRADLSARL---DRDVRLDNDANCFALSE  113 (117)
T ss_dssp             TCTTTTTSCHHHHHHHHH---TSCEEEEEHHHHHHHHH
T ss_pred             CCCCCCCCCHHHHHHHHH---CCCEEEEEHHHHHHHHC
T ss_conf             765557975899998876---99899974787667640

>d1z05a3 c.55.1.10 (A:81-208) Transcriptional regulator VC2007 {Vibrio cholerae [TaxId: 666]}

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Actin-like ATPase domain
family: ROK
domain: Transcriptional regulator VC2007
species: Vibrio cholerae [TaxId: 666]

Probab=94.82  E-value=0.024  Score=30.61  Aligned_cols=102  Identities=17%  Similarity=0.175  Sum_probs=60.2

Q ss_pred             CCEEEEEECCCCEEEEEEEC--CC-EEEEEEEEECCC-HHH----HHHHHHHHHHCC-----CCEEEEEECCCCCCCCC-
Q ss_conf             95299993599819999852--97-234405677256-258----999999998739-----99899941479999998-
Q 028759           62 GGFSLGVDLGLSRTGLALSK--GF-CVRPLTVLKLRG-EKL----ELQLLEIAQREE-----TDEFIIGLPKSWDGSET-  127 (204)
Q Consensus        62 ~~~iLglD~G~krIGiAisD--~~-~A~Pl~vi~~~~-~~~----~~~L~~li~e~~-----v~~iVIGlP~~~dGt~s-  127 (204)
                      +-.+||+|.|..++-+|+.|  +. ...-...+.... ...    ...+.+++.+.+     +.++-||.|=..|...+ 
T Consensus         3 g~~~lgi~ig~~~i~~~l~d~~G~il~~~~~~~~~~~~~~~~~~i~~~i~~~~~~~~~~~~~i~gIgi~~pG~vd~~~~~   82 (128)
T d1z05a3           3 GWQFLSMRLGRGYLTIALHELGGEVLIDTKIDIHEIDQDDVLARLLFEIEEFFQTYAAQLDRVTSIAITLPGLVNSEQGI   82 (128)
T ss_dssp             TEEEEEEEEETTEEEEEEEETTSCEEEEEEEECCCCBHHHHHHHHHHHHHHHHHHTTTTCCEEEEEEEEESSEEETTTTE
T ss_pred             CCEEEEEEECCCEEEEEEECCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCEEEEEEEEEEEECCCEE
T ss_conf             88999999899999999995989999999721346898999999999999999974324466157876210014022104


Q ss_pred             ------HHHHHHHHHHHHHHHHHCCCCCCEEEECCCCCHHHHHHHH
Q ss_conf             ------4579999999999886332897289971877289999999
Q 028759          128 ------PQSNKVRSVAGRLAVRAAERGWRVYLLDEHRTSAEAVDRM  167 (204)
Q Consensus       128 ------~~~~~i~~Fa~~L~~~~~~~~lpV~l~DER~ST~~A~~~L  167 (204)
                            ..... ..+.+.|++++   ++||.+.+.-.....|+..+
T Consensus        83 ~~~~~~~~~~~-~~l~~~l~~~~---~~PV~l~NDana~a~aE~~~  124 (128)
T d1z05a3          83 VLQMPHYNVKN-LALGPEIYKAT---GLPVFVANDTRAWALAEKLF  124 (128)
T ss_dssp             EEECSSSBCSS-BCHHHHHHHHH---CSCEEEEEHHHHHHHHHHHH
T ss_pred             EECCCCCCCCC-CCHHHHHHHHC---CCCEEEEEHHHHHHHHHHHH
T ss_conf             20112578788-63689999851---99899986688999999863

>d2hoea3 c.55.1.10 (A:72-199) N-acetylglucosamine kinase {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Actin-like ATPase domain
family: ROK
domain: N-acetylglucosamine kinase
species: Thermotoga maritima [TaxId: 2336]

Probab=94.77  E-value=0.061  Score=28.29  Aligned_cols=103  Identities=13%  Similarity=0.132  Sum_probs=60.8

Q ss_pred             CCEEEEEECCCCEEEEEEECC--C-EEEEEEEEECC-C-HHHHHHHHHHH-------H--HCCCCEEEEEECCCCCCCCC
Q ss_conf             952999935998199998529--7-23440567725-6-25899999999-------8--73999899941479999998
Q 028759           62 GGFSLGVDLGLSRTGLALSKG--F-CVRPLTVLKLR-G-EKLELQLLEIA-------Q--REETDEFIIGLPKSWDGSET  127 (204)
Q Consensus        62 ~~~iLglD~G~krIGiAisD~--~-~A~Pl~vi~~~-~-~~~~~~L~~li-------~--e~~v~~iVIGlP~~~dGt~s  127 (204)
                      ...++|+|+|..++-+++.|.  . ..+-...+... . ......+.+++       .  ..++.++-||.|=..|...+
T Consensus         3 ~~~~igidig~~~i~~~l~d~~G~il~~~~~~~~~~~~~~~~~~~i~~~i~~~~~~~~~~~~~i~gigi~~pG~vd~~~g   82 (128)
T d2hoea3           3 CAYVLGIEVTRDEIAACLIDASMNILAHEAHPLPSQSDREETLNVMYRIIDRAKDMMEKLGSKLSALTVAAPGPIDTERG   82 (128)
T ss_dssp             GCEEEEEEECSSEEEEEEEETTCCEEEEEEEECCSSCCHHHHHHHHHHHHHHHHHHHHHTTCCCCEEEEEESSCEETTTT
T ss_pred             CEEEEEEEECCCEEEEEEECCCCCEEEEEEEECCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCEEEEECCEEEEECCCCC
T ss_conf             57999999999999999995999899999885145789899999999999999997142468557985140511848889


Q ss_pred             -----HHH-HHHHHHHHHHHHHHCCCCCCEEEECCCCCHHHHHHHH
Q ss_conf             -----457-9999999999886332897289971877289999999
Q 028759          128 -----PQS-NKVRSVAGRLAVRAAERGWRVYLLDEHRTSAEAVDRM  167 (204)
Q Consensus       128 -----~~~-~~i~~Fa~~L~~~~~~~~lpV~l~DER~ST~~A~~~L  167 (204)
                           +.. -.-..+.+.|++++   ++||++.++-.....|+..+
T Consensus        83 ~i~~~~~l~w~~~~l~~~l~~~~---~~pv~i~NDa~~~alaE~~f  125 (128)
T d2hoea3          83 IIIDPRNFPLSQIPLANLLKEKY---GIEVWVENDADMGAVGEKWY  125 (128)
T ss_dssp             EECCCSSCTTBTSCHHHHHHHHH---CSEEEEEEHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCCCCHHHHHHHHC---CCCEEEEEHHHHHHHHHHHH
T ss_conf             89851222224886699999872---99899984888999999986

>d1z6ra2 c.55.1.10 (A:82-210) Mlc protein {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Actin-like ATPase domain
family: ROK
domain: Mlc protein
species: Escherichia coli [TaxId: 562]

Probab=94.15  E-value=0.045  Score=29.04  Aligned_cols=103  Identities=19%  Similarity=0.141  Sum_probs=63.7

Q ss_pred             CCEEEEEECCCCEEEEEEEC--CC-EEEEEEEEEC-CCHH----HHHHHHHHHHH-----CCCCEEEEEECCCCCCCC--
Q ss_conf             95299993599819999852--97-2344056772-5625----89999999987-----399989994147999999--
Q 028759           62 GGFSLGVDLGLSRTGLALSK--GF-CVRPLTVLKL-RGEK----LELQLLEIAQR-----EETDEFIIGLPKSWDGSE--  126 (204)
Q Consensus        62 ~~~iLglD~G~krIGiAisD--~~-~A~Pl~vi~~-~~~~----~~~~L~~li~e-----~~v~~iVIGlP~~~dGt~--  126 (204)
                      ...+||+|+|...+-+++.|  +. ..+....+.. ....    ....+.+++++     .++.++-|+.|=..|...  
T Consensus         3 ~~~~l~i~i~~~~i~~~l~Dl~G~~l~~~~~~~~~~~~~~~~~~l~~~i~~~l~~~~~~~~~i~gIgi~~pG~v~~~~~~   82 (129)
T d1z6ra2           3 AWHYLSLRISRGEIFLALRDLSSKLVVEESQELALKDDLPLLDRIISHIDQFFIRHQKKLERLTSIAITLPGIIDTENGI   82 (129)
T ss_dssp             TCEEEEEEEETTEEEEEEEETTCCEEEEEEEECCSSCSSCHHHHHHHHHHHHHHHTGGGCCCEEEEEEEESSEEETTTTE
T ss_pred             CEEEEEEEECCCEEEEEEECCCCCEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCEEEEEEEEEEEEECCCC
T ss_conf             35999999899999999995999988787740245544689999999999999853754333036887331126640460


Q ss_pred             ---CHHH--HHHHHHHHHHHHHHCCCCCCEEEECCCCCHHHHHHHH
Q ss_conf             ---8457--9999999999886332897289971877289999999
Q 028759          127 ---TPQS--NKVRSVAGRLAVRAAERGWRVYLLDEHRTSAEAVDRM  167 (204)
Q Consensus       127 ---s~~~--~~i~~Fa~~L~~~~~~~~lpV~l~DER~ST~~A~~~L  167 (204)
                         .+..  -.--.+.+.|++.+   ++||.+.+.-.....|+.++
T Consensus        83 ~~~~~~~~~w~~~~l~~~l~~~~---~~pV~~~NDa~a~alaE~~~  125 (129)
T d1z6ra2          83 VHRMPFYEDVKEMPLGEALEQHT---GVPVYIQHDISAWTMAEALF  125 (129)
T ss_dssp             EEECTTCTTCSSBCHHHHHHHHH---SSCEEEEEHHHHHHHHHHHH
T ss_pred             EECCCCCHHCCCCCHHHHHHHHC---CCCEEEEEHHHHHHHHHHHH
T ss_conf             30467611105833699999861---99899986488999999734

>d2aa4a1 c.55.1.10 (A:1-119) N-acetylmannosamine kinase NanK {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Actin-like ATPase domain
family: ROK
domain: N-acetylmannosamine kinase NanK
species: Escherichia coli [TaxId: 562]

Probab=92.19  E-value=0.18  Score=25.65  Aligned_cols=98  Identities=13%  Similarity=0.037  Sum_probs=60.0

Q ss_pred             EEEEEECCCCEEEEEEECC--C-EEEEEEEEEC-CC-HHHHHHHHHHHHHC--CCCEEEEEECCCCCCCC----C-HHH-
Q ss_conf             2999935998199998529--7-2344056772-56-25899999999873--99989994147999999----8-457-
Q 028759           64 FSLGVDLGLSRTGLALSKG--F-CVRPLTVLKL-RG-EKLELQLLEIAQRE--ETDEFIIGLPKSWDGSE----T-PQS-  130 (204)
Q Consensus        64 ~iLglD~G~krIGiAisD~--~-~A~Pl~vi~~-~~-~~~~~~L~~li~e~--~v~~iVIGlP~~~dGt~----s-~~~-  130 (204)
                      ++||+|+|-.++=+|+.|.  . ..+-....+. .. ..+.+.+.+++++.  ++..+-||.|=..|...    + +.. 
T Consensus         2 ~~lgiDiGgT~i~~~l~d~~G~i~~~~~~~~~~~~~~~~~~~~i~~~i~~~~~~~~~igI~~pG~v~~~~~~~~~~~~l~   81 (119)
T d2aa4a1           2 TTLAIDIGGTKLAAALIGADGQIRDRRELPTPASQTPEALRDALSALVSPLQAHAQRVAIASTGIIRDGSLLALNPHNLG   81 (119)
T ss_dssp             CEEEEEECSSEEEEEEECTTCCEEEEEEEECCSSCCHHHHHHHHHHHHTTTGGGCSEEEEEESSEEETTEEECSSGGGGG
T ss_pred             EEEEEEECCCEEEEEEECCCCCEEEEEEEECCCCCCHHHHHHHHHHHHHHHHCCCCEEEEEEEEEECCCCCEEECCCCCC
T ss_conf             09999968687999999499989876777036667688999999999997533476389984326739986897267544


Q ss_pred             -HHHHHHHHHHHHHHCCCCCCEEEECCCCCHHHHH
Q ss_conf             -9999999999886332897289971877289999
Q 028759          131 -NKVRSVAGRLAVRAAERGWRVYLLDEHRTSAEAV  164 (204)
Q Consensus       131 -~~i~~Fa~~L~~~~~~~~lpV~l~DER~ST~~A~  164 (204)
                       -.-..+++.|++++   ++||++.+.-..-.-|+
T Consensus        82 ~w~~~~l~~~l~~~~---~~pv~i~NDanaaalgE  113 (119)
T d2aa4a1          82 GLLHFPLVKTLEQLT---NLPTIAINDAQAAAWAE  113 (119)
T ss_dssp             GGTTCCHHHHHHHHH---CSCEEEEEHHHHHHHHH
T ss_pred             CCCCCCHHHHHHHHH---CCCEEEEEHHHHHHHHH
T ss_conf             356997899999986---99999984588799997

>d2gupa1 c.55.1.10 (A:1-114) Hypothetical protein SP2142 {Streptococcus pneumoniae [TaxId: 1313]}

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Actin-like ATPase domain
family: ROK
domain: Hypothetical protein SP2142
species: Streptococcus pneumoniae [TaxId: 1313]

Probab=91.71  E-value=0.27  Score=24.66  Aligned_cols=97  Identities=13%  Similarity=-0.012  Sum_probs=58.7

Q ss_pred             EEEEEECCCCEEEEEEECCC-EEEEEEEEECC--CHHHHHHHHHHHHHCCCCEEEEEECCCCC---CCC--CHH--HHHH
Q ss_conf             29999359981999985297-23440567725--62589999999987399989994147999---999--845--7999
Q 028759           64 FSLGVDLGLSRTGLALSKGF-CVRPLTVLKLR--GEKLELQLLEIAQREETDEFIIGLPKSWD---GSE--TPQ--SNKV  133 (204)
Q Consensus        64 ~iLglD~G~krIGiAisD~~-~A~Pl~vi~~~--~~~~~~~L~~li~e~~v~~iVIGlP~~~d---Gt~--s~~--~~~i  133 (204)
                      .++|+|+|-.++=+|+.|.. ...-...++..  -......+.+.+.++++.++-||.|=..|   |..  ++.  .-.-
T Consensus         2 ~i~~iDiGgT~i~~~l~d~~g~i~~~~~~~t~~~~~~~~~~i~~~~~~~~i~gIGi~~pG~vd~~~g~i~~~~~l~~~~~   81 (114)
T d2gupa1           2 TIATIDIGGTGIKFASLTPDGKILDKTSISTPENLEDLLAWLDQRLSEQDYSGIAMSVPGAVNQETGVIDGFSAVPYIHG   81 (114)
T ss_dssp             CEEEEEEETTEEEEEEECTTCCEEEEEEECCCSSHHHHHHHHHHHHTTSCCSEEEEEESSEECTTTCBEESCCSSGGGSS
T ss_pred             EEEEEEECCCCEEEEEECCCCCEEEEEEECCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCCCEEECCCCCCCCCC
T ss_conf             69999968103999999099979999997143559999999999861144535999656653577538974445675458


Q ss_pred             HHHHHHHHHHHCCCCCCEEEECCCCCHHHHH
Q ss_conf             9999999886332897289971877289999
Q 028759          134 RSVAGRLAVRAAERGWRVYLLDEHRTSAEAV  164 (204)
Q Consensus       134 ~~Fa~~L~~~~~~~~lpV~l~DER~ST~~A~  164 (204)
                      ..+.+.++ ++   ++||++-+.-....-|+
T Consensus        82 ~~l~~~l~-~~---~~pV~veNDanaaalgE  108 (114)
T d2gupa1          82 FSWYEALS-SY---QLPVHLENDANCVGLSE  108 (114)
T ss_dssp             SBHHHHTG-GG---CCCEEEEEHHHHHHHHH
T ss_pred             CCHHHHHH-HC---CCCEEEEHHHHHHHHHH
T ss_conf             83799998-67---99799971999999999

>d1woqa1 c.55.1.10 (A:11-139) Inorganic polyphosphate/ATP-glucomannokinase PPGMK {Arthrobacter sp. KM [TaxId: 184230]}

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Actin-like ATPase domain
family: ROK
domain: Inorganic polyphosphate/ATP-glucomannokinase PPGMK
species: Arthrobacter sp. KM [TaxId: 184230]

Probab=90.33  E-value=0.41  Score=23.57  Aligned_cols=102  Identities=12%  Similarity=0.076  Sum_probs=56.8

Q ss_pred             CEEEEEECCCCEEEEEEECC---CEEEEEEEEEC--C-C-HHHHHHHHHHHHH----C----CCCEEEEEECCCCCCC--
Q ss_conf             52999935998199998529---72344056772--5-6-2589999999987----3----9998999414799999--
Q 028759           63 GFSLGVDLGLSRTGLALSKG---FCVRPLTVLKL--R-G-EKLELQLLEIAQR----E----ETDEFIIGLPKSWDGS--  125 (204)
Q Consensus        63 ~~iLglD~G~krIGiAisD~---~~A~Pl~vi~~--~-~-~~~~~~L~~li~e----~----~v~~iVIGlP~~~dGt--  125 (204)
                      ..+||+|+|-.+|=+|+.|.   ....-...++.  . . ....+.+.+++++    .    .+..+-||.|-..|..  
T Consensus         2 ~~vlGiDiGgT~i~~~l~d~~~g~i~~~~~~~~t~~~~~~~~~~~~i~~~~~~l~~~~~~~~~~~gIGi~~pG~vd~~~~   81 (129)
T d1woqa1           2 APLIGIDIGGTGIKGGIVDLKKGKLLGERFRVPTPQPATPESVAEAVALVVAELSARPEAPAAGSPVGVTFPGIIQHGVV   81 (129)
T ss_dssp             CCEEEEEECSSEEEEEEEETTTTEEEEEEEEEECCSSCCHHHHHHHHHHHHHHHHTSTTCCCTTCCEEEEESSCEETTEE
T ss_pred             CCEEEEEECCCEEEEEEEECCCCEEEEEEEECCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCEEEECCEEEEECCEE
T ss_conf             98899998836699999989999899998601424677899999999999999874014355310463032104864708


Q ss_pred             ---CCH-HHHHHHHHHHHHHHHHCCCCCCEEEECCCCCHHHHHHHH
Q ss_conf             ---984-579999999999886332897289971877289999999
Q 028759          126 ---ETP-QSNKVRSVAGRLAVRAAERGWRVYLLDEHRTSAEAVDRM  167 (204)
Q Consensus       126 ---~s~-~~~~i~~Fa~~L~~~~~~~~lpV~l~DER~ST~~A~~~L  167 (204)
                         .+. ..-.-..+.+.|++++   ++||++.+.-....-|+..+
T Consensus        82 ~~~~~~~~~w~~~~l~~~l~~~~---~~pv~i~NDan~aalgE~~~  124 (129)
T d1woqa1          82 HSAANVDKSWLNTDIDALLTARL---GRPVEVINDADAAGLAEARY  124 (129)
T ss_dssp             CCCTTSCGGGTTCBHHHHHHHHH---TSCEEEEEHHHHHHHHHHHH
T ss_pred             EEECCCCCCCCCCCCHHHHHHHC---CCCEEEEEHHHHHHHHHHHH
T ss_conf             98134478741036156689862---99589987699999999835

>d1bupa1 c.55.1.1 (A:4-188) Heat shock protein 70kDa, ATPase fragment {Cow (Bos taurus) [TaxId: 9913]}

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Actin-like ATPase domain
family: Actin/HSP70
domain: Heat shock protein 70kDa, ATPase fragment
species: Cow (Bos taurus) [TaxId: 9913]

Probab=86.65  E-value=0.2  Score=25.41  Aligned_cols=53  Identities=19%  Similarity=0.347  Sum_probs=24.3

Q ss_pred             HHHHHHHHHH---CCCCEEEEEECCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCC-EEEECCCCCHHHH
Q ss_conf             9999999987---399989994147999999845799999999998863328972-8997187728999
Q 028759           99 ELQLLEIAQR---EETDEFIIGLPKSWDGSETPQSNKVRSVAGRLAVRAAERGWR-VYLLDEHRTSAEA  163 (204)
Q Consensus        99 ~~~L~~li~e---~~v~~iVIGlP~~~dGt~s~~~~~i~~Fa~~L~~~~~~~~lp-V~l~DER~ST~~A  163 (204)
                      +..|.+.+++   ..+..+||+.|.+.+.    ..   +.....-.+..   +++ +.+++|  .|.+|
T Consensus       121 l~~l~~~a~~~~~~~~~~~VitvPa~f~~----~q---r~~~~~Aa~~A---Gl~~~~li~E--P~AAA  177 (185)
T d1bupa1         121 LTKMKEIAEAYLGKTVTNAVVTVPAYFND----SQ---RQATKDAGTIA---GLNVLRIINE--PTAAA  177 (185)
T ss_dssp             HHHHHHHHHHHHTSCCCEEEEEECTTCCH----HH---HHHHHHHHHHT---TCEEEEEEEH--HHHHH
T ss_pred             HHHHHHHHHHHHCCCCCCEEEEECCCCCH----HH---HHHHHHHHHHC---CCCEEEEECC--HHHHH
T ss_conf             99999999998599767099998998877----99---99999999986---9976898728--89999

>d1okja1 c.55.1.9 (A:1-106) Hypothetical protein YeaZ {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Actin-like ATPase domain
family: YeaZ-like
domain: Hypothetical protein YeaZ
species: Escherichia coli [TaxId: 562]

Probab=85.20  E-value=1  Score=21.36  Aligned_cols=91  Identities=14%  Similarity=0.082  Sum_probs=61.9

Q ss_pred             EEEEEECCCCEEEEEEECCC-EEEEEEEEEC-CCHHHHHHHHHHHHH-----CCCCEEEEEECCCCCCCCCHHHHHHHHH
Q ss_conf             29999359981999985297-2344056772-562589999999987-----3999899941479999998457999999
Q 028759           64 FSLGVDLGLSRTGLALSKGF-CVRPLTVLKL-RGEKLELQLLEIAQR-----EETDEFIIGLPKSWDGSETPQSNKVRSV  136 (204)
Q Consensus        64 ~iLglD~G~krIGiAisD~~-~A~Pl~vi~~-~~~~~~~~L~~li~e-----~~v~~iVIGlP~~~dGt~s~~~~~i~~F  136 (204)
                      ++|++|--.+.++||+.+.. ...-.....+ +.+.+...+.+++++     .+++.++++.-.   |+.+ -.+-...|
T Consensus         1 kiLaIdTS~~~~sval~~~~~i~~~~~~~~~~h~~~l~~~i~~~l~~~~~~~~di~~i~v~~GP---GsfT-glRig~s~   76 (106)
T d1okja1           1 RILAIDTATEACSVALWNDGTVNAHFELCPREHTQRILPMVQDILTTSGTSLTDINALAYGRGP---GSFT-GVRIGIGI   76 (106)
T ss_dssp             EEEEEECSSSEEEEEEEETTEEEEEEEECCSSTTTTHHHHHHHHHHHTTCCGGGCCEEEEEEES---SCHH-HHHHHHHH
T ss_pred             CEEEEECCCCCEEEEEEECCEEEEEEEECCHHHHHHHHHHHHHHHHHCCCCCEEEEEEEEEECC---CCCC-CCHHHHHH
T ss_conf             9999997771329999999999999997558999999999999998608750025678885036---7654-20599999


Q ss_pred             HHHHHHHHCCCCCCEEEECCCCCHHHHHH
Q ss_conf             99998863328972899718772899999
Q 028759          137 AGRLAVRAAERGWRVYLLDEHRTSAEAVD  165 (204)
Q Consensus       137 a~~L~~~~~~~~lpV~l~DER~ST~~A~~  165 (204)
                      ++.|...+   ++|++-++    |.++..
T Consensus        77 akgla~~~---~ip~~~v~----sl~~la   98 (106)
T d1okja1          77 AQGLALGA---ELPMIGVS----TLMTMA   98 (106)
T ss_dssp             HHHHHHHT---TCCEEEEE----HHHHHH
T ss_pred             HHHHHHHC---CCCEEEEC----HHHHHH
T ss_conf             99999982---99999868----799999

>d1dkgd1 c.55.1.1 (D:3-185) Heat shock protein 70kDa, ATPase fragment {Escherichia coli, gene dnaK [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Actin-like ATPase domain
family: Actin/HSP70
domain: Heat shock protein 70kDa, ATPase fragment
species: Escherichia coli, gene dnaK [TaxId: 562]

Probab=84.47  E-value=0.23  Score=25.00  Aligned_cols=18  Identities=28%  Similarity=0.534  Sum_probs=11.9

Q ss_pred             EEEEEECCCCEEEEEEEC
Q ss_conf             299993599819999852
Q 028759           64 FSLGVDLGLSRTGLALSK   81 (204)
Q Consensus        64 ~iLglD~G~krIGiAisD   81 (204)
                      +++|||+|+..+.+|+.+
T Consensus         1 ~VvGIDfGTt~s~va~~~   18 (183)
T d1dkgd1           1 KIIGIDLGTTNSCVAIMD   18 (183)
T ss_dssp             CCCEEECCSSEEEEEEEE
T ss_pred             CEEEEECCHHCEEEEEEE
T ss_conf             999998582028999999