Citrus Sinensis ID: 030761

---

Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170--
Protein Sequence
MAGVVATAEACDSNAALLASGDLRVLQPVFQIYGQCRSFSGPVVTLKVFEDNVLVRELLETRGEGKVLVIDGGGSMRCALVGGNLGQLAHNNGWSGIVVNGCIRDVDEINGCGIGVRALGSHPLKSNKKGHGDKHVPVYIAGVYIAGSFIRDGEWLYADSDGILVSKSELSI
Secondary Structure (PSIPRED)
ccccccccccccccccccccccEEEcccccEEcccccEEEEEEEEEEEcccHHHHHHHHHccccccEEEEEcccccccccHHHHHHHHHHHcccEEEEEEcccccHHHHHcccccEEEEEEccccccccccccccccEEEccEEEcccccccccEEEEccccEEEEcccccc
Secondary Structure Prediction (SSPRO)
cccccccHHHHHHcHHHHHccHcEEcccccEEccccccEEEEEEEEEcccEcHHHHHHHccccccEEEEEEcccccccEEEcHHHHHHHHHccccEEEEEEEEccHHHHcccccEEEEEEEcccEcEcccccEEcccEEEccEEEcccEEccccEEEEccccEEEEcccccc
Coil and Loop (DISEMBL)
MAGVVATAEACDSNAAllasgdlrvlqPVFQIYgqcrsfsgpvvtlkVFEDNVLVRELLETRGEGKVLVIDgggsmrcalvggnlgqlahnngwsgivvngcirdvdeingcgigvralgshplksnkkghgdkhvPVYIAGVYIagsfirdgewlyadsdgilvskselsi
Flexible Loop (DISEMBL)
MAGVVATAEACDSNAALLASGDLRVLQPVFQIYGQCRSFSGPVVTLKVFEDNVLVRELletrgegkvlviDGGGSMRCALVGGNLGQLAHNNGWSGIVVNGCIRDVDEINGCGIGVRALgshplksnkkghgdkhVPVYIAGVYIAGSFIRDGEWLYADsdgilvskselsi
Low Complexity Region (SEG)
MAGVVATAEACDSNAALLASGDLRVLQPVFQIYGQCRSFSGPVVTLKVFEDNVLVRELLETRGEGKVLVIDGGGSMRCALVGGNLGQLAHNNGWSGIVVNGCIRDVDEINGCGIGVRALGSHPLKSNKKGHGDKHVPVYIAGVYIAGSFIRDGEWLYADSDGILVSKSELSI
Disordered region (IsUnstruct)
*******AEACDSNAALLASGDLRVLQPVFQIYGQCRSFSGPVVTLKVFEDNVLVRELLETRGEGKVLVIDGGGSMRCALVGGNLGQLAHNNGWSGIVVNGCIRDVDEINGCGIGVRALGSHP********GDKHVPVYIAGVYIAGSFIRDGEWLYADSDGILV*******
Disordered Region (DISOPRED)
**GVVATAEACDSNAALLASGDLRVLQPVFQIYGQCRSFSGPVVTLKVFEDNVLVRELLETRGEGKVLVIDGGGSMRCALVGGNLGQLAHNNGWSGIVVNGCIRDVDEINGCGIGVRALGSHPLKSNKKGHGDKHVPVYIAGVYIAGSFIRDGEWLYADSDGILVSKSELSI
Disordered Region (DISEMBL)
MAGVVATAEACDSNAALLASGDLRVLQPVFQIYGQCRSFSGPVVTLKVFEDNVLVRELLETRGEGKVLVIDGGGSMRCALVGGNLGQLAHNNGWSGIVVNGCIRDVDEINGCGIGVRALGSHPLKSNKKGHGDKHVPVYIAGVYIAGSFIRDGEWLYADSDGILVSKSELSI
Disordered Region (DISPRO)
***VVATAEACDSNAALLASGDLRVLQPVFQIYGQCRSFSGPVVTLKVFEDNVLVRELLETRGEGKVLVIDGGGSMRCALVGGNLGQLAHNNGWSGIVVNGCIRDVDEINGCGIGVRALGSHPLKSNKKGHGDKHVPVYIAGVYIAGSFIRDGEWLYADSDGILVSKS****
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MAGVVATAEACDSNAALLASGDLRVLQPVFQIYGQCRSFSGPVVTLKVFEDNVLVRELLETRGEGKVLVIDGGGSMRCALVGGNLGQLAHNNGWSGIVVNGCIRDVDEINGCGIGVRALGSHPLKSNKKGHGDKHVPVYIAGVYIAGSFIRDGEWLYADSDGILVSKSELSI
Positional Conservation
no confident homologs detected

---

Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	172	2.2.26 [Sep-21-2011]
Q9FH13	166	Regulator of ribonuclease	yes	no	0.941	0.975	0.784	7e-72
Q9FFE0	166	Regulator of ribonuclease	no	no	0.947	0.981	0.666	3e-60
Q9M8R9	166	Regulator of ribonuclease	no	no	0.947	0.981	0.654	8e-59
Q46ZV6	165	Putative regulator of rib	yes	no	0.924	0.963	0.554	2e-50
Q2SX33	165	Putative regulator of rib	yes	no	0.941	0.981	0.574	3e-49
A9AHQ6	164	Putative regulator of rib	yes	no	0.936	0.981	0.566	3e-49
Q63SX7	165	Putative regulator of rib	yes	no	0.941	0.981	0.562	9e-49
A3NAY8	165	Putative regulator of rib	yes	no	0.941	0.981	0.562	9e-49
Q3JQZ3	165	Putative regulator of rib	yes	no	0.941	0.981	0.562	9e-49
A3NWR9	165	Putative regulator of rib	yes	no	0.941	0.981	0.562	9e-49

>sp|Q9FH13|RRAA3_ARATH Regulator of ribonuclease-like protein 3 OS=Arabidopsis thaliana GN=At5g56260 PE=2 SV=1

 Score =  269 bits (687), Expect = 7e-72,   Method: Compositional matrix adjust.
 Identities = 131/167 (78%), Positives = 148/167 (88%), Gaps = 5/167 (2%)

Query: 6   ATAEACDSNAALLASGDLRVLQPVFQIYGQCRSFSGPVVTLKVFEDNVLVRELLETRGEG 65
           ATAEACDSNA L+++GDLR L P+F+IYGQ R FSGP+VTLKVFEDNVLVR  LET+GEG
Sbjct: 5   ATAEACDSNAELISNGDLRALHPIFKIYGQRRCFSGPIVTLKVFEDNVLVRNQLETKGEG 64

Query: 66  KVLVIDGGGSMRCALVGGNLGQLAHNNGWSGIVVNGCIRDVDEINGCGIGVRALGSHPLK 125
            VLVIDGGGSMRCALVGGNLGQLA NNGWSGIVVNGC+RDVDEIN C +GVRALGS+PLK
Sbjct: 65  GVLVIDGGGSMRCALVGGNLGQLAQNNGWSGIVVNGCVRDVDEINDCDVGVRALGSNPLK 124

Query: 126 SNKKGHGDKHVPVYIAGVYIAGSFIRDGEWLYADSDGILVSKSELSI 172
           S KKGHG+K+VP     V+I G+ IRDGEWLYADSDGIL+SK+ELS+
Sbjct: 125 STKKGHGEKNVP-----VHIGGTLIRDGEWLYADSDGILISKTELSV 166

Potential inhibitor of endonuclease activity of RNase proteins. It probably does not have any methyltransferase activity.
Arabidopsis thaliana (taxid: 3702)

>sp|Q9FFE0|RRAA2_ARATH Regulator of ribonuclease-like protein 2 OS=Arabidopsis thaliana GN=At5g16450 PE=2 SV=1

 Score =  230 bits (587), Expect = 3e-60,   Method: Compositional matrix adjust.
 Identities = 112/168 (66%), Positives = 135/168 (80%), Gaps = 5/168 (2%)

Query: 5   VATAEACDSNAALLASGDLRVLQPVFQIYGQCRSFSGPVVTLKVFEDNVLVRELLETRGE 64
           V TAE CD+N  L+ SG LR LQP+FQIYG+ + FSGPVVT+KVFEDN L+R+ +E +G 
Sbjct: 4   VTTAEVCDANQELIRSGQLRALQPIFQIYGRRQIFSGPVVTVKVFEDNGLIRQFIEEKGN 63

Query: 65  GKVLVIDGGGSMRCALVGGNLGQLAHNNGWSGIVVNGCIRDVDEINGCGIGVRALGSHPL 124
           G+VLV+DGGGS RCA++GGN    A NNGW+GIVVNGCIRDVDEINGC IGVRAL SHP+
Sbjct: 64  GRVLVVDGGGSQRCAILGGNPVVQAQNNGWAGIVVNGCIRDVDEINGCDIGVRALASHPI 123

Query: 125 KSNKKGHGDKHVPVYIAGVYIAGSFIRDGEWLYADSDGILVSKSELSI 172
           K++KKG G++ VPV IAG  I      DGEWLYAD+DGILVS+ ELS+
Sbjct: 124 KASKKGLGEQRVPVNIAGTRIC-----DGEWLYADTDGILVSQIELSV 166

Possible inhibitor of endonuclease activity of RNase proteins. It probably does not have any methyltransferase activity.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9M8R9|RRAA1_ARATH Regulator of ribonuclease-like protein 1 OS=Arabidopsis thaliana GN=At3g02770 PE=2 SV=1

 Score =  226 bits (575), Expect = 8e-59,   Method: Compositional matrix adjust.
 Identities = 110/168 (65%), Positives = 134/168 (79%), Gaps = 5/168 (2%)

Query: 5   VATAEACDSNAALLASGDLRVLQPVFQIYGQCRSFSGPVVTLKVFEDNVLVRELLETRGE 64
           V TAE CD+N  ++ SG LR LQPVFQIYG+ + FSGPVVT+KVFEDN L+R  LE +G 
Sbjct: 4   VTTAEVCDANQEMIRSGQLRALQPVFQIYGRRQIFSGPVVTVKVFEDNGLIRHFLEEKGN 63

Query: 65  GKVLVIDGGGSMRCALVGGNLGQLAHNNGWSGIVVNGCIRDVDEINGCGIGVRALGSHPL 124
           G+VLV+DGGGS+RCA++GGN    A NNGW+GI+VNGCIRDVDEINGC IGVRAL SHP+
Sbjct: 64  GRVLVVDGGGSLRCAILGGNPVVQAQNNGWAGIIVNGCIRDVDEINGCDIGVRALASHPI 123

Query: 125 KSNKKGHGDKHVPVYIAGVYIAGSFIRDGEWLYADSDGILVSKSELSI 172
           K++KKG G++ V + IAG  I      DGEWLYAD+DGILVS+ ELS+
Sbjct: 124 KASKKGLGEQRVSLNIAGTRIC-----DGEWLYADTDGILVSQIELSV 166

Possible inhibitor of endonuclease activity of RNase proteins. It probably does not have any methyltransferase activity.

Arabidopsis thaliana (taxid: 3702)

>sp|Q46ZV6|RRAA_CUPPJ Putative regulator of ribonuclease activity OS=Cupriavidus pinatubonensis (strain JMP134 / LMG 1197) GN=Reut_A1963 PE=3 SV=1

 Score =  197 bits (502), Expect = 2e-50,   Method: Compositional matrix adjust.
 Identities = 91/164 (55%), Positives = 123/164 (75%), Gaps = 5/164 (3%)

Query: 7   TAEACDSNAALLASGDLRVLQPVFQIYGQCRSFSGPVVTLKVFEDNVLVRELLETRGEGK 66
           T + CD+N   LA G LRV+ PVF+ +G+ ++F+GP  TLK+FEDN LVRE LE+ G+G+
Sbjct: 5   TTDLCDANEPRLADGTLRVMAPVFRAFGKQQAFAGPAATLKIFEDNSLVREALESPGQGR 64

Query: 67  VLVIDGGGSMRCALVGGNLGQLAHNNGWSGIVVNGCIRDVDEINGCGIGVRALGSHPLKS 126
           VLV+DGGGS+RCALVGGNLG LA  NGW GI+VNGC+RD  E++ C IG+RAL +HP KS
Sbjct: 65  VLVVDGGGSLRCALVGGNLGLLAEKNGWVGIIVNGCVRDTGELDVCDIGIRALAAHPQKS 124

Query: 127 NKKGHGDKHVPVYIAGVYIAGSFIRDGEWLYADSDGILVSKSEL 170
            K+G G++ V      V + G+ +R G W+Y D+DG+LVS+ +L
Sbjct: 125 QKRGAGERDV-----AVQMPGAVVRPGNWIYVDADGVLVSEEKL 163

Cupriavidus pinatubonensis (strain JMP134 / LMG 1197) (taxid: 264198)

>sp|Q2SX33|RRAAH_BURTA Putative regulator of ribonuclease activity OS=Burkholderia thailandensis (strain E264 / ATCC 700388 / DSM 13276 / CIP 106301) GN=BTH_I1992 PE=3 SV=1

 Score =  194 bits (492), Expect = 3e-49,   Method: Compositional matrix adjust.
 Identities = 96/167 (57%), Positives = 120/167 (71%), Gaps = 5/167 (2%)

Query: 4   VVATAEACDSNAALLASGDLRVLQPVFQIYGQCRSFSGPVVTLKVFEDNVLVRELLETRG 63
           + AT + CD+N   LA+G LRV++PVF+ +G  R F+GP  TLK+FEDN LVR  LE  G
Sbjct: 2   MFATTDLCDANEERLAAGTLRVIEPVFRSFGGVRRFAGPAATLKLFEDNTLVRAALEQDG 61

Query: 64  EGKVLVIDGGGSMRCALVGGNLGQLAHNNGWSGIVVNGCIRDVDEINGCGIGVRALGSHP 123
            G+VLV+DGGGS+RCALVGGNLG+LA  NGW GIVVNGC+RD  E+  C  GV AL +HP
Sbjct: 62  AGRVLVVDGGGSLRCALVGGNLGKLAEKNGWVGIVVNGCVRDSAELAECRAGVLALAAHP 121

Query: 124 LKSNKKGHGDKHVPVYIAGVYIAGSFIRDGEWLYADSDGILVSKSEL 170
            KS+K+G G   VPV + G  IA      G+W+YAD+DGILVS + L
Sbjct: 122 RKSDKRGAGVSDVPVDVRGTRIA-----PGDWIYADADGILVSDAAL 163

Burkholderia thailandensis (strain E264 / ATCC 700388 / DSM 13276 / CIP 106301) (taxid: 271848)

>sp|A9AHQ6|RRAAH_BURM1 Putative regulator of ribonuclease activity OS=Burkholderia multivorans (strain ATCC 17616 / 249) GN=Bmul_1223 PE=3 SV=1

 Score =  194 bits (492), Expect = 3e-49,   Method: Compositional matrix adjust.
 Identities = 94/166 (56%), Positives = 118/166 (71%), Gaps = 5/166 (3%)

Query: 6   ATAEACDSNAALLASGDLRVLQPVFQIYGQCRSFSGPVVTLKVFEDNVLVRELLETRGEG 65
           AT + CD++   LA+G LRVLQP  + YG    F+GP  TLKVFEDN LVR  LE  G G
Sbjct: 4   ATTDLCDAHEDKLAAGTLRVLQPALRPYGGAARFAGPAATLKVFEDNTLVRAALEQDGGG 63

Query: 66  KVLVIDGGGSMRCALVGGNLGQLAHNNGWSGIVVNGCIRDVDEINGCGIGVRALGSHPLK 125
           +VLV+DGG S+RCALVGGNLG LA  NGW+GIVV+GC+RD  E+  C +GV AL +HP K
Sbjct: 64  RVLVVDGGASLRCALVGGNLGALAEKNGWAGIVVHGCVRDAAELRECKVGVLALATHPRK 123

Query: 126 SNKKGHGDKHVPVYIAGVYIAGSFIRDGEWLYADSDGILVSKSELS 171
           S+K+G G++ VPV + G  IA      GEW+YAD DG+LVS + L+
Sbjct: 124 SDKRGAGERDVPVTVLGTRIA-----PGEWIYADDDGVLVSATSLT 164

Burkholderia multivorans (strain ATCC 17616 / 249) (taxid: 395019)

>sp|Q63SX7|RRAAH_BURPS Putative regulator of ribonuclease activity OS=Burkholderia pseudomallei (strain K96243) GN=BPSL2194 PE=3 SV=1

 Score =  192 bits (488), Expect = 9e-49,   Method: Compositional matrix adjust.
 Identities = 94/167 (56%), Positives = 120/167 (71%), Gaps = 5/167 (2%)

Query: 4   VVATAEACDSNAALLASGDLRVLQPVFQIYGQCRSFSGPVVTLKVFEDNVLVRELLETRG 63
           + AT + CD++   LA+G LRVL+PVF+ +G  R F+GP  TLK+FEDN LVR  LE  G
Sbjct: 2   MFATTDLCDAHEDRLAAGTLRVLEPVFRPFGGVRRFAGPAATLKLFEDNSLVRTALEQDG 61

Query: 64  EGKVLVIDGGGSMRCALVGGNLGQLAHNNGWSGIVVNGCIRDVDEINGCGIGVRALGSHP 123
            G+VLV+DGGGS+RCALVGGNLG+LA  NGW+GIVVNGC+RD DE+  C +GV AL +HP
Sbjct: 62  AGRVLVVDGGGSLRCALVGGNLGKLAEKNGWAGIVVNGCVRDSDELAECRVGVLALAAHP 121

Query: 124 LKSNKKGHGDKHVPVYIAGVYIAGSFIRDGEWLYADSDGILVSKSEL 170
            KS+K+G G    PV + G  I       G+W+YAD+DG+LVS   L
Sbjct: 122 RKSDKRGAGVSDAPVDVRGTRIV-----PGDWIYADADGVLVSDDAL 163

Burkholderia pseudomallei (strain K96243) (taxid: 272560)

>sp|A3NAY8|RRAAH_BURP6 Putative regulator of ribonuclease activity OS=Burkholderia pseudomallei (strain 668) GN=BURPS668_2477 PE=3 SV=1

 Score =  192 bits (488), Expect = 9e-49,   Method: Compositional matrix adjust.
 Identities = 94/167 (56%), Positives = 120/167 (71%), Gaps = 5/167 (2%)

Query: 4   VVATAEACDSNAALLASGDLRVLQPVFQIYGQCRSFSGPVVTLKVFEDNVLVRELLETRG 63
           + AT + CD++   LA+G LRVL+PVF+ +G  R F+GP  TLK+FEDN LVR  LE  G
Sbjct: 2   MFATTDLCDAHEDRLAAGTLRVLEPVFRPFGGVRRFAGPAATLKLFEDNSLVRTALEQDG 61

Query: 64  EGKVLVIDGGGSMRCALVGGNLGQLAHNNGWSGIVVNGCIRDVDEINGCGIGVRALGSHP 123
            G+VLV+DGGGS+RCALVGGNLG+LA  NGW+GIVVNGC+RD DE+  C +GV AL +HP
Sbjct: 62  AGRVLVVDGGGSLRCALVGGNLGKLAEKNGWAGIVVNGCVRDSDELAECRVGVLALAAHP 121

Query: 124 LKSNKKGHGDKHVPVYIAGVYIAGSFIRDGEWLYADSDGILVSKSEL 170
            KS+K+G G    PV + G  I       G+W+YAD+DG+LVS   L
Sbjct: 122 RKSDKRGAGVSDAPVDVRGTRIV-----PGDWIYADADGVLVSDDAL 163

Burkholderia pseudomallei (strain 668) (taxid: 320373)

>sp|Q3JQZ3|RRAAH_BURP1 Putative regulator of ribonuclease activity OS=Burkholderia pseudomallei (strain 1710b) GN=BURPS1710b_2618 PE=3 SV=1

 Score =  192 bits (488), Expect = 9e-49,   Method: Compositional matrix adjust.
 Identities = 94/167 (56%), Positives = 120/167 (71%), Gaps = 5/167 (2%)

Query: 4   VVATAEACDSNAALLASGDLRVLQPVFQIYGQCRSFSGPVVTLKVFEDNVLVRELLETRG 63
           + AT + CD++   LA+G LRVL+PVF+ +G  R F+GP  TLK+FEDN LVR  LE  G
Sbjct: 2   MFATTDLCDAHEDRLAAGTLRVLEPVFRPFGGVRRFAGPAATLKLFEDNSLVRTALEQDG 61

Query: 64  EGKVLVIDGGGSMRCALVGGNLGQLAHNNGWSGIVVNGCIRDVDEINGCGIGVRALGSHP 123
            G+VLV+DGGGS+RCALVGGNLG+LA  NGW+GIVVNGC+RD DE+  C +GV AL +HP
Sbjct: 62  AGRVLVVDGGGSLRCALVGGNLGKLAEKNGWAGIVVNGCVRDSDELAECRVGVLALAAHP 121

Query: 124 LKSNKKGHGDKHVPVYIAGVYIAGSFIRDGEWLYADSDGILVSKSEL 170
            KS+K+G G    PV + G  I       G+W+YAD+DG+LVS   L
Sbjct: 122 RKSDKRGAGVSDAPVDVRGTRIV-----PGDWIYADADGVLVSDDAL 163

Burkholderia pseudomallei (strain 1710b) (taxid: 320372)

>sp|A3NWR9|RRAAH_BURP0 Putative regulator of ribonuclease activity OS=Burkholderia pseudomallei (strain 1106a) GN=BURPS1106A_2531 PE=3 SV=1

 Score =  192 bits (488), Expect = 9e-49,   Method: Compositional matrix adjust.
 Identities = 94/167 (56%), Positives = 120/167 (71%), Gaps = 5/167 (2%)

Query: 4   VVATAEACDSNAALLASGDLRVLQPVFQIYGQCRSFSGPVVTLKVFEDNVLVRELLETRG 63
           + AT + CD++   LA+G LRVL+PVF+ +G  R F+GP  TLK+FEDN LVR  LE  G
Sbjct: 2   MFATTDLCDAHEDRLAAGTLRVLEPVFRPFGGVRRFAGPAATLKLFEDNSLVRTALEQDG 61

Query: 64  EGKVLVIDGGGSMRCALVGGNLGQLAHNNGWSGIVVNGCIRDVDEINGCGIGVRALGSHP 123
            G+VLV+DGGGS+RCALVGGNLG+LA  NGW+GIVVNGC+RD DE+  C +GV AL +HP
Sbjct: 62  AGRVLVVDGGGSLRCALVGGNLGKLAEKNGWAGIVVNGCVRDSDELAECRVGVLALAAHP 121

Query: 124 LKSNKKGHGDKHVPVYIAGVYIAGSFIRDGEWLYADSDGILVSKSEL 170
            KS+K+G G    PV + G  I       G+W+YAD+DG+LVS   L
Sbjct: 122 RKSDKRGAGVSDAPVDVRGTRIV-----PGDWIYADADGVLVSDDAL 163

Burkholderia pseudomallei (strain 1106a) (taxid: 357348)

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	172
255576633	166	Regulator of ribonuclease activity A, pu	0.947	0.981	0.845	1e-75
225463540	166	PREDICTED: regulator of ribonuclease-lik	0.947	0.981	0.821	1e-73
147859276	166	hypothetical protein VITISV_040370 [Viti	0.947	0.981	0.815	5e-73
15241161	166	Regulator of ribonuclease-like protein 3	0.941	0.975	0.784	3e-70
357446205	686	Regulator of ribonuclease-like protein [	0.936	0.234	0.765	8e-70
297796499	166	dimethylmenaquinone methyltransferase fa	0.941	0.975	0.784	1e-69
357446201	169	Regulator of ribonuclease-like protein [	0.936	0.952	0.765	5e-68
224122216	166	predicted protein [Populus trichocarpa]	0.947	0.981	0.767	6e-68
226491520	168	regulator of ribonuclease activity A [Ze	0.947	0.970	0.726	5e-66
195608760	168	regulator of ribonuclease activity A [Ze	0.947	0.970	0.720	2e-65

>gi|255576633|ref|XP_002529206.1| Regulator of ribonuclease activity A, putative [Ricinus communis] gi|223531324|gb|EEF33162.1| Regulator of ribonuclease activity A, putative [Ricinus communis]

 Score =  287 bits (735), Expect = 1e-75,   Method: Compositional matrix adjust.
 Identities = 142/168 (84%), Positives = 153/168 (91%), Gaps = 5/168 (2%)

Query: 5   VATAEACDSNAALLASGDLRVLQPVFQIYGQCRSFSGPVVTLKVFEDNVLVRELLETRGE 64
           VATAEACDSNAAL ASGDLR LQPVF+IYGQ R+FSGP+VTLKVFEDNVLVRELLETRGE
Sbjct: 4   VATAEACDSNAALSASGDLRALQPVFKIYGQRRAFSGPIVTLKVFEDNVLVRELLETRGE 63

Query: 65  GKVLVIDGGGSMRCALVGGNLGQLAHNNGWSGIVVNGCIRDVDEINGCGIGVRALGSHPL 124
           G+VLVIDGGGSMRCALVGGNLGQLA N GW+GI+VNGCIRDVDEINGC IGVRAL SHP+
Sbjct: 64  GRVLVIDGGGSMRCALVGGNLGQLAQNMGWAGIIVNGCIRDVDEINGCDIGVRALASHPM 123

Query: 125 KSNKKGHGDKHVPVYIAGVYIAGSFIRDGEWLYADSDGILVSKSELSI 172
           KSNKKG G+KHV      V+IAG+ IRDGEWLYADSDGIL+SKSELSI
Sbjct: 124 KSNKKGMGEKHVT-----VHIAGTLIRDGEWLYADSDGILISKSELSI 166

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225463540|ref|XP_002265968.1| PREDICTED: regulator of ribonuclease-like protein 3 [Vitis vinifera] gi|296090048|emb|CBI39867.3| unnamed protein product [Vitis vinifera]

 Score =  280 bits (717), Expect = 1e-73,   Method: Compositional matrix adjust.
 Identities = 138/168 (82%), Positives = 150/168 (89%), Gaps = 5/168 (2%)

Query: 5   VATAEACDSNAALLASGDLRVLQPVFQIYGQCRSFSGPVVTLKVFEDNVLVRELLETRGE 64
           +ATAE CDSNAA L SGDLRVLQP+FQ YGQCR+FSGP+VTLKVFEDNVLVR LLETRGE
Sbjct: 4   LATAEVCDSNAAHLTSGDLRVLQPIFQSYGQCRAFSGPIVTLKVFEDNVLVRALLETRGE 63

Query: 65  GKVLVIDGGGSMRCALVGGNLGQLAHNNGWSGIVVNGCIRDVDEINGCGIGVRALGSHPL 124
           G+VLVIDGGGSMRCALVGGN+GQLA N GW+GIVVNGCIRDVDEI  C IGVRALG+HP+
Sbjct: 64  GRVLVIDGGGSMRCALVGGNIGQLAQNMGWAGIVVNGCIRDVDEIKDCDIGVRALGAHPM 123

Query: 125 KSNKKGHGDKHVPVYIAGVYIAGSFIRDGEWLYADSDGILVSKSELSI 172
           KSNKKG G+KHVP     VYIAG+ IRDGEWLYADSDGILVSK ELS+
Sbjct: 124 KSNKKGIGEKHVP-----VYIAGALIRDGEWLYADSDGILVSKFELSL 166

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147859276|emb|CAN79693.1| hypothetical protein VITISV_040370 [Vitis vinifera]

 Score =  278 bits (711), Expect = 5e-73,   Method: Compositional matrix adjust.
 Identities = 137/168 (81%), Positives = 149/168 (88%), Gaps = 5/168 (2%)

Query: 5   VATAEACDSNAALLASGDLRVLQPVFQIYGQCRSFSGPVVTLKVFEDNVLVRELLETRGE 64
           +ATAE CDSNAA L SGDLRVLQP+FQ YG CR+FSGP+VTLKVFEDNVLVR LLETRGE
Sbjct: 4   LATAEVCDSNAAHLTSGDLRVLQPIFQSYGHCRAFSGPIVTLKVFEDNVLVRALLETRGE 63

Query: 65  GKVLVIDGGGSMRCALVGGNLGQLAHNNGWSGIVVNGCIRDVDEINGCGIGVRALGSHPL 124
           G+VLVIDGGGSMRCALVGGN+GQLA N GW+GIVVNGCIRDVDEI  C IGVRALG+HP+
Sbjct: 64  GRVLVIDGGGSMRCALVGGNIGQLAQNMGWAGIVVNGCIRDVDEIKDCDIGVRALGAHPM 123

Query: 125 KSNKKGHGDKHVPVYIAGVYIAGSFIRDGEWLYADSDGILVSKSELSI 172
           KSNKKG G+KHVP     VYIAG+ IRDGEWLYADSDGILVSK ELS+
Sbjct: 124 KSNKKGIGEKHVP-----VYIAGALIRDGEWLYADSDGILVSKFELSL 166

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15241161|ref|NP_200437.1| Regulator of ribonuclease-like protein 3 [Arabidopsis thaliana] gi|17368897|sp|Q9FH13.1|RRAA3_ARATH RecName: Full=Regulator of ribonuclease-like protein 3 gi|9758753|dbj|BAB09117.1| S-adenosylmethionine:2-demethylmenaquinone methyltransferase-like [Arabidopsis thaliana] gi|38603850|gb|AAR24670.1| At5g56260 [Arabidopsis thaliana] gi|38603934|gb|AAR24712.1| At5g56260 [Arabidopsis thaliana] gi|332009359|gb|AED96742.1| Regulator of ribonuclease-like protein 3 [Arabidopsis thaliana]

 Score =  269 bits (687), Expect = 3e-70,   Method: Compositional matrix adjust.
 Identities = 131/167 (78%), Positives = 148/167 (88%), Gaps = 5/167 (2%)

Query: 6   ATAEACDSNAALLASGDLRVLQPVFQIYGQCRSFSGPVVTLKVFEDNVLVRELLETRGEG 65
           ATAEACDSNA L+++GDLR L P+F+IYGQ R FSGP+VTLKVFEDNVLVR  LET+GEG
Sbjct: 5   ATAEACDSNAELISNGDLRALHPIFKIYGQRRCFSGPIVTLKVFEDNVLVRNQLETKGEG 64

Query: 66  KVLVIDGGGSMRCALVGGNLGQLAHNNGWSGIVVNGCIRDVDEINGCGIGVRALGSHPLK 125
            VLVIDGGGSMRCALVGGNLGQLA NNGWSGIVVNGC+RDVDEIN C +GVRALGS+PLK
Sbjct: 65  GVLVIDGGGSMRCALVGGNLGQLAQNNGWSGIVVNGCVRDVDEINDCDVGVRALGSNPLK 124

Query: 126 SNKKGHGDKHVPVYIAGVYIAGSFIRDGEWLYADSDGILVSKSELSI 172
           S KKGHG+K+VP     V+I G+ IRDGEWLYADSDGIL+SK+ELS+
Sbjct: 125 STKKGHGEKNVP-----VHIGGTLIRDGEWLYADSDGILISKTELSV 166

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357446205|ref|XP_003593380.1| Regulator of ribonuclease-like protein [Medicago truncatula] gi|355482428|gb|AES63631.1| Regulator of ribonuclease-like protein [Medicago truncatula]

 Score =  268 bits (684), Expect = 8e-70,   Method: Composition-based stats.
 Identities = 127/166 (76%), Positives = 142/166 (85%), Gaps = 5/166 (3%)

Query: 7   TAEACDSNAALLASGDLRVLQPVFQIYGQCRSFSGPVVTLKVFEDNVLVRELLETRGEGK 66
           TAE CD+NA  L +GDLR+L PVFQ YGQ ++FSGP VT+KVFEDNVLVRELLET+GEG+
Sbjct: 526 TAEICDTNATHLTNGDLRILHPVFQKYGQSQAFSGPAVTVKVFEDNVLVRELLETKGEGR 585

Query: 67  VLVIDGGGSMRCALVGGNLGQLAHNNGWSGIVVNGCIRDVDEINGCGIGVRALGSHPLKS 126
           VLV+DGGGSMRCALVGGNL QLA N GWSGIVVNGCIRDVDEIN C +GVRAL SHPLKS
Sbjct: 586 VLVVDGGGSMRCALVGGNLVQLAQNKGWSGIVVNGCIRDVDEINLCQVGVRALASHPLKS 645

Query: 127 NKKGHGDKHVPVYIAGVYIAGSFIRDGEWLYADSDGILVSKSELSI 172
           NK G G+KHV      VY+ G+FIRDGEWLYAD+DGI+VSK ELSI
Sbjct: 646 NKNGTGEKHV-----AVYVGGTFIRDGEWLYADNDGIIVSKFELSI 686

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297796499|ref|XP_002866134.1| dimethylmenaquinone methyltransferase family protein [Arabidopsis lyrata subsp. lyrata] gi|297311969|gb|EFH42393.1| dimethylmenaquinone methyltransferase family protein [Arabidopsis lyrata subsp. lyrata]

 Score =  267 bits (683), Expect = 1e-69,   Method: Compositional matrix adjust.
 Identities = 131/167 (78%), Positives = 147/167 (88%), Gaps = 5/167 (2%)

Query: 6   ATAEACDSNAALLASGDLRVLQPVFQIYGQCRSFSGPVVTLKVFEDNVLVRELLETRGEG 65
           ATAEACDSNA L+++GDLR L P+F+IYGQ R FSGPVVTLKVFEDNVLVR  LET+GEG
Sbjct: 5   ATAEACDSNAELISNGDLRALHPIFKIYGQRRCFSGPVVTLKVFEDNVLVRNQLETKGEG 64

Query: 66  KVLVIDGGGSMRCALVGGNLGQLAHNNGWSGIVVNGCIRDVDEINGCGIGVRALGSHPLK 125
            VLVIDGGGSMRCALVGGNLGQLA NNGWSGIVVNGC+RDVDEIN C +GVRALGS+PLK
Sbjct: 65  GVLVIDGGGSMRCALVGGNLGQLAQNNGWSGIVVNGCVRDVDEINDCDVGVRALGSNPLK 124

Query: 126 SNKKGHGDKHVPVYIAGVYIAGSFIRDGEWLYADSDGILVSKSELSI 172
           S KKGHG+K+VP     V+I G+ IRDGEWLYADSDGIL+S +ELS+
Sbjct: 125 STKKGHGEKNVP-----VHIGGTLIRDGEWLYADSDGILISMTELSV 166

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357446201|ref|XP_003593378.1| Regulator of ribonuclease-like protein [Medicago truncatula] gi|355482426|gb|AES63629.1| Regulator of ribonuclease-like protein [Medicago truncatula]

 Score =  261 bits (668), Expect = 5e-68,   Method: Compositional matrix adjust.
 Identities = 127/166 (76%), Positives = 144/166 (86%), Gaps = 5/166 (3%)

Query: 7   TAEACDSNAALLASGDLRVLQPVFQIYGQCRSFSGPVVTLKVFEDNVLVRELLETRGEGK 66
           TAE CD+NA  +ASGDLR+L PVFQIYG CR+FSGP+VT+KVFEDNVL RELLET+GEG+
Sbjct: 6   TAEICDTNATHIASGDLRILHPVFQIYGHCRAFSGPIVTVKVFEDNVLARELLETKGEGR 65

Query: 67  VLVIDGGGSMRCALVGGNLGQLAHNNGWSGIVVNGCIRDVDEINGCGIGVRALGSHPLKS 126
           VLVID GGSMRCALVGGNL QLA N GWSGI+VNGC+RDVDEIN C +GVRALGS+PL S
Sbjct: 66  VLVIDRGGSMRCALVGGNLVQLAQNTGWSGIIVNGCVRDVDEINLCQVGVRALGSYPLGS 125

Query: 127 NKKGHGDKHVPVYIAGVYIAGSFIRDGEWLYADSDGILVSKSELSI 172
           N+KG G+KHV      VY+ G+FIRDGEWLYADSDGI+VSK ELSI
Sbjct: 126 NEKGTGEKHVD-----VYVGGTFIRDGEWLYADSDGIIVSKFELSI 166

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224122216|ref|XP_002330568.1| predicted protein [Populus trichocarpa] gi|222872126|gb|EEF09257.1| predicted protein [Populus trichocarpa]

 Score =  261 bits (668), Expect = 6e-68,   Method: Compositional matrix adjust.
 Identities = 129/168 (76%), Positives = 144/168 (85%), Gaps = 5/168 (2%)

Query: 5   VATAEACDSNAALLASGDLRVLQPVFQIYGQCRSFSGPVVTLKVFEDNVLVRELLETRGE 64
           + TAEACDSN  LLASGDLRVL P+F+IYGQ R+FSGP+ TLKVFEDNVLVRELLET GE
Sbjct: 4   ITTAEACDSNVPLLASGDLRVLPPIFKIYGQSRAFSGPIATLKVFEDNVLVRELLETEGE 63

Query: 65  GKVLVIDGGGSMRCALVGGNLGQLAHNNGWSGIVVNGCIRDVDEINGCGIGVRALGSHPL 124
           G+VLV+DGGGSMRCALVGGNLGQLA   GW+GI+VNGCIRDVDEINGC IGVRALGSHP 
Sbjct: 64  GRVLVVDGGGSMRCALVGGNLGQLAQTMGWAGILVNGCIRDVDEINGCDIGVRALGSHPT 123

Query: 125 KSNKKGHGDKHVPVYIAGVYIAGSFIRDGEWLYADSDGILVSKSELSI 172
           KS KKG G+KHV      V+I G+ I DGEWLYADSDGIL+S+ ELS+
Sbjct: 124 KSFKKGVGEKHV-----AVHIGGTLICDGEWLYADSDGILISRCELSL 166

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|226491520|ref|NP_001148311.1| regulator of ribonuclease activity A [Zea mays] gi|195617414|gb|ACG30537.1| regulator of ribonuclease activity A [Zea mays]

 Score =  255 bits (651), Expect = 5e-66,   Method: Compositional matrix adjust.
 Identities = 122/168 (72%), Positives = 143/168 (85%), Gaps = 5/168 (2%)

Query: 5   VATAEACDSNAALLASGDLRVLQPVFQIYGQCRSFSGPVVTLKVFEDNVLVRELLETRGE 64
           +ATAEACD+NAAL+ +GDLR LQP+FQIYG  + F+GPVVTLK+FEDNVL+RE LE +G 
Sbjct: 6   LATAEACDANAALIMNGDLRSLQPIFQIYGGRQIFAGPVVTLKIFEDNVLLREFLEEKGH 65

Query: 65  GKVLVIDGGGSMRCALVGGNLGQLAHNNGWSGIVVNGCIRDVDEINGCGIGVRALGSHPL 124
           G+VLV+D GGSMRCA++GGNL QL  NNGW+GIVVNGCIRDVDEINGC +GVRAL SHP+
Sbjct: 66  GRVLVVDAGGSMRCAVLGGNLAQLMQNNGWAGIVVNGCIRDVDEINGCDVGVRALNSHPM 125

Query: 125 KSNKKGHGDKHVPVYIAGVYIAGSFIRDGEWLYADSDGILVSKSELSI 172
           KSNKKG G+KHVPV  AG  I      DGEWLYADSDGIL+S+SELS+
Sbjct: 126 KSNKKGVGEKHVPVTFAGTRIC-----DGEWLYADSDGILISRSELSV 168

Source: Zea mays

Species: Zea mays

Genus: Zea

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|195608760|gb|ACG26210.1| regulator of ribonuclease activity A [Zea mays] gi|223974573|gb|ACN31474.1| unknown [Zea mays] gi|414876314|tpg|DAA53445.1| TPA: hypothetical protein ZEAMMB73_524650 [Zea mays]

 Score =  253 bits (647), Expect = 2e-65,   Method: Compositional matrix adjust.
 Identities = 121/168 (72%), Positives = 143/168 (85%), Gaps = 5/168 (2%)

Query: 5   VATAEACDSNAALLASGDLRVLQPVFQIYGQCRSFSGPVVTLKVFEDNVLVRELLETRGE 64
           +ATAEACD+NAAL+ +GDLR LQP+F+IYG  + F+GPVVTLK+FEDNVL+RE LE +G 
Sbjct: 6   LATAEACDANAALIMNGDLRSLQPIFRIYGGRQIFAGPVVTLKIFEDNVLLREFLEEKGH 65

Query: 65  GKVLVIDGGGSMRCALVGGNLGQLAHNNGWSGIVVNGCIRDVDEINGCGIGVRALGSHPL 124
           G+VLV+D GGSMRCA++GGNL QL  NNGW+GIVVNGCIRDVDEINGC +GVRAL SHP+
Sbjct: 66  GRVLVVDAGGSMRCAVLGGNLAQLMQNNGWAGIVVNGCIRDVDEINGCDVGVRALNSHPM 125

Query: 125 KSNKKGHGDKHVPVYIAGVYIAGSFIRDGEWLYADSDGILVSKSELSI 172
           KSNKKG G+KHVPV  AG  I      DGEWLYADSDGIL+S+SELS+
Sbjct: 126 KSNKKGVGEKHVPVTFAGTRIC-----DGEWLYADSDGILISRSELSV 168

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	172
TAIR|locus:2156430	166	AT5G56260 [Arabidopsis thalian	0.941	0.975	0.784	4.4e-68
TAIR|locus:2171397	166	AT5G16450 [Arabidopsis thalian	0.947	0.981	0.666	2.8e-57
TAIR|locus:2075432	166	AT3G02770 [Arabidopsis thalian	0.947	0.981	0.654	4.2e-56
TIGR_CMR|SO_4197	161	SO_4197 "S-adenosylmethionine:	0.906	0.968	0.415	6.2e-30
UNIPROTKB|Q47VZ9	165	rraA "Regulator of ribonucleas	0.906	0.945	0.451	2.1e-29
TIGR_CMR|CPS_4374	165	CPS_4374 "protein of unknown f	0.906	0.945	0.451	2.1e-29
UNIPROTKB|P0A8R0	161	rraA "ribonuclease E inhibitor	0.906	0.968	0.409	2.4e-28
UNIPROTKB|Q489G8	163	CPS_0538 "Putative uncharacter	0.843	0.889	0.44	2.8e-27
TIGR_CMR|CPS_0538	163	CPS_0538 "protein of unknown f	0.843	0.889	0.44	2.8e-27
TIGR_CMR|SO_2567	164	SO_2567 "S-adenosylmethionine:	0.837	0.878	0.409	1.9e-26

TAIR|locus:2156430 AT5G56260 [Arabidopsis thaliana (taxid:3702)]

 Score = 691 (248.3 bits), Expect = 4.4e-68, P = 4.4e-68
 Identities = 131/167 (78%), Positives = 148/167 (88%)

Query:     6 ATAEACDSNAALLASGDLRVLQPVFQIYGQCRSFSGPVVTLKVFEDNVLVRELLETRGEG 65
             ATAEACDSNA L+++GDLR L P+F+IYGQ R FSGP+VTLKVFEDNVLVR  LET+GEG
Sbjct:     5 ATAEACDSNAELISNGDLRALHPIFKIYGQRRCFSGPIVTLKVFEDNVLVRNQLETKGEG 64

Query:    66 KVLVIDGGGSMRCALVGGNLGQLAHNNGWSGIVVNGCIRDVDEINGCGIGVRALGSHPLK 125
              VLVIDGGGSMRCALVGGNLGQLA NNGWSGIVVNGC+RDVDEIN C +GVRALGS+PLK
Sbjct:    65 GVLVIDGGGSMRCALVGGNLGQLAQNNGWSGIVVNGCVRDVDEINDCDVGVRALGSNPLK 124

Query:   126 SNKKGHGDKHVPVYIAGVYIAGSFIRDGEWLYADSDGILVSKSELSI 172
             S KKGHG+K+VPV+I G     + IRDGEWLYADSDGIL+SK+ELS+
Sbjct:   125 STKKGHGEKNVPVHIGG-----TLIRDGEWLYADSDGILISKTELSV 166

GO:0005737 "cytoplasm" evidence=ISM

GO:0008428 "ribonuclease inhibitor activity" evidence=IEA

GO:0051252 "regulation of RNA metabolic process" evidence=IEA

TAIR|locus:2171397 AT5G16450 [Arabidopsis thaliana (taxid:3702)]

 Score = 589 (212.4 bits), Expect = 2.8e-57, P = 2.8e-57
 Identities = 112/168 (66%), Positives = 135/168 (80%)

Query:     5 VATAEACDSNAALLASGDLRVLQPVFQIYGQCRSFSGPVVTLKVFEDNVLVRELLETRGE 64
             V TAE CD+N  L+ SG LR LQP+FQIYG+ + FSGPVVT+KVFEDN L+R+ +E +G 
Sbjct:     4 VTTAEVCDANQELIRSGQLRALQPIFQIYGRRQIFSGPVVTVKVFEDNGLIRQFIEEKGN 63

Query:    65 GKVLVIDGGGSMRCALVGGNLGQLAHNNGWSGIVVNGCIRDVDEINGCGIGVRALGSHPL 124
             G+VLV+DGGGS RCA++GGN    A NNGW+GIVVNGCIRDVDEINGC IGVRAL SHP+
Sbjct:    64 GRVLVVDGGGSQRCAILGGNPVVQAQNNGWAGIVVNGCIRDVDEINGCDIGVRALASHPI 123

Query:   125 KSNKKGHGDKHVPVYIAGVYIAGSFIRDGEWLYADSDGILVSKSELSI 172
             K++KKG G++ VPV IAG  I      DGEWLYAD+DGILVS+ ELS+
Sbjct:   124 KASKKGLGEQRVPVNIAGTRIC-----DGEWLYADTDGILVSQIELSV 166

GO:0005737 "cytoplasm" evidence=ISM

GO:0008428 "ribonuclease inhibitor activity" evidence=IEA

GO:0051252 "regulation of RNA metabolic process" evidence=IEA

TAIR|locus:2075432 AT3G02770 [Arabidopsis thaliana (taxid:3702)]

 Score = 578 (208.5 bits), Expect = 4.2e-56, P = 4.2e-56
 Identities = 110/168 (65%), Positives = 134/168 (79%)

Query:     5 VATAEACDSNAALLASGDLRVLQPVFQIYGQCRSFSGPVVTLKVFEDNVLVRELLETRGE 64
             V TAE CD+N  ++ SG LR LQPVFQIYG+ + FSGPVVT+KVFEDN L+R  LE +G 
Sbjct:     4 VTTAEVCDANQEMIRSGQLRALQPVFQIYGRRQIFSGPVVTVKVFEDNGLIRHFLEEKGN 63

Query:    65 GKVLVIDGGGSMRCALVGGNLGQLAHNNGWSGIVVNGCIRDVDEINGCGIGVRALGSHPL 124
             G+VLV+DGGGS+RCA++GGN    A NNGW+GI+VNGCIRDVDEINGC IGVRAL SHP+
Sbjct:    64 GRVLVVDGGGSLRCAILGGNPVVQAQNNGWAGIIVNGCIRDVDEINGCDIGVRALASHPI 123

Query:   125 KSNKKGHGDKHVPVYIAGVYIAGSFIRDGEWLYADSDGILVSKSELSI 172
             K++KKG G++ V + IAG  I      DGEWLYAD+DGILVS+ ELS+
Sbjct:   124 KASKKGLGEQRVSLNIAGTRIC-----DGEWLYADTDGILVSQIELSV 166

GO:0005737 "cytoplasm" evidence=ISM

GO:0008428 "ribonuclease inhibitor activity" evidence=IEA

GO:0051252 "regulation of RNA metabolic process" evidence=IEA

TIGR_CMR|SO_4197 SO_4197 "S-adenosylmethionine:2-demethylmenaquinone methyltransferase" [Shewanella oneidensis MR-1 (taxid:211586)]

 Score = 331 (121.6 bits), Expect = 6.2e-30, P = 6.2e-30
 Identities = 69/166 (41%), Positives = 106/166 (63%)

Query:     7 TAEACDSNAALLASGDLRVLQPVFQIYGQCRSFSGPVVTLKVFEDNVLVRELLETRGEGK 66
             T+E CD    ++   D  V++P+F  YG C SF G + T+K FEDN L+ ++L+  G+GK
Sbjct:     5 TSELCDMYLDVV---D--VVEPMFSNYGGCSSFGGSISTIKCFEDNGLITDVLQEDGQGK 59

Query:    67 VLVIDGGGSMRCALVGGNLGQLAHNNGWSGIVVNGCIRDVDEINGCGIGVRALGSHPLKS 126
             VL++DGGGS+R AL+ G + +LA +N W GI+V G +RDVD +    IG++AL S P+ +
Sbjct:    60 VLLVDGGGSLRRALIDGTIAELAVSNNWEGIIVYGSVRDVDALEELDIGIQALASIPVGA 119

Query:   127 NKKGHGDKHVPVYIAGVYIAGSFIRDGEWLYADSDGILVSKSELSI 172
             +    G+  +PV   GV    +F+  G+ +YAD+ GI++S   L I
Sbjct:   120 DGNSVGEVDIPVNFGGV----TFL-PGDHIYADNTGIILSPEPLDI 160

GO:0008757 "S-adenosylmethionine-dependent methyltransferase activity" evidence=ISS

GO:0009234 "menaquinone biosynthetic process" evidence=ISS

UNIPROTKB|Q47VZ9 rraA "Regulator of ribonuclease activity A" [Colwellia psychrerythraea 34H (taxid:167879)]

 Score = 326 (119.8 bits), Expect = 2.1e-29, P = 2.1e-29
 Identities = 75/166 (45%), Positives = 106/166 (63%)

Query:     7 TAEACDSNAALLASGDLRVLQPVFQIYGQCRSFSGPVVTLKVFEDNVLVRELLETRGEGK 66
             T+E CD  A L+   D  V+ P+F  YG   SF+G VVTLK FE   L+ EL+ T G GK
Sbjct:     5 TSELCDFYADLI---D--VVDPIFCNYGGRSSFAGKVVTLKCFEHLGLINELVATYGTGK 59

Query:    67 VLVIDGGGSMRCALVGGNLGQLAHNNGWSGIVVNGCIRDVDEINGCGIGVRALGSHPLKS 126
             VLVIDGGGS R AL+   + Q A NNGW GIV  G +RDVD ++G  IG++ALG+ P+ +
Sbjct:    60 VLVIDGGGSTRRALIDLGIAQCAANNGWEGIVCYGSVRDVDALDGVDIGIQALGAIPVGA 119

Query:   127 NKKGHGDKHVPVYIAGVYIAGSFIRDGEWLYADSDGILVSKSELSI 172
             +++  G+  + +  AGV    + + D +++YAD+ GI++S   L I
Sbjct:   120 SEQNIGETDMAINFAGV----TLLPD-DYIYADNTGIILSPEALEI 160

GO:0003674 "molecular_function" evidence=ND

GO:0008150 "biological_process" evidence=ND

TIGR_CMR|CPS_4374 CPS_4374 "protein of unknown function" [Colwellia psychrerythraea 34H (taxid:167879)]

 Score = 326 (119.8 bits), Expect = 2.1e-29, P = 2.1e-29
 Identities = 75/166 (45%), Positives = 106/166 (63%)

Query:     7 TAEACDSNAALLASGDLRVLQPVFQIYGQCRSFSGPVVTLKVFEDNVLVRELLETRGEGK 66
             T+E CD  A L+   D  V+ P+F  YG   SF+G VVTLK FE   L+ EL+ T G GK
Sbjct:     5 TSELCDFYADLI---D--VVDPIFCNYGGRSSFAGKVVTLKCFEHLGLINELVATYGTGK 59

Query:    67 VLVIDGGGSMRCALVGGNLGQLAHNNGWSGIVVNGCIRDVDEINGCGIGVRALGSHPLKS 126
             VLVIDGGGS R AL+   + Q A NNGW GIV  G +RDVD ++G  IG++ALG+ P+ +
Sbjct:    60 VLVIDGGGSTRRALIDLGIAQCAANNGWEGIVCYGSVRDVDALDGVDIGIQALGAIPVGA 119

Query:   127 NKKGHGDKHVPVYIAGVYIAGSFIRDGEWLYADSDGILVSKSELSI 172
             +++  G+  + +  AGV    + + D +++YAD+ GI++S   L I
Sbjct:   120 SEQNIGETDMAINFAGV----TLLPD-DYIYADNTGIILSPEALEI 160

GO:0003674 "molecular_function" evidence=ND

GO:0008150 "biological_process" evidence=ND

UNIPROTKB|P0A8R0 rraA "ribonuclease E inhibitor protein" [Escherichia coli K-12 (taxid:83333)]

 Score = 316 (116.3 bits), Expect = 2.4e-28, P = 2.4e-28
 Identities = 68/166 (40%), Positives = 103/166 (62%)

Query:     7 TAEACDSNAALLASGDLRVLQPVFQIYGQCRSFSGPVVTLKVFEDNVLVRELLETRGEGK 66
             T+E CD     +   D+ V++P+F  +G   SF G ++T+K FEDN L+ +LLE  G G+
Sbjct:     5 TSELCD-----IYQEDVNVVEPLFSNFGGRASFGGQIITVKCFEDNGLLYDLLEQNGRGR 59

Query:    67 VLVIDGGGSMRCALVGGNLGQLAHNNGWSGIVVNGCIRDVDEINGCGIGVRALGSHPLKS 126
             VLV+DGGGS+R ALV   L +LA  N W G+V+ G +R VD++    IG++A+ + P+ +
Sbjct:    60 VLVVDGGGSVRRALVDAELARLAVQNEWEGLVIYGAVRQVDDLEELDIGIQAMAAIPVGA 119

Query:   127 NKKGHGDKHVPVYIAGVYIAGSFIRDGEWLYADSDGILVSKSELSI 172
               +G G+  V V   GV    +F   G+ LYAD+ GI++S+  L I
Sbjct:   120 AGEGIGESDVRVNFGGV----TFF-SGDHLYADNTGIILSEDPLDI 160

GO:0051252 "regulation of RNA metabolic process" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0060702 "negative regulation of endoribonuclease activity" evidence=IDA

GO:0005515 "protein binding" evidence=IPI

GO:0008428 "ribonuclease inhibitor activity" evidence=IEA;IDA

GO:0006401 "RNA catabolic process" evidence=IDA

UNIPROTKB|Q489G8 CPS_0538 "Putative uncharacterized protein" [Colwellia psychrerythraea 34H (taxid:167879)]

 Score = 306 (112.8 bits), Expect = 2.8e-27, P = 2.8e-27
 Identities = 66/150 (44%), Positives = 91/150 (60%)

Query:    23 LRVLQPVFQIYGQCRSFSGPVVTLKVFEDNVLVRELLETRGEGKVLVIDGGGSMRCALVG 82
             L +    F  YG+   F G +VT+  FEDN  V+E+L T G GKVLV+DG GSM  AL+G
Sbjct:    16 LSLANQAFTDYGKNTIFYGEIVTVSCFEDNSKVKEILATDGSGKVLVVDGKGSMNRALLG 75

Query:    83 GNLGQLAHNNGWSGIVVNGCIRDVDEINGCGIGVRALGSHPLKSNKKGHGDKHVPVYIAG 142
               + + A  N W  +V+NGCIRD   I    I V+A+G +P+K+ K G GD ++ V  A 
Sbjct:    76 DMIAENAVKNNWQAVVINGCIRDAGTIRTLEIAVKAIGCNPIKTEKLGVGDTNIVVNFAN 135

Query:   143 VYIAGSFIRDGEWLYADSDGILVSKSELSI 172
             V     FI  G ++Y D +G+ VSKS+LS+
Sbjct:   136 V----EFI-PGWYVYGDENGLAVSKSKLSV 160

GO:0003674 "molecular_function" evidence=ND

GO:0008150 "biological_process" evidence=ND

TIGR_CMR|CPS_0538 CPS_0538 "protein of unknown function" [Colwellia psychrerythraea 34H (taxid:167879)]

 Score = 306 (112.8 bits), Expect = 2.8e-27, P = 2.8e-27
 Identities = 66/150 (44%), Positives = 91/150 (60%)

Query:    23 LRVLQPVFQIYGQCRSFSGPVVTLKVFEDNVLVRELLETRGEGKVLVIDGGGSMRCALVG 82
             L +    F  YG+   F G +VT+  FEDN  V+E+L T G GKVLV+DG GSM  AL+G
Sbjct:    16 LSLANQAFTDYGKNTIFYGEIVTVSCFEDNSKVKEILATDGSGKVLVVDGKGSMNRALLG 75

Query:    83 GNLGQLAHNNGWSGIVVNGCIRDVDEINGCGIGVRALGSHPLKSNKKGHGDKHVPVYIAG 142
               + + A  N W  +V+NGCIRD   I    I V+A+G +P+K+ K G GD ++ V  A 
Sbjct:    76 DMIAENAVKNNWQAVVINGCIRDAGTIRTLEIAVKAIGCNPIKTEKLGVGDTNIVVNFAN 135

Query:   143 VYIAGSFIRDGEWLYADSDGILVSKSELSI 172
             V     FI  G ++Y D +G+ VSKS+LS+
Sbjct:   136 V----EFI-PGWYVYGDENGLAVSKSKLSV 160

GO:0003674 "molecular_function" evidence=ND

GO:0008150 "biological_process" evidence=ND

TIGR_CMR|SO_2567 SO_2567 "S-adenosylmethionine:2-demethylmenaquinone methyltransferase" [Shewanella oneidensis MR-1 (taxid:211586)]

 Score = 298 (110.0 bits), Expect = 1.9e-26, P = 1.9e-26
 Identities = 61/149 (40%), Positives = 92/149 (61%)

Query:    23 LRVLQPVFQIYGQCRSFSGPVVTLKVFEDNVLVRELLETRGEGKVLVIDGGGSMRCALVG 82
             L +L   F+ +G  R F G VVT+K FEDN  V+E+L   G GKVL++DGGGS R AL+G
Sbjct:    16 LTLLPLAFRAFGGKRLFWGEVVTVKCFEDNSKVKEVLAQPGHGKVLIVDGGGSSRRALLG 75

Query:    83 GNLGQLAHNNGWSGIVVNGCIRDVDEINGCGIGVRALGSHPLKSNKKGHGDKHVPVYIAG 142
               + Q A +NGW G+++NG +RD   ++   +GV ALG+ P+K+ K   G  +VP+ +  
Sbjct:    76 DLIAQSAMDNGWQGVIINGYVRDAARLSSFNLGVYALGAMPMKTEKLDQGQINVPIELGC 135

Query:   143 VYIAGSFIRDGEWLYADSDGILVSKSELS 171
             V +     + G  +Y D +GI +S+  L+
Sbjct:   136 VTV-----KPGMMVYVDENGIAISEESLN 159

GO:0008757 "S-adenosylmethionine-dependent methyltransferase activity" evidence=ISS

GO:0009234 "menaquinone biosynthetic process" evidence=ISS

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q02KR3	RRAAH_PSEAB	No assigned EC number	0.4879	0.9069	0.9629	yes	no
Q48JZ3	RRAAH_PSE14	No assigned EC number	0.4642	0.9069	0.9512	yes	no
Q4ZUN7	RRAAH_PSEU2	No assigned EC number	0.4819	0.9069	0.9629	yes	no
A4XU32	RRAAH_PSEMY	No assigned EC number	0.4939	0.9069	0.9629	yes	no
Q47BF5	RRAAH_DECAR	No assigned EC number	0.5636	0.9244	0.9754	yes	no
Q9RW10	RRAAH_DEIRA	No assigned EC number	0.4260	0.9186	0.9875	yes	no
B7VBA7	RRAAH_PSEA8	No assigned EC number	0.4879	0.9069	0.9629	yes	no
Q88L51	RRAAH_PSEPK	No assigned EC number	0.4759	0.9069	0.9570	yes	no
Q13X79	RRAAH_BURXL	No assigned EC number	0.5361	0.9360	0.9817	yes	no
Q0A9G6	RRAAH_ALHEH	No assigned EC number	0.5120	0.9069	0.9689	yes	no
A3NWR9	RRAAH_BURP0	No assigned EC number	0.5628	0.9418	0.9818	yes	no
A1V5A8	RRAAH_BURMS	No assigned EC number	0.5628	0.9418	0.9818	yes	no
A1WU91	RRAAH_HALHL	No assigned EC number	0.5060	0.9302	0.9756	yes	no
A3NAY8	RRAAH_BURP6	No assigned EC number	0.5628	0.9418	0.9818	yes	no
Q3KFE1	RRAAH_PSEPF	No assigned EC number	0.4759	0.9069	0.9570	yes	no
A9AHQ6	RRAAH_BURM1	No assigned EC number	0.5662	0.9360	0.9817	yes	no
Q9I2W7	RRAAH_PSEAE	No assigned EC number	0.4879	0.9069	0.9629	yes	no
A2SB35	RRAAH_BURM9	No assigned EC number	0.5628	0.9418	0.9818	yes	no
A4VL60	RRAAH_PSEU5	No assigned EC number	0.4518	0.9069	0.9629	yes	no
Q46ZV6	RRAA_CUPPJ	No assigned EC number	0.5548	0.9244	0.9636	yes	no
Q63SX7	RRAAH_BURPS	No assigned EC number	0.5628	0.9418	0.9818	yes	no
C1DHC2	RRAAH_AZOVD	No assigned EC number	0.4819	0.9069	0.9629	yes	no
B1J596	RRAAH_PSEPW	No assigned EC number	0.4759	0.9069	0.9570	yes	no
B0KG79	RRAAH_PSEPG	No assigned EC number	0.4819	0.9069	0.9570	yes	no
B2JIG2	RRAAH_BURP8	No assigned EC number	0.5515	0.9302	0.9756	yes	no
B2SXN2	RRAAH_BURPP	No assigned EC number	0.5421	0.9360	0.9817	yes	no
Q7NXI6	RRAAH_CHRVO	No assigned EC number	0.4759	0.9069	0.9811	yes	no
A6V753	RRAAH_PSEA7	No assigned EC number	0.4759	0.9069	0.9629	yes	no
C1D7M1	RRAAH_LARHH	No assigned EC number	0.5	0.8953	0.9685	yes	no
Q3JQZ3	RRAAH_BURP1	No assigned EC number	0.5628	0.9418	0.9818	yes	no
A3MKY3	RRAAH_BURM7	No assigned EC number	0.5628	0.9418	0.9818	yes	no
Q2SX33	RRAAH_BURTA	No assigned EC number	0.5748	0.9418	0.9818	yes	no
Q0K9J4	RRAA_CUPNH	No assigned EC number	0.5609	0.9244	0.9636	yes	no
Q2SK70	RRAAH_HAHCH	No assigned EC number	0.4337	0.9069	0.9512	yes	no
Q883Q6	RRAAH_PSESM	No assigned EC number	0.4518	0.9069	0.9629	yes	no
Q62J86	RRAAH_BURMA	No assigned EC number	0.5628	0.9418	0.9818	yes	no
Q607E7	RRAAH_METCA	No assigned EC number	0.4727	0.9127	0.9751	yes	no
Q9FH13	RRAA3_ARATH	No assigned EC number	0.7844	0.9418	0.9759	yes	no
Q1ICM4	RRAAH_PSEE4	No assigned EC number	0.4698	0.9069	0.9570	yes	no
B3R2J3	RRAAH_CUPTR	No assigned EC number	0.5575	0.9302	0.9696	yes	no
C3K0T6	RRAAH_PSEFS	No assigned EC number	0.4819	0.9069	0.9570	yes	no
Q4KFJ3	RRAAH_PSEF5	No assigned EC number	0.4819	0.9069	0.9570	yes	no
Q5P203	RRAAH_AROAE	No assigned EC number	0.5060	0.8953	0.9685	yes	no
B8GM40	RRAAH_THISH	No assigned EC number	0.5090	0.9011	0.9627	yes	no
A5W6M0	RRAAH_PSEP1	No assigned EC number	0.4819	0.9069	0.9570	yes	no
Q21X23	RRAAH_RHOFD	No assigned EC number	0.4662	0.9534	0.9479	yes	no
Q8XZP1	RRAAH_RALSO	No assigned EC number	0.5329	0.9418	0.9818	yes	no

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	172
PRK09372	159	PRK09372, PRK09372, ribonuclease activity regulato	3e-80
TIGR01935	150	TIGR01935, NOT-MenG, RraA famliy	2e-70
COG0684	210	COG0684, MenG, Demethylmenaquinone methyltransfera	4e-53
PRK12487	163	PRK12487, PRK12487, ribonuclease activity regulato	2e-52
TIGR02998	161	TIGR02998, RraA_entero, regulator of ribonuclease	4e-44
pfam03737	154	pfam03737, Methyltransf_6, Demethylmenaquinone met	1e-43
PRK06201	221	PRK06201, PRK06201, hypothetical protein; Validate	5e-17
PRK07028	430	PRK07028, PRK07028, bifunctional hexulose-6-phosph	1e-09
PRK12764	500	PRK12764, PRK12764, hypothetical protein; Provisio	5e-08
PRK08245	240	PRK08245, PRK08245, hypothetical protein; Validate	9e-06

>gnl|CDD|236487 PRK09372, PRK09372, ribonuclease activity regulator protein RraA; Provisional

 Score =  234 bits (600), Expect = 3e-80
 Identities = 85/166 (51%), Positives = 114/166 (68%), Gaps = 10/166 (6%)

Query: 6   ATAEACDSNAALLASGDLRVLQPVFQIYGQCRSFSGPVVTLKVFEDNVLVRELLETRGEG 65
            T++ CD         D+RV++P+F  +G   SF GP+ T+K FEDN LV+ELLE  GEG
Sbjct: 4   DTSDLCDIYP-----DDVRVVEPLFSSFGGRSSFGGPITTVKCFEDNGLVKELLEEPGEG 58

Query: 66  KVLVIDGGGSMRCALVGGNLGQLAHNNGWSGIVVNGCIRDVDEINGCGIGVRALGSHPLK 125
           +VLV+DGGGS+R ALVG NL +LA +NGW GIVV GC+RDVDE+    IG++AL + P+K
Sbjct: 59  RVLVVDGGGSLRRALVGDNLAELAVDNGWEGIVVYGCVRDVDELAELDIGIQALAAIPVK 118

Query: 126 SNKKGHGDKHVPVYIAGVYIAGSFIRDGEWLYADSDGILVSKSELS 171
           S+K+G G++ VPV   GV         G++LYAD+DGI+VS   L 
Sbjct: 119 SDKEGIGERDVPVNFGGVT-----FFPGDYLYADNDGIIVSPEPLD 159

Length = 159

>gnl|CDD|130990 TIGR01935, NOT-MenG, RraA famliy

 Score =  209 bits (533), Expect = 2e-70
 Identities = 84/160 (52%), Positives = 112/160 (70%), Gaps = 10/160 (6%)

Query: 7   TAEACDSNAALLASGDLRVLQPVFQIYGQCRSFSGPVVTLKVFEDNVLVRELLETRGEGK 66
           T + CD+         +RVL+P+F+ +G   +F+GP+VT+K FEDN LVRE+LE  G G+
Sbjct: 1   TPDLCDAYPD-----KVRVLEPMFRNFGGRAAFAGPIVTVKCFEDNSLVREVLEQPGAGR 55

Query: 67  VLVIDGGGSMRCALVGGNLGQLAHNNGWSGIVVNGCIRDVDEINGCGIGVRALGSHPLKS 126
           VLV+DGGGS+RCAL+G NL  LA  NGW G++VNGC+RDV E+ G  +GV+AL +HP K+
Sbjct: 56  VLVVDGGGSLRCALLGDNLAVLAEENGWEGVIVNGCVRDVAELAGMDLGVKALAAHPRKT 115

Query: 127 NKKGHGDKHVPVYIAGVYIAGSFIRDGEWLYADSDGILVS 166
            K+G G+  VPV  AGV         G++LYAD DGILVS
Sbjct: 116 EKRGAGEVDVPVTFAGVT-----FVPGDYLYADEDGILVS 150

The E. coli member of this family has been characterized as a regulator of RNase E and its crystal structure has been analyzed. This model was initially classified as a "hypothetical equivalog" expressing the tentative hypothesis that all members might have the same function as the E. coli enzyme. Considering the second clade of enterobacterial sequences within this family, that appears to be less tenable. The function of these sequences outside of the narrow RraA equivalog model (TIGR02998) remains obscure. All of these were initially annotated as MenG, AKA S-adenosylmethionine: 2-demethylmenaquinone methyltransferase (EC 2.1.-.-). See the references characterizing this as a case of transitive annotation error in the case of the E. coli protein [Unknown function, General]. Length = 150

>gnl|CDD|223756 COG0684, MenG, Demethylmenaquinone methyltransferase [Coenzyme metabolism]

 Score =  167 bits (425), Expect = 4e-53
 Identities = 66/166 (39%), Positives = 95/166 (57%), Gaps = 5/166 (3%)

Query: 5   VATAEACDSNAALLASGDLRVLQPVFQIYGQCRSFSGPVVTLKVFEDNVLVRELLETRGE 64
           + T + CD+     A G + V+ P  + +G   SF GP VT++ F D+ L+   LE  G 
Sbjct: 11  IETLDLCDAATVSDALGRVGVVDPGIRPFGGRSSFVGPAVTVRCFPDDWLLHVALEQAGP 70

Query: 65  GKVLVIDGGGSMRCALVGGNLGQLAHNNGWSGIVVNGCIRDVDEINGCGIGVRALGSHPL 124
           G VLVIDGGG +R AL G  L  LA   GW+G+V++G +RDVDE+      V A G  P 
Sbjct: 71  GDVLVIDGGGDLRRALWGDLLATLAKVRGWAGVVIDGAVRDVDELRELDFPVFARGVTPR 130

Query: 125 KSNKKGHGDKHVPVYIAGVYIAGSFIRDGEWLYADSDGILVSKSEL 170
            + K+G G+ +VPV   GV      +  G+ + AD+DG++V  +EL
Sbjct: 131 GATKRGIGEVNVPVTCGGVT-----VNPGDIVVADADGVVVVPAEL 171

Length = 210

>gnl|CDD|183553 PRK12487, PRK12487, ribonuclease activity regulator protein RraA; Reviewed

 Score =  164 bits (417), Expect = 2e-52
 Identities = 69/151 (45%), Positives = 98/151 (64%), Gaps = 5/151 (3%)

Query: 22  DLRVLQPVFQIYGQCRSFSGPVVTLKVFEDNVLVRELLETRGEGKVLVIDGGGSMRCALV 81
            L +L   F+ +G  R F G +VT++ FEDN  V+E+L   G+GKVLV+DGGGS R AL+
Sbjct: 15  KLTLLNLPFKNFGGKRIFWGEIVTVRCFEDNSKVKEVLAQDGKGKVLVVDGGGSCRRALL 74

Query: 82  GGNLGQLAHNNGWSGIVVNGCIRDVDEINGCGIGVRALGSHPLKSNKKGHGDKHVPVYIA 141
           G  + Q A +NGW GIV+NGC+RDV  ++   +GV+ALG+ P+K+ K+G G+ +V + + 
Sbjct: 75  GDQIAQSALDNGWEGIVINGCVRDVGALSTMDLGVKALGASPIKTEKRGQGEVNVTLTMG 134

Query: 142 GVYIAGSFIRDGEWLYADSDGILVSKSELSI 172
            V      I  G+ LYAD +GI VSK  L  
Sbjct: 135 NV-----IIEPGDMLYADENGIAVSKEALDF 160

Length = 163

>gnl|CDD|132043 TIGR02998, RraA_entero, regulator of ribonuclease activity A

 Score =  143 bits (361), Expect = 4e-44
 Identities = 73/166 (43%), Positives = 103/166 (62%), Gaps = 10/166 (6%)

Query: 7   TAEACDSNAALLASGDLRVLQPVFQIYGQCRSFSGPVVTLKVFEDNVLVRELLETRGEGK 66
           T+E CD       +  + V++P+F  +G   SF G VVT+K FE N L+ ELLE  G G+
Sbjct: 5   TSELCD-----FYADLVDVVEPIFSNFGGRSSFGGKVVTVKCFEHNGLINELLEQNGTGR 59

Query: 67  VLVIDGGGSMRCALVGGNLGQLAHNNGWSGIVVNGCIRDVDEINGCGIGVRALGSHPLKS 126
           VLVIDGGGS R AL+   L QLA NNGW GIVV G +R VD +    IG++AL + P+ +
Sbjct: 60  VLVIDGGGSTRRALIDAELAQLAANNGWEGIVVYGAVRQVDALEELDIGIQALAAIPVGA 119

Query: 127 NKKGHGDKHVPVYIAGVYIAGSFIRDGEWLYADSDGILVSKSELSI 172
           +++G G+  + V  AGV    +F    +++YAD+ GI++S   L I
Sbjct: 120 DEQGIGESDIAVNFAGV----TFF-PDDYIYADNTGIILSPEPLEI 160

This family includes a number of closely related sequences from certain enterobacteria. The E. coli member of this family has been characterized as a regulator of RNase E and its crystal structure has been analyzed. The broader subfamily which includes this equivalog, TIGR01935, was initially classified as a "hypothetical equivalog" with the name "regulator of ribonuclease activity A" based on the same evidence for this model. It now appears that, considering the second group of enterobacterial sequences within TIGR01935, the functional assignment is unsupported. THIS PROTEIN IS _NOT_ MenG, AKA S-adenosylmethionine: 2-demethylmenaquinone methyltransferase (EC 2.1.-.-). See the references characterizing this as a case of transitive annotation error [Transcription, Degradation of RNA, Regulatory functions, Protein interactions]. Length = 161

>gnl|CDD|217703 pfam03737, Methyltransf_6, Demethylmenaquinone methyltransferase

 Score =  141 bits (357), Expect = 1e-43
 Identities = 66/146 (45%), Positives = 94/146 (64%), Gaps = 6/146 (4%)

Query: 21  GDLRVLQPVFQIYGQCRSFSGPVVTLKVFE-DNVLVRELLETRGEGKVLVIDGGGSMRCA 79
             + V++P+   +G   SF GP VT++  E DN LVRE+L+  G G+VLV+DGGGS+R A
Sbjct: 14  SQVGVVEPILSNFGGRSSFVGPAVTVRCSEIDNGLVREVLDQAGPGRVLVVDGGGSLRRA 73

Query: 80  LVGGNLGQLAHNNGWSGIVVNGCIRDVDEINGCGIGVRALGSHPLKSNKKGHGDKHVPVY 139
           L G  L  LA  NGW G+VV GC+RDVD +    + + ALG+ P  + K G G+ +VPV 
Sbjct: 74  LWGDLLSTLAKKNGWEGVVVYGCVRDVDALRELDLPIFALGTTPCAAVKTGIGEVNVPVT 133

Query: 140 IAGVYIAGSFIRDGEWLYADSDGILV 165
             GV      +R G+++YAD++GI+V
Sbjct: 134 CGGV-----TVRPGDYIYADNNGIVV 154

Members of this family are demethylmenaquinone methyltransferases that convert dimethylmenaquinone (DMK) to menaquinone (MK) in the final step of menaquinone biosynthesis. This region is also found at the C-terminus of the DlpA protein. Length = 154

>gnl|CDD|180465 PRK06201, PRK06201, hypothetical protein; Validated

 Score = 74.6 bits (184), Expect = 5e-17
 Identities = 41/130 (31%), Positives = 67/130 (51%), Gaps = 6/130 (4%)

Query: 37  RSFSGPVVTLKVFE-DNVLVRELLETRGEGKVLVIDGGGSMRCALVGGNLGQLAHNNGWS 95
              +G  +T++    DN+++   L+    G V+V+DGGG +  ALVG  +  +A   G +
Sbjct: 51  GRLAGTALTVRTRPGDNLMIHRALDLARPGDVIVVDGGGDLTNALVGEIMLAIAARRGVA 110

Query: 96  GIVVNGCIRDVDEINGCGIGVRALGSHPLKSNKKGHGDKHVPVYIAGVYIAGSFIRDGEW 155
           G+V++G +RDV  +   G  V A G       K G G+ +VPV I G+      I  G+ 
Sbjct: 111 GVVIDGAVRDVAALREMGFPVFARGVTHRGPYKDGPGEINVPVAIGGM-----VIEPGDL 165

Query: 156 LYADSDGILV 165
           +  D DG++ 
Sbjct: 166 IVGDDDGLVA 175

Length = 221

>gnl|CDD|235912 PRK07028, PRK07028, bifunctional hexulose-6-phosphate synthase/ribonuclease regulator; Validated

 Score = 55.4 bits (134), Expect = 1e-09
 Identities = 40/138 (28%), Positives = 59/138 (42%), Gaps = 11/138 (7%)

Query: 32  IYGQCRS--FSGPVVTLKVFE-DNVLVRELLETRGEGKVLVIDGGGSMRCALVGGNLGQL 88
           I    R     G  VT++ F  D     E ++    G V+VI            G L  L
Sbjct: 254 IKPLVRGTKMVGKAVTVQTFAGDWAKPVEAIDVAKPGDVIVIYNSSKD--IAPWGELATL 311

Query: 89  -AHNNGWSGIVVNGCIRDVDEINGCGIGVRALGSHPLKSNKKGHGDKHVPVYIAGVYIAG 147
              N G +G+V++G +RDVDEI   G  V A    P     KG G+ +  +   G     
Sbjct: 312 SCLNKGIAGVVIDGAVRDVDEIRKLGFPVFARAIVPNAGEPKGFGEINAEIVCGGQT--- 368

Query: 148 SFIRDGEWLYADSDGILV 165
             +R G+W+  D +G++V
Sbjct: 369 --VRPGDWIIGDENGVVV 384

Length = 430

>gnl|CDD|237193 PRK12764, PRK12764, hypothetical protein; Provisional

 Score = 50.9 bits (122), Expect = 5e-08
 Identities = 31/109 (28%), Positives = 53/109 (48%), Gaps = 8/109 (7%)

Query: 59  LETRGEGKVLVIDGGGSMRCALVGGNLGQLAHNNGWSGIVVNGCIRDVDEINGCGIGVRA 118
            ++   G+VLVI+  G      +G  L   A   G +G+V +G +RD   +   G+ V  
Sbjct: 340 FDSVNPGEVLVIEARGEKGTGTLGDILALRAQVRGAAGVVTDGGVRDYAAVAELGLPVFF 399

Query: 119 LGSHPLKSNKKGHGDKHVPVYIAGVYIA--GSFIRDGEWLYADSDGILV 165
            G HP        G +HVP +   + +A  G+ ++ G+ +  D DG++V
Sbjct: 400 AGPHPAVL-----GRRHVP-WDVDITVACGGATVQPGDVIVGDDDGVVV 442

Length = 500

>gnl|CDD|236200 PRK08245, PRK08245, hypothetical protein; Validated

 Score = 44.1 bits (105), Expect = 9e-06
 Identities = 38/132 (28%), Positives = 49/132 (37%), Gaps = 29/132 (21%)

Query: 5   VATAEACDSNAALLASG-------DLRVLQPVFQIYGQCRSFSGPVVTLK---------- 47
           V+TA       AL   G        +R L+P     G  R   GP  TL+          
Sbjct: 17  VSTATLT---TALFKRGLRNQFIRGVRPLRP-----GGPR-MVGPAFTLRFVPAREDLNT 67

Query: 48  --VFED-NVLVRELLETRGEGKVLVIDGGGSMRCALVGGNLGQLAHNNGWSGIVVNGCIR 104
              F D     R  +ET   G VLV+D  G  R    G  L       G +G+V +G +R
Sbjct: 68  PESFADPESPQRAAIETCPPGCVLVVDARGDARAGSFGDILCTRLKKRGVAGLVTDGGVR 127

Query: 105 DVDEINGCGIGV 116
           D   I   G+ V
Sbjct: 128 DSPGIAALGLPV 139

Length = 240

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	172
TIGR02998	161	RraA_entero regulator of ribonuclease activity A.	100.0
PRK09372	159	ribonuclease activity regulator protein RraA; Prov	100.0
PRK12487	163	ribonuclease activity regulator protein RraA; Revi	100.0
PRK06201	221	hypothetical protein; Validated	100.0
TIGR01935	150	NOT-MenG RraA famliy. This model was initially cla	100.0
PRK09262	225	hypothetical protein; Provisional	100.0
TIGR02798	222	ligK_PcmE 4-carboxy-4-hydroxy-2-oxoadipate aldolas	100.0
COG0684	210	MenG Demethylmenaquinone methyltransferase [Coenzy	100.0
PF03737	154	Methyltransf_6: Demethylmenaquinone methyltransfer	100.0
PRK08245	240	hypothetical protein; Validated	100.0
PRK07028	430	bifunctional hexulose-6-phosphate synthase/ribonuc	100.0
PRK12764	500	hypothetical protein; Provisional	100.0

>TIGR02998 RraA_entero regulator of ribonuclease activity A

Probab=100.00  E-value=2.7e-53  Score=331.00  Aligned_cols=158  Identities=45%  Similarity=0.775  Sum_probs=152.6

Q ss_pred             CCChhhHhHhhhccccCCceecccccceecCCCceEEEEEEEEEeecCcHHHHHHHhhCCCCcEEEEEcCCCCCcceehH
Q 030761            4 VVATAEACDSNAALLASGDLRVLQPVFQIYGQCRSFSGPVVTLKVFEDNVLVRELLETRGEGKVLVIDGGGSMRCALVGG   83 (172)
Q Consensus         4 ~~~t~~v~Dal~~~~~~g~~~~l~p~~~~~~~~~~~~G~A~Tv~~~~d~~~~~~~~~~~~~G~VlVid~~g~~~~a~~G~   83 (172)
                      ++.|++|||++.+     .++.++|.|++||+.+|++|+|+||++.+||..+++++++++||||||||++++.++|+|||
T Consensus         2 ~~~t~dl~d~~~~-----~~~~~~~~~~~~g~~~~~~G~A~TV~~~~d~~~~~~aid~~~pGdVlVid~~g~~~~A~~G~   76 (161)
T TIGR02998         2 QYDTSELCDFYAD-----LVDVVEPIFSNFGGRSSFGGKVVTVKCFEHNGLINELLEQNGTGRVLVIDGGGSTRRALIDA   76 (161)
T ss_pred             CCCchhHhhcCcc-----cccEecccccccCCCCEEEEEEEEEEeeCCcHHHHHHHhccCCCeEEEEECCCCCceEeeCH
Confidence            4799999999987     57899999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHCCCcEEEecCccCCHHHHhcCCCcEEEcceecCCCCCCccceeceeEEEeeeccCCeEEccCCEEEEcCCce
Q 030761           84 NLGQLAHNNGWSGIVVNGCIRDVDEINGCGIGVRALGSHPLKSNKKGHGDKHVPVYIAGVYIAGSFIRDGEWLYADSDGI  163 (172)
Q Consensus        84 l~a~~a~~~G~~G~VidG~vRD~~~i~~~~~pvfa~g~~p~~~~~~~~~~~~vpV~ig~~~~~gv~V~pGD~v~aD~dGV  163 (172)
                      +|+++|++||++|+|+||++||++||++++|||||+|++|..+.+...+++|+||+||     |++|+|||+|+||+|||
T Consensus        77 ~la~~a~~~G~aGvVidG~vRD~~~i~~l~~PVfa~g~~p~~~~~~~~g~~nvpV~ig-----gv~V~PGD~IvaD~DGV  151 (161)
T TIGR02998        77 ELAQLAANNGWEGIVVYGAVRQVDALEELDIGIQALAAIPVGADEQGIGESDIAVNFA-----GVTFFPDDYIYADNTGI  151 (161)
T ss_pred             HHHHHHHHCCCeEEEEeecccCHHHHhhCCCCcEEeeccCCCCCCCCcceeCCCEEEC-----CEEECCCCEEEEcCCcE
Confidence            9999999999999999999999999999999999999999988777899999999999     99999999999999999


Q ss_pred             EEecCCcC
Q 030761          164 LVSKSELS  171 (172)
Q Consensus       164 vviP~~l~  171 (172)
                      +|||++|.
T Consensus       152 vVip~~~~  159 (161)
T TIGR02998       152 ILSPEPLE  159 (161)
T ss_pred             EEECcccc
Confidence            99999984

THIS PROTEIN IS _NOT_ MenG, AKA S-adenosylmethionine: 2-demethylmenaquinone methyltransferase (EC 2.1.-.-). See the references characterizing this as a case of transitive annotation error .

>PRK09372 ribonuclease activity regulator protein RraA; Provisional

Probab=100.00  E-value=4.3e-51  Score=318.43  Aligned_cols=158  Identities=53%  Similarity=0.943  Sum_probs=149.0

Q ss_pred             CCChhhHhHhhhccccCCceecccccceecCCCceEEEEEEEEEeecCcHHHHHHHhhCCCCcEEEEEcCCCCCcceehH
Q 030761            4 VVATAEACDSNAALLASGDLRVLQPVFQIYGQCRSFSGPVVTLKVFEDNVLVRELLETRGEGKVLVIDGGGSMRCALVGG   83 (172)
Q Consensus         4 ~~~t~~v~Dal~~~~~~g~~~~l~p~~~~~~~~~~~~G~A~Tv~~~~d~~~~~~~~~~~~~G~VlVid~~g~~~~a~~G~   83 (172)
                      ++.|++|||++..     .++.+.|.++++++++|++|+|+||++.+|+...++++++++|||||||++.++.++|+|||
T Consensus         2 ~~~ta~l~D~~~~-----~~~~~~~~i~~~~~~~~~~G~A~TV~~~~d~~~~~~~i~~~~~GdVlVid~~g~~~~a~~G~   76 (159)
T PRK09372          2 EYDTSDLCDIYPD-----DVRVVEPLFSSFGGRSSFGGPITTVKCFEDNGLVKELLEEPGEGRVLVVDGGGSLRRALVGD   76 (159)
T ss_pred             CCCcceeeccccC-----cccCcCccccccCCCCEEEEEEEEEEEeCCcHHHHHHHhcCCCCeEEEEECCCCcCcEeehH
Confidence            6899999999864     34567888888888899999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHCCCcEEEecCccCCHHHHhcCCCcEEEcceecCCCCCCccceeceeEEEeeeccCCeEEccCCEEEEcCCce
Q 030761           84 NLGQLAHNNGWSGIVVNGCIRDVDEINGCGIGVRALGSHPLKSNKKGHGDKHVPVYIAGVYIAGSFIRDGEWLYADSDGI  163 (172)
Q Consensus        84 l~a~~a~~~G~~G~VidG~vRD~~~i~~~~~pvfa~g~~p~~~~~~~~~~~~vpV~ig~~~~~gv~V~pGD~v~aD~dGV  163 (172)
                      +|+++|+++|++|+|+||++||++||++++|||||+|++|..+.+...+++|+||+|+     |++|+|||+|+||.|||
T Consensus        77 ~~~~~a~~~G~~G~VidG~vRD~~~i~~~~~Pvfa~g~~p~~~~~~~~~~~n~pV~ig-----gv~V~PGD~I~aD~dGV  151 (159)
T PRK09372         77 NLAELAVDNGWEGIVVYGCVRDVDELAELDIGIQALAAIPVKSDKEGIGERDVPVNFG-----GVTFFPGDYLYADNDGI  151 (159)
T ss_pred             HHHHHHHHcCCeEEEecccccCHHHHhhCCCCeEEeeecCCCCCCCCccEecccEEEC-----CEEECCCCEEEEcCCCE
Confidence            9999999999999999999999999999999999999999888777899999999999     99999999999999999


Q ss_pred             EEecCCcC
Q 030761          164 LVSKSELS  171 (172)
Q Consensus       164 vviP~~l~  171 (172)
                      +|||++|.
T Consensus       152 vviP~~l~  159 (159)
T PRK09372        152 IVSPEPLD  159 (159)
T ss_pred             EEECCcCC
Confidence            99999973

>PRK12487 ribonuclease activity regulator protein RraA; Reviewed

Probab=100.00  E-value=5.9e-51  Score=318.39  Aligned_cols=158  Identities=44%  Similarity=0.786  Sum_probs=150.6

Q ss_pred             CCChhhHhHhhhccccCCceecccccceecCCCceEEEEEEEEEeecCcHHHHHHHhhCCCCcEEEEEcCCCCCcceehH
Q 030761            4 VVATAEACDSNAALLASGDLRVLQPVFQIYGQCRSFSGPVVTLKVFEDNVLVRELLETRGEGKVLVIDGGGSMRCALVGG   83 (172)
Q Consensus         4 ~~~t~~v~Dal~~~~~~g~~~~l~p~~~~~~~~~~~~G~A~Tv~~~~d~~~~~~~~~~~~~G~VlVid~~g~~~~a~~G~   83 (172)
                      .+.|++|||.+..     .++.+.|.++++++.++++|+|+||++.+++..+++++++++||||||||++++.++|+|||
T Consensus         2 ~~~~~dl~d~~~~-----~~~~l~~~i~~~~~~~~~~G~A~TV~~~~d~~~~~~al~~~~~GdVlVid~~g~~~~a~~G~   76 (163)
T PRK12487          2 LDLLPDLFDHYED-----KLTLLNLPFKNFGGKRIFWGEIVTVRCFEDNSKVKEVLAQDGKGKVLVVDGGGSCRRALLGD   76 (163)
T ss_pred             CCCchhHhhcchh-----hhcccCHhheecCCCCEEEEEEEEEEeeCCcHHHHHHHhcCCCCeEEEEECCCCCCcEeehH
Confidence            4689999999987     57889999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHCCCcEEEecCccCCHHHHhcCCCcEEEcceecCCCCCCccceeceeEEEeeeccCCeEEccCCEEEEcCCce
Q 030761           84 NLGQLAHNNGWSGIVVNGCIRDVDEINGCGIGVRALGSHPLKSNKKGHGDKHVPVYIAGVYIAGSFIRDGEWLYADSDGI  163 (172)
Q Consensus        84 l~a~~a~~~G~~G~VidG~vRD~~~i~~~~~pvfa~g~~p~~~~~~~~~~~~vpV~ig~~~~~gv~V~pGD~v~aD~dGV  163 (172)
                      +|+++|++||++|+|+||++||+++|++++|||||+|++|.++.+...+++|+||+|+     |++|+|||+|+||+|||
T Consensus        77 ~~a~~a~~~G~aG~VidG~vRD~~~i~~l~fPVfa~g~~p~~~~~~~~~~~nvPV~ig-----gv~V~PGDiI~aD~dGV  151 (163)
T PRK12487         77 QIAQSALDNGWEGIVINGCVRDVGALSTMDLGVKALGASPIKTEKRGQGEVNVTLTMG-----NVIIEPGDMLYADENGI  151 (163)
T ss_pred             HHHHHHHHCCCeEEEEeecccCHHHHhhCCCCeEEeecCCCCCCCCCcceecccEEEC-----CEEECCCCEEEEcCCCE
Confidence            9999999999999999999999999999999999999999887777899999999999     99999999999999999


Q ss_pred             EEecCCcC
Q 030761          164 LVSKSELS  171 (172)
Q Consensus       164 vviP~~l~  171 (172)
                      +|||++|.
T Consensus       152 vvip~~l~  159 (163)
T PRK12487        152 AVSKEALD  159 (163)
T ss_pred             EEECchhh
Confidence            99999874

>PRK06201 hypothetical protein; Validated

Probab=100.00  E-value=4.1e-50  Score=327.88  Aligned_cols=160  Identities=28%  Similarity=0.453  Sum_probs=146.2

Q ss_pred             CCCCCChhhHhHhhhccccCCceecccccceecCCCceEEEEEEEEEeec-CcHHHHHHHhhCCCCcEEEEEcCCCCCcc
Q 030761            1 MAGVVATAEACDSNAALLASGDLRVLQPVFQIYGQCRSFSGPVVTLKVFE-DNVLVRELLETRGEGKVLVIDGGGSMRCA   79 (172)
Q Consensus         1 ~l~~~~t~~v~Dal~~~~~~g~~~~l~p~~~~~~~~~~~~G~A~Tv~~~~-d~~~~~~~~~~~~~G~VlVid~~g~~~~a   79 (172)
                      +|++++|++|||+|++++.      +.+.++++.+.++++|+|+|+++.+ |+...+++++.++||+|||||+.++.++|
T Consensus        21 ~l~~l~t~~v~Dal~~~g~------~~~~i~p~~~~~~~~G~A~Tv~~~~~d~~~~~~ai~~~~pG~VlVid~~g~~~~a   94 (221)
T PRK06201         21 AFRELPVANISDSMNRMTA------GGAGLRPMHRGGRLAGTALTVRTRPGDNLMIHRALDLARPGDVIVVDGGGDLTNA   94 (221)
T ss_pred             HHhcCCchHHHHHHcccCC------CcccceecCCCCEEEEEEEEEEeeCCCcHHHHHHHhccCCCcEEEEECCCCCCcc
Confidence            5789999999999998653      2233445555689999999999997 78889999999999999999999999999


Q ss_pred             eehHHHHHHHHHCCCcEEEecCccCCHHHHhcCCCcEEEcceecCCCCCCccceeceeEEEeeeccCCeEEccCCEEEEc
Q 030761           80 LVGGNLGQLAHNNGWSGIVVNGCIRDVDEINGCGIGVRALGSHPLKSNKKGHGDKHVPVYIAGVYIAGSFIRDGEWLYAD  159 (172)
Q Consensus        80 ~~G~l~a~~a~~~G~~G~VidG~vRD~~~i~~~~~pvfa~g~~p~~~~~~~~~~~~vpV~ig~~~~~gv~V~pGD~v~aD  159 (172)
                      +|||+++++|+++|++|+|+||++||+++|++++|||||+|++|.++.+...+++|+||+||     |++|+|||+|+||
T Consensus        95 ~~G~~~a~~a~~~G~~G~VidG~vRD~~~i~~~~fPvfa~g~~p~~~~~~~~~~~n~pV~ig-----Gv~V~PGD~I~aD  169 (221)
T PRK06201         95 LVGEIMLAIAARRGVAGVVIDGAVRDVAALREMGFPVFARGVTHRGPYKDGPGEINVPVAIG-----GMVIEPGDLIVGD  169 (221)
T ss_pred             chhHHHHHHHHHCCCeEEEEeeccCCHHHHhhCCCCeEEeccCCCCCCCCCccccCccEEEC-----CEEEcCCCEEEEc
Confidence            99999999999999999999999999999999999999999999877667789999999999     9999999999999


Q ss_pred             CCceEEecCCcC
Q 030761          160 SDGILVSKSELS  171 (172)
Q Consensus       160 ~dGVvviP~~l~  171 (172)
                      +|||+|||++++
T Consensus       170 ~dGVvviP~~~a  181 (221)
T PRK06201        170 DDGLVAVPPADA  181 (221)
T ss_pred             CCceEEEcHHHH
Confidence            999999999864

>TIGR01935 NOT-MenG RraA famliy

Probab=100.00  E-value=8.8e-50  Score=308.37  Aligned_cols=150  Identities=55%  Similarity=1.042  Sum_probs=144.4

Q ss_pred             hhhHhHhhhccccCCceecccccceecCCCceEEEEEEEEEeecCcHHHHHHHhhCCCCcEEEEEcCCCCCcceehHHHH
Q 030761            7 TAEACDSNAALLASGDLRVLQPVFQIYGQCRSFSGPVVTLKVFEDNVLVRELLETRGEGKVLVIDGGGSMRCALVGGNLG   86 (172)
Q Consensus         7 t~~v~Dal~~~~~~g~~~~l~p~~~~~~~~~~~~G~A~Tv~~~~d~~~~~~~~~~~~~G~VlVid~~g~~~~a~~G~l~a   86 (172)
                      |++|||.+.+     .++.++|.|++|++.+|++|+|+||++.+|+..+++++++++|||||||+++++.+.|+|||+|+
T Consensus         1 t~~l~d~~~~-----~~~~~~~~~~~~g~~~~i~G~A~TV~~~~d~~~~~~ai~~~~~GdVlVid~~g~~~~a~~G~~~~   75 (150)
T TIGR01935         1 TPDLCDAYPD-----KVRVLEPMFRNFGGRAAFAGPIVTVKCFEDNSLVREVLEQPGAGRVLVVDGGGSLRCALLGDNLA   75 (150)
T ss_pred             CchHHhCCcc-----hhcccChhhhhcCCCCEEEEEEEEEEEECCcHHHHHHHhcCCCCeEEEEECCCCCceEeehHHHH
Confidence            7899999976     57889999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHCCCcEEEecCccCCHHHHhcCCCcEEEcceecCCCCCCccceeceeEEEeeeccCCeEEccCCEEEEcCCceEEe
Q 030761           87 QLAHNNGWSGIVVNGCIRDVDEINGCGIGVRALGSHPLKSNKKGHGDKHVPVYIAGVYIAGSFIRDGEWLYADSDGILVS  166 (172)
Q Consensus        87 ~~a~~~G~~G~VidG~vRD~~~i~~~~~pvfa~g~~p~~~~~~~~~~~~vpV~ig~~~~~gv~V~pGD~v~aD~dGVvvi  166 (172)
                      ++|+++|++|+|+||++||++||++++|||||+|++|..+.+...+++|+||+|+     |++|+|||+|+||.|||+|.
T Consensus        76 ~~a~~~G~~G~VidG~vRD~~~i~~~~~Pvfa~g~~p~~~~~~~~~~~nvPV~ig-----Gv~V~PGD~IvaD~dGVvv~  150 (150)
T TIGR01935        76 VLAEENGWEGVIVNGCVRDVAELAGMDLGVKALAAHPRKTEKRGAGEVDVPVTFA-----GVTFVPGDYLYADEDGILVS  150 (150)
T ss_pred             HHHHHCCCEEEEEeecccCHHHHhhCCCCEEEeeecCCCCCCCcceEecceEEEC-----CEEECCCCEEEEcCCCEEEC
Confidence            9999999999999999999999999999999999999988777899999999999     99999999999999999984

This model was initially classified as a "hypothetical equivalog" expressing the tentative hypothesis that all members might have the same function as the E. coli enzyme. Considering the second clade of enterobacterial sequences within this family, that appears to be less tenable. The function of these sequences outside of the narrow RraA equivalog model (TIGR02998) remains obscure. All of these were initially annotated as MenG, AKA S-adenosylmethionine: 2-demethylmenaquinone methyltransferase (EC 2.1.-.-). See the references characterizing this as a case of transitive annotation error in the case of the E. coli protein.

>PRK09262 hypothetical protein; Provisional

Probab=100.00  E-value=1e-49  Score=326.16  Aligned_cols=160  Identities=24%  Similarity=0.332  Sum_probs=146.7

Q ss_pred             CCCCCChhhHhHhhhccccCCceecccccceecCCCceEEEEEEEEEeec-CcHHHHHHHhhCCCCcEEEEEcCCCCCcc
Q 030761            1 MAGVVATAEACDSNAALLASGDLRVLQPVFQIYGQCRSFSGPVVTLKVFE-DNVLVRELLETRGEGKVLVIDGGGSMRCA   79 (172)
Q Consensus         1 ~l~~~~t~~v~Dal~~~~~~g~~~~l~p~~~~~~~~~~~~G~A~Tv~~~~-d~~~~~~~~~~~~~G~VlVid~~g~~~~a   79 (172)
                      +|++++|++|||+|++++.      +.+.++++.++++++|+|+||++.+ |++.++++++.++||+||||++.++.++|
T Consensus        19 ~l~~~~ta~v~Dal~~~g~------~~~~i~p~~~~~~~~G~A~TV~~~~~d~~~~~~ai~~~~pGdVlVid~~g~~~~a   92 (225)
T PRK09262         19 RLAEFGVATVHEAQGRVGL------LKPYMRPIYQGARIAGTAVTVLVQPGDNWMMHVAVEQCQPGDVLVVAPTSPCTDG   92 (225)
T ss_pred             HhcCCCCccHHHHhcccCC------CCcceEECCCCCeEEEEEEEEEeecCCcHHHHHHHHccCCCCEEEEECCCCCcee
Confidence            5889999999999998653      3334555556679999999999995 88999999999999999999999999999


Q ss_pred             eehHHHHHHHHHCCCcEEEecCccCCHHHHhcCCCcEEEcceecCCCCCCccceeceeEEEeeeccCCeEEccCCEEEEc
Q 030761           80 LVGGNLGQLAHNNGWSGIVVNGCIRDVDEINGCGIGVRALGSHPLKSNKKGHGDKHVPVYIAGVYIAGSFIRDGEWLYAD  159 (172)
Q Consensus        80 ~~G~l~a~~a~~~G~~G~VidG~vRD~~~i~~~~~pvfa~g~~p~~~~~~~~~~~~vpV~ig~~~~~gv~V~pGD~v~aD  159 (172)
                      +|||+|+++|+++|++|+|+||++||+++|++++|||||+|++|.++.+...+++|+||+||     |++|+|||+||||
T Consensus        93 ~~Ge~~a~~a~~~G~~GiVidG~vRD~~~i~~l~~Pvfa~g~~p~~~~~~~~~~~nvpV~ig-----gv~V~PGD~IvaD  167 (225)
T PRK09262         93 FFGDLLATSLQARGVRGLVIDAGVRDVRTLTEMGFPVWSRAISAQGTVKATLGSVNVPVVCA-----GALVNPGDVVVAD  167 (225)
T ss_pred             eehHHHHHHHHHCCCeEEEEeceeCCHHHHhhCCCceEEeecCCCCCCCCCcceecccEEEC-----CEEECCCCEEEEE
Confidence            99999999999999999999999999999999999999999999877777799999999999     9999999999999


Q ss_pred             CCceEEecCCcC
Q 030761          160 SDGILVSKSELS  171 (172)
Q Consensus       160 ~dGVvviP~~l~  171 (172)
                      +|||+|||++++
T Consensus       168 ~dGVvvIP~~~~  179 (225)
T PRK09262        168 DDGVVVVPRAQA  179 (225)
T ss_pred             CCcEEEECHHHH
Confidence            999999999763

>TIGR02798 ligK_PcmE 4-carboxy-4-hydroxy-2-oxoadipate aldolase/oxaloacetate decarboxylase

Probab=100.00  E-value=9.5e-50  Score=325.66  Aligned_cols=160  Identities=21%  Similarity=0.284  Sum_probs=147.0

Q ss_pred             CCCCCChhhHhHhhhccccCCceecccccceecCCCceEEEEEEEEEeec-CcHHHHHHHhhCCCCcEEEEEcCCCCCcc
Q 030761            1 MAGVVATAEACDSNAALLASGDLRVLQPVFQIYGQCRSFSGPVVTLKVFE-DNVLVRELLETRGEGKVLVIDGGGSMRCA   79 (172)
Q Consensus         1 ~l~~~~t~~v~Dal~~~~~~g~~~~l~p~~~~~~~~~~~~G~A~Tv~~~~-d~~~~~~~~~~~~~G~VlVid~~g~~~~a   79 (172)
                      +|+.++|++|||+|++++.      +.+.++++.+++|++|+|+||++.+ ||..++++++.++||||||||+.++.++|
T Consensus        17 ~l~~~~ta~v~Dal~~~g~------~~~~I~p~~~~~ki~G~A~TV~~~~~d~~~~~~ai~~~~pGdVlVid~~g~~~~a   90 (222)
T TIGR02798        17 GLAAFGVATVHEAMGRVGL------LAPYMRPIYTGARVCGTAVTVLLQPGDNWMMHVAAEQIQEGDVVVAACTAECEDG   90 (222)
T ss_pred             HHhCCCCccHHHHhcccCC------CCccceEcCCCCEEEEEEEEEEeecCCchHHHHHHHhCCCCeEEEEECCCCcceE
Confidence            4789999999999998763      3334555556789999999999995 88999999999999999999999999999


Q ss_pred             eehHHHHHHHHHCCCcEEEecCccCCHHHHhcCCCcEEEcceecCCCCCCccceeceeEEEeeeccCCeEEccCCEEEEc
Q 030761           80 LVGGNLGQLAHNNGWSGIVVNGCIRDVDEINGCGIGVRALGSHPLKSNKKGHGDKHVPVYIAGVYIAGSFIRDGEWLYAD  159 (172)
Q Consensus        80 ~~G~l~a~~a~~~G~~G~VidG~vRD~~~i~~~~~pvfa~g~~p~~~~~~~~~~~~vpV~ig~~~~~gv~V~pGD~v~aD  159 (172)
                      +|||+|+++|+++|++|+|+||++||+++|++++|||||+|++|.++.+...+++|+||+||     |++|+|||+|+||
T Consensus        91 ~~G~~~a~~a~~~G~~GiVidG~vRD~~~i~~l~~Pvfa~g~~p~~~~~~~~~~~nvpv~ig-----gv~V~PGD~i~aD  165 (222)
T TIGR02798        91 YFGDLLATSFQARGCRGLIIDAGVRDVRDLTEMNFPVWSKAIHAKGTVKATLGSVNIPVVCA-----NALVNPGDVVVAD  165 (222)
T ss_pred             eehHHHHHHHHHCCCeEEEEecccCCHHHHhhCCCceEEeecCCCCCCCCCccccCCCEEEC-----CEEECCCCEEEEc
Confidence            99999999999999999999999999999999999999999999877777899999999999     9999999999999


Q ss_pred             CCceEEecCCcC
Q 030761          160 SDGILVSKSELS  171 (172)
Q Consensus       160 ~dGVvviP~~l~  171 (172)
                      +|||||||++++
T Consensus       166 ~dGVvviP~~~~  177 (222)
T TIGR02798       166 DDGVVVVPRANA  177 (222)
T ss_pred             CCcEEEEcHHHH
Confidence            999999999864

Members of this protein family 4-carboxy-4-hydroxy-2-oxoadipate aldolase, also called 4-oxalocitramalate aldolase. This enzyme of the protocatechuate 4,5-cleavage pathway converts its substrate to pyruvate plus oxaloacetate. Protocatechuate is an intermediate in many pathways for degrading aromatic compounds, including lignin, fluorene, etc. Hara, et al. showed the LigK gene was not only a 4-carboxy-4-hydroxy-2-oxoadipate aldolase but also the enzyme of the following step, oxaloacetate decarboxylase.

>COG0684 MenG Demethylmenaquinone methyltransferase [Coenzyme metabolism]

Probab=100.00  E-value=6.6e-49  Score=316.90  Aligned_cols=160  Identities=41%  Similarity=0.697  Sum_probs=143.4

Q ss_pred             hhhHhHhhhccccCCceecccccceecCCCceEEEEEEEEEeecCcHHHHHHHhhCCCCcEEEEEcCCCCCcceehHHHH
Q 030761            7 TAEACDSNAALLASGDLRVLQPVFQIYGQCRSFSGPVVTLKVFEDNVLVRELLETRGEGKVLVIDGGGSMRCALVGGNLG   86 (172)
Q Consensus         7 t~~v~Dal~~~~~~g~~~~l~p~~~~~~~~~~~~G~A~Tv~~~~d~~~~~~~~~~~~~G~VlVid~~g~~~~a~~G~l~a   86 (172)
                      |.++||++..+.-.+....+.|.+++++++++|+|+|+||||.++|+..+.+|++++||||||||++++.++|+||++|+
T Consensus        13 ~~~~~d~~~~~~a~~~~g~~~~~i~p~~~~~~~~G~A~TV~~~~~d~~~~~al~~~~~GdVLVid~~g~~~~A~~Gd~la   92 (210)
T COG0684          13 TLDLCDAATVSDALGRVGVVDPGIRPFGGRSSFVGPAVTVRCFPDDWLLHVALEQAGPGDVLVIDGGGDLRRALWGDLLA   92 (210)
T ss_pred             hhhhcCcccchhhhhhcCCcccccccCCCCCcceeEEEEEEEeCCCchhhheeecCCCCCEEEEeCCCCcceeehHHHHH
Confidence            44444444332212233445667888888899999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHCCCcEEEecCccCCHHHHhcCCCcEEEcceecCCCCCCccceeceeEEEeeeccCCeEEccCCEEEEcCCceEEe
Q 030761           87 QLAHNNGWSGIVVNGCIRDVDEINGCGIGVRALGSHPLKSNKKGHGDKHVPVYIAGVYIAGSFIRDGEWLYADSDGILVS  166 (172)
Q Consensus        87 ~~a~~~G~~G~VidG~vRD~~~i~~~~~pvfa~g~~p~~~~~~~~~~~~vpV~ig~~~~~gv~V~pGD~v~aD~dGVvvi  166 (172)
                      ++|+.|||+|+||||+|||++++++|+||+||++++|.++.|...+++|+||+||     |++|+|||+||||+|||||+
T Consensus        93 ~~a~~~G~~GvVidG~vRDv~~l~el~~pv~a~~~~p~~~~k~~~geinvpV~~g-----Gv~v~PGD~vvgD~dGvVVv  167 (210)
T COG0684          93 TLAKVRGWAGVVIDGAVRDVDELRELDFPVFARGVTPRGATKRGIGEVNVPVTCG-----GVTVNPGDIVVADADGVVVV  167 (210)
T ss_pred             HHHHHcCccEEEEeceeechHHHhhcCCCeEeccccCCCCCcCCcceecccEEEC-----CEEECCCCEEEEcCCceEEe
Confidence            9999999999999999999999999999999999999999999999999999999     99999999999999999999


Q ss_pred             cCCcC
Q 030761          167 KSELS  171 (172)
Q Consensus       167 P~~l~  171 (172)
                      |++++
T Consensus       168 p~~~~  172 (210)
T COG0684         168 PAELA  172 (210)
T ss_pred             ccchh
Confidence            99874

>PF03737 Methyltransf_6: Demethylmenaquinone methyltransferase; InterPro: IPR005493 This entry represents a structural motif found in demethylmenaquinone methyltransferases and in the regulator of ribonuclease E activity A (RraA)

Probab=100.00  E-value=4.5e-48  Score=300.17  Aligned_cols=152  Identities=38%  Similarity=0.665  Sum_probs=137.3

Q ss_pred             CCChhhHhHhhhccccCCceecccccceecCCCceEEEEEEEEEeec-CcHHHHHHHhhCCCCcEEEEEcCCCCCcceeh
Q 030761            4 VVATAEACDSNAALLASGDLRVLQPVFQIYGQCRSFSGPVVTLKVFE-DNVLVRELLETRGEGKVLVIDGGGSMRCALVG   82 (172)
Q Consensus         4 ~~~t~~v~Dal~~~~~~g~~~~l~p~~~~~~~~~~~~G~A~Tv~~~~-d~~~~~~~~~~~~~G~VlVid~~g~~~~a~~G   82 (172)
                      .++|++|||+|++     .++.+.|.++++.+.++++|+|+|+++.+ ++...+++++.++||+|||+++.++.++|+||
T Consensus         2 ~i~ta~l~Dal~~-----~~~~~~~~~~~~~~~~~~~G~A~Tv~~~~~~~~~~~~~i~~~~~G~VlVid~~~~~~~a~~G   76 (154)
T PF03737_consen    2 NISTADLCDALGK-----RLGGMNPIIRPLPPGMKIVGPAVTVRFAPGDNLLVREAIDAAPPGDVLVIDGGGDTDCAVWG   76 (154)
T ss_dssp             HCHHHHHHHHHGG-----TSEEEESTSEESSSCSSEEEEEEEEEESSTBSHHHHHHHTSS-TTEEEEEEETTGSSSEEE-
T ss_pred             ccchhhHhHCccc-----ccCEeccccccCCCCCEEEEEEEEEEEECCCCHHHHHHHhcCCCCeEEEEECCCCcceeeEC
Confidence            4789999999985     24556677777788899999999999998 88899999999999999999999988999999


Q ss_pred             HHHHHHHHHCCCcEEEecCccCCHHHHhcCCCcEEEcceecCCCCCCccceeceeEEEeeeccCCeEEccCCEEEEcCCc
Q 030761           83 GNLGQLAHNNGWSGIVVNGCIRDVDEINGCGIGVRALGSHPLKSNKKGHGDKHVPVYIAGVYIAGSFIRDGEWLYADSDG  162 (172)
Q Consensus        83 ~l~a~~a~~~G~~G~VidG~vRD~~~i~~~~~pvfa~g~~p~~~~~~~~~~~~vpV~ig~~~~~gv~V~pGD~v~aD~dG  162 (172)
                      |+|+++|+++|++|+|+||++||++||++++||+||+|++|..+.++..+++|+||+|+     |++|+|||+||||.||
T Consensus        77 ~~~a~~a~~~G~~G~VidG~vRD~~~i~~~~~Pvfa~g~~p~~~~~~~~~~~~~pv~~g-----Gv~V~pGD~I~aD~dG  151 (154)
T PF03737_consen   77 ELMATAAKARGVAGVVIDGAVRDVDEIRELGFPVFARGTTPRGGKKRGVGEINVPVTIG-----GVTVNPGDIIVADDDG  151 (154)
T ss_dssp             HHHHHHHHHTTBSEEEEEEEES-HHHHTTSSSEEEEEEE-SSBTBCSSESEESSEEEET-----TEEE-TTSEEEEETTE
T ss_pred             HHHHHHHHHCCCeEEECCCcccCHHHHhhcCCCeEecccCcccCcceeeeeeCCeEEEC-----CEEECCCCEEEECCCc
Confidence            99999999999999999999999999999999999999999987778899999999999     9999999999999999


Q ss_pred             eEE
Q 030761          163 ILV  165 (172)
Q Consensus       163 Vvv  165 (172)
                      |||
T Consensus       152 VvV  154 (154)
T PF03737_consen  152 VVV  154 (154)
T ss_dssp             EEE
T ss_pred             EEC
Confidence            997

These proteins contain a swivelling 3-layer beta/beta/alpha domain that appears to be mobile in most multi-domain proteins known to contain it. These proteins are structurally similar, and may have distant homology, to the phosphohistidine domain of pyruvate phosphate dikinase. The RraA fold is an ancient platform that has been adapted for a wide range of functions. RraA had been identified as a putative demethylmenaquinone methyltransferase and was annotated as MenG, but further analysis showed that RraA lacked the structural motifs usually required for methylases. The Escherichia coli protein regulator RraA acts as a trans-acting modulator of RNA turnover, binding essential endonuclease RNase E and inhibiting RNA processing []. RNase E forms the core of a large RNA-catalysis machine termed the degradosomes. RraA (and RraB) causes remodelling of degradosome composition, which is associated with alterations in RNA decay and global transcript abundance and as such is a bacterial mechanism for the regulation of RNA cleavage. Demethylmenaquinone methyltransferases convert dimethylmenaquinone (DMK) to menaquinone (MK) in the final step of menaquinone biosynthesis. This region is also found at the C terminus of the DlpA protein Q48806 from SWISSPROT.; PDB: 3C8O_A 2PCN_A 3K4I_B 2YJV_A 1Q5X_B 2C5Q_D 2YJT_B 1NXJ_B 3NOJ_A 1J3L_A ....

>PRK08245 hypothetical protein; Validated

Probab=100.00  E-value=4.4e-48  Score=319.31  Aligned_cols=162  Identities=26%  Similarity=0.324  Sum_probs=143.4

Q ss_pred             CCCCCChhhHhHhhhcccc-CCceecccccceecCCC-ceEEEEEEEEEeec-Cc------------HHHHHHHhhCCCC
Q 030761            1 MAGVVATAEACDSNAALLA-SGDLRVLQPVFQIYGQC-RSFSGPVVTLKVFE-DN------------VLVRELLETRGEG   65 (172)
Q Consensus         1 ~l~~~~t~~v~Dal~~~~~-~g~~~~l~p~~~~~~~~-~~~~G~A~Tv~~~~-d~------------~~~~~~~~~~~~G   65 (172)
                      +|++++|++|||+|+++|+ .+++..++|.++    . .+++|+|+||++.+ ++            ...+++++.++||
T Consensus        13 ~l~~l~t~~v~Dal~~~g~~~~~~~~i~pl~p----~~~~~~G~A~TV~~~p~~~~~~~~~~~~~~~~~~~~aid~~~~G   88 (240)
T PRK08245         13 ALKRVSTATLTTALFKRGLRNQFIRGVRPLRP----GGPRMVGPAFTLRFVPAREDLNTPESFADPESPQRAAIETCPPG   88 (240)
T ss_pred             HHhcCChhHHHHHHHhcCCccccCCCceecCC----CCCeEEEEEEEEEeecCCCcccccccccccchhHHHHHhccCCC
Confidence            4789999999999999876 334555565443    3 48999999999985 21            1378999999999


Q ss_pred             cEEEEEcCCCCCcceehHHHHHHHHHCCCcEEEecCccCCHHHHhcCCCcEEEcceecCCCC-CCccceeceeEEEeeec
Q 030761           66 KVLVIDGGGSMRCALVGGNLGQLAHNNGWSGIVVNGCIRDVDEINGCGIGVRALGSHPLKSN-KKGHGDKHVPVYIAGVY  144 (172)
Q Consensus        66 ~VlVid~~g~~~~a~~G~l~a~~a~~~G~~G~VidG~vRD~~~i~~~~~pvfa~g~~p~~~~-~~~~~~~~vpV~ig~~~  144 (172)
                      ||||||+.+..+.|+|||+|+++|+++|++|+|+||++||+++|++++|||||+|++|..+. +..++++|+||+||   
T Consensus        89 dVlVid~~g~~~~a~~G~~~~~~a~~~G~~G~VidG~vRD~~ei~~~gfPvfarg~~p~~~~~~~~~~~~nvPV~ig---  165 (240)
T PRK08245         89 CVLVVDARGDARAGSFGDILCTRLKKRGVAGLVTDGGVRDSPGIAALGLPVWCAGPSAPTNLTGLTAVDINVPIGCG---  165 (240)
T ss_pred             eEEEEECCCCCCccccHHHHHHHHHHCCCeEEEEeeccCCHHHHhhCCCceEecccCCCCCCCCCceEeecCCEEEC---
Confidence            99999999988999999999999999999999999999999999999999999999997664 56789999999999   


Q ss_pred             cCCeEEccCCEEEEcCCceEEecCCcC
Q 030761          145 IAGSFIRDGEWLYADSDGILVSKSELS  171 (172)
Q Consensus       145 ~~gv~V~pGD~v~aD~dGVvviP~~l~  171 (172)
                        |++|+|||+|+||+|||+|||++++
T Consensus       166 --Gv~V~PGD~I~aD~dGVvvIP~~~a  190 (240)
T PRK08245        166 --GVAVFPGDIIVADDDGVVVIPAALA  190 (240)
T ss_pred             --CEEEcCCCEEEEcCCceEEEcHHHH
Confidence              9999999999999999999998864

>PRK07028 bifunctional hexulose-6-phosphate synthase/ribonuclease regulator; Validated

Probab=100.00  E-value=2.9e-45  Score=323.58  Aligned_cols=158  Identities=28%  Similarity=0.425  Sum_probs=143.7

Q ss_pred             CCCCCChhhHhHhhhccccCCceecccccceecCCCceEEEEEEEEEeec-CcHHHHHHHhhCCCCcEEEEEcCCCCCcc
Q 030761            1 MAGVVATAEACDSNAALLASGDLRVLQPVFQIYGQCRSFSGPVVTLKVFE-DNVLVRELLETRGEGKVLVIDGGGSMRCA   79 (172)
Q Consensus         1 ~l~~~~t~~v~Dal~~~~~~g~~~~l~p~~~~~~~~~~~~G~A~Tv~~~~-d~~~~~~~~~~~~~G~VlVid~~g~~~~a   79 (172)
                      +|++++|++|||+|+++|.   +..++|.+    ++.+++|+|+|+++.+ |+...+++++.++|||||||++ ++.++|
T Consensus       232 ~l~~~~t~~i~d~l~~~g~---~~~i~p~~----~~~~~~G~A~Tv~~~~~d~~~~~~~~~~~~~G~VlVi~~-~~~~~a  303 (430)
T PRK07028        232 IFMQVSTPNISDAMHRKGA---MKGIKPLV----RGTKMVGKAVTVQTFAGDWAKPVEAIDVAKPGDVIVIYN-SSKDIA  303 (430)
T ss_pred             HhcCCCCCcHHhhhhccCC---CceeeecC----CCCeEEEEEEEEEeeCCCcHHHHHHHhcCCCCeEEEEEC-CCCCce
Confidence            4789999999999998653   44555554    3579999999999996 7778899999999999999999 778999


Q ss_pred             eehHHHHHHHHHCCCcEEEecCccCCHHHHhcCCCcEEEcceecCCCCCCccceeceeEEEeeeccCCeEEccCCEEEEc
Q 030761           80 LVGGNLGQLAHNNGWSGIVVNGCIRDVDEINGCGIGVRALGSHPLKSNKKGHGDKHVPVYIAGVYIAGSFIRDGEWLYAD  159 (172)
Q Consensus        80 ~~G~l~a~~a~~~G~~G~VidG~vRD~~~i~~~~~pvfa~g~~p~~~~~~~~~~~~vpV~ig~~~~~gv~V~pGD~v~aD  159 (172)
                      +|||+|+++|+++|++|+|+||++||++++++++|||||+|++|.++.+...+++|+||+||     |++|+|||+|+||
T Consensus       304 ~~G~~~~~~a~~~G~~G~VidG~vRD~~~i~~~~~pv~~~g~~p~~~~~~~~~~~nvpv~~g-----gv~V~pGD~i~aD  378 (430)
T PRK07028        304 PWGELATLSCLNKGIAGVVIDGAVRDVDEIRKLGFPVFARAIVPNAGEPKGFGEINAEIVCG-----GQTVRPGDWIIGD  378 (430)
T ss_pred             eecHHHHHHHHHCCCeEEEEeeccCCHHHHhhCCCCeEeeecCCCCCCCCCccccCCCEEEC-----CEEECCCCEEEEc
Confidence            99999999999999999999999999999999999999999999877666789999999999     9999999999999


Q ss_pred             CCceEEecCCcC
Q 030761          160 SDGILVSKSELS  171 (172)
Q Consensus       160 ~dGVvviP~~l~  171 (172)
                      +|||||||++++
T Consensus       379 ~dGvvvip~~~~  390 (430)
T PRK07028        379 ENGVVVVPKERA  390 (430)
T ss_pred             CCceEEEcHHHH
Confidence            999999998864

>PRK12764 hypothetical protein; Provisional

Probab=100.00  E-value=2.5e-44  Score=323.10  Aligned_cols=162  Identities=24%  Similarity=0.336  Sum_probs=144.1

Q ss_pred             CCCCCChhhHhHhhhccccCC-ceecccccceecCCCceEEEEEEEEEeec-Cc----------HHHHHHHhhCCCCcEE
Q 030761            1 MAGVVATAEACDSNAALLASG-DLRVLQPVFQIYGQCRSFSGPVVTLKVFE-DN----------VLVRELLETRGEGKVL   68 (172)
Q Consensus         1 ~l~~~~t~~v~Dal~~~~~~g-~~~~l~p~~~~~~~~~~~~G~A~Tv~~~~-d~----------~~~~~~~~~~~~G~Vl   68 (172)
                      +|++++|++|||+|+++++.+ .+..++|.+    +++|++|+|+|+++.+ ++          ...+++++.++|||||
T Consensus       274 ~l~~l~ta~vsdal~~~g~~~~~~~~i~p~~----p~~k~vG~A~Tv~~~p~~~~~~~~~~~~~~~~~~aid~~~pGdVl  349 (500)
T PRK12764        274 KLASVATATLSAQLRKRGLNNVSIDGLTPTR----PGRRMVGRARTLRYVPNREDLFKEHGGGFNAQKRAFDSVNPGEVL  349 (500)
T ss_pred             HHhcCCcchHHHHHhhcCCCcccccCceecC----CCCeEEEEEEEEEeecCCcccccccccchhHHHHHHhcCCCCeEE
Confidence            588999999999999987643 345556544    4579999999999985 22          3467999999999999


Q ss_pred             EEEcCCCCCcceehHHHHHHHHHCCCcEEEecCccCCHHHHhcCCCcEEEcceecCCCCCC-ccceeceeEEEeeeccCC
Q 030761           69 VIDGGGSMRCALVGGNLGQLAHNNGWSGIVVNGCIRDVDEINGCGIGVRALGSHPLKSNKK-GHGDKHVPVYIAGVYIAG  147 (172)
Q Consensus        69 Vid~~g~~~~a~~G~l~a~~a~~~G~~G~VidG~vRD~~~i~~~~~pvfa~g~~p~~~~~~-~~~~~~vpV~ig~~~~~g  147 (172)
                      |||+.++.++|+|||+|+++|+++|++|+|+||+|||+++|++++|||||+|++|..+.+. ..+++|+||+||     |
T Consensus       350 VId~~g~~~~a~~Gel~a~~a~~~G~~G~ViDG~vRD~~ei~~lg~PVfarg~~p~~~~~~~~~~~~nvpV~~g-----G  424 (500)
T PRK12764        350 VIEARGEKGTGTLGDILALRAQVRGAAGVVTDGGVRDYAAVAELGLPVFFAGPHPAVLGRRHVPWDVDITVACG-----G  424 (500)
T ss_pred             EEECCCCCCeEchHHHHHHHHHHCCCeEEEEeecccCHHHHHhCCCCeEEeecCCCCCCcCcccceeCCcEEEC-----C
Confidence            9999999999999999999999999999999999999999999999999999999866543 568999999999     9


Q ss_pred             eEEccCCEEEEcCCceEEecCCcC
Q 030761          148 SFIRDGEWLYADSDGILVSKSELS  171 (172)
Q Consensus       148 v~V~pGD~v~aD~dGVvviP~~l~  171 (172)
                      ++|+|||+|+||+|||||||++++
T Consensus       425 v~V~PGDiIvaD~dGVvvIP~~~a  448 (500)
T PRK12764        425 ATVQPGDVIVGDDDGVVVIPPALA  448 (500)
T ss_pred             EEEcCCCEEEEcCCcEEEEcHHHH
Confidence            999999999999999999999864

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	172
3c8o_A	162	The Crystal Structure Of Rraa From Pao1 Length = 16		5e-37
2pcn_A	161	Crystal Structure Of S-Adenosylmethionine: 2-Dimeth		6e-32
1j3l_A	164	Structure Of The Rna-Processing Inhibitor Rraa From		1e-30
1q5x_A	161	Structure Of Of Rraa (Meng), A Protein Inhibitor Of		4e-28
1nxj_A	183	Structure Of Rv3853 From Mycobacterium Tuberculosis		9e-27
1vi4_A	174	Crystal Structure Of Regulator Of Ribonuclease Aciv		8e-24

>pdb|3C8O|A Chain A, The Crystal Structure Of Rraa From Pao1 Length = 162

Iteration: 1
 Score =  150 bits (378), Expect = 5e-37,   Method: Compositional matrix adjust.
 Identities = 81/166 (48%), Positives = 111/166 (66%), Gaps = 10/166 (6%)
Query: 7   TAEACDSNAALLASGDLRVLQPVFQIYGQCRSFSGPVVTLKVFEDNVLVRELLETRGEGK 66
           T + CD+   L+     +V++P+F  +G   SF G +VT+K FEDN LV+E ++  G+GK
Sbjct: 5   TPDLCDAYPELV-----QVVEPMFSNFGGRDSFGGEIVTIKCFEDNSLVKEQVDKDGKGK 59
Query: 67  VLVIDGGGSMRCALVGGNLGQLAHNNGWSGIVVNGCIRDVDEINGCGIGVRALGSHPLKS 126
           VLV+DGGGS+R AL+G  L + A  NGW GIVV GCIRDVD I    +GV+AL SHPLK+
Sbjct: 60  VLVVDGGGSLRRALLGDMLAEKAAKNGWEGIVVYGCIRDVDVIAQTDLGVQALASHPLKT 119
Query: 127 NKKGHGDKHVPVYIAGVYIAGSFIRDGEWLYADSDGILVSKSELSI 172
           +K+G GD +V V   GV       R GE++YAD++GI+VS   L +
Sbjct: 120 DKRGIGDLNVAVTFGGVT-----FRPGEFVYADNNGIIVSPQALKM 160

>pdb|2PCN|A Chain A, Crystal Structure Of S-Adenosylmethionine: 2-Dimethylmenaquinone Methyltransferase (Gk_1813) From Geobacillus Kaustophilus Hta426 Length = 161

Iteration: 1
 Score =  133 bits (334), Expect = 6e-32,   Method: Compositional matrix adjust.
 Identities = 75/166 (45%), Positives = 103/166 (62%), Gaps = 10/166 (6%)
Query: 5   VATAEACDSNAALLASGDLRVLQPVFQIYGQCRSFSGPVVTLKVFEDNVLVRELLETRGE 64
           + TA+ CD         +L+V +  FQ YG  R FSGP+ T+ VFEDNVLVRE LET   
Sbjct: 1   MKTADLCDQFL-----DELQVCELPFQSYGGKRMFSGPIATVDVFEDNVLVREALETVPP 55
Query: 65  GKVLVIDGGGSMRCALVGGNLGQLAHNNGWSGIVVNGCIRDVDEINGCGIGVRALGSHPL 124
           G VLV+DG GS R AL+G  L Q+A   G +G++++GCIRD  EI    IGV A+G+ P+
Sbjct: 56  GTVLVVDGKGSRRVALLGDRLAQIACERGLAGVIIHGCIRDSAEIGAMPIGVMAIGTCPV 115
Query: 125 KSNKKGHGDKHVPVYIAGVYIAGSFIRDGEWLYADSDGILVSKSEL 170
           KS K+G G + V +   GV         G ++YAD+DG++V+  +L
Sbjct: 116 KSKKEGKGARDVVLEFGGVR-----WEPGAYVYADADGVVVANKDL 156

>pdb|1J3L|A Chain A, Structure Of The Rna-Processing Inhibitor Rraa From Thermus Thermophilis Length = 164

Iteration: 1
 Score =  129 bits (323), Expect = 1e-30,   Method: Compositional matrix adjust.
 Identities = 66/140 (47%), Positives = 93/140 (66%), Gaps = 5/140 (3%)
Query: 26  LQPVFQIYGQCRSFSGPVVTLKVFEDNVLVRELLETRGEGKVLVIDGGGSMRCALVGGNL 85
           L  VF+ +G    F+G V TL+VFEDN LVR++LE  G G+VL +DGGGS+R AL+GGNL
Sbjct: 18  LPXVFKSFGGRARFAGRVRTLRVFEDNALVRKVLEEEGAGQVLFVDGGGSLRTALLGGNL 77
Query: 86  GQLAHNNGWSGIVVNGCIRDVDEINGCGIGVRALGSHPLKSNKKGHGDKHVPVYIAGVYI 145
            + A   GW+G+VV+G +RD +E+    IG+ AL + P KS K+G G+  VP+ + GV +
Sbjct: 78  ARRAWEKGWAGVVVHGAVRDTEELREVPIGLLALAATPKKSAKEGKGEVDVPLKVLGVEV 137
Query: 146 AGSFIRDGEWLYADSDGILV 165
                  G +L AD DG+L+
Sbjct: 138 L-----PGSFLLADEDGLLL 152

>pdb|1Q5X|A Chain A, Structure Of Of Rraa (Meng), A Protein Inhibitor Of Rna Processing Length = 161

Iteration: 1
 Score =  120 bits (301), Expect = 4e-28,   Method: Compositional matrix adjust.
 Identities = 68/166 (40%), Positives = 103/166 (62%), Gaps = 10/166 (6%)
Query: 7   TAEACDSNAALLASGDLRVLQPVFQIYGQCRSFSGPVVTLKVFEDNVLVRELLETRGEGK 66
           T+E CD     +   D+ V++P+F  +G   SF G ++T+K FEDN L+ +LLE  G G+
Sbjct: 5   TSELCD-----IYQEDVNVVEPLFSNFGGRASFGGQIITVKCFEDNGLLYDLLEQNGRGR 59
Query: 67  VLVIDGGGSMRCALVGGNLGQLAHNNGWSGIVVNGCIRDVDEINGCGIGVRALGSHPLKS 126
           VLV+DGGGS+R ALV   L +LA  N W G+V+ G +R VD++    IG++A+ + P+ +
Sbjct: 60  VLVVDGGGSVRRALVDAELARLAVQNEWEGLVIYGAVRQVDDLEELDIGIQAMAAIPVGA 119
Query: 127 NKKGHGDKHVPVYIAGVYIAGSFIRDGEWLYADSDGILVSKSELSI 172
             +G G+  V V   GV    +F   G+ LYAD+ GI++S+  L I
Sbjct: 120 AGEGIGESDVRVNFGGV----TFFS-GDHLYADNTGIILSEDPLDI 160

>pdb|1NXJ|A Chain A, Structure Of Rv3853 From Mycobacterium Tuberculosis Length = 183

Iteration: 1
 Score =  115 bits (289), Expect = 9e-27,   Method: Compositional matrix adjust.
 Identities = 58/144 (40%), Positives = 92/144 (63%), Gaps = 5/144 (3%)
Query: 22  DLRVLQPVFQIYGQCRSFSGPVVTLKVFEDNVLVRELLETRGEGKVLVIDGGGSMRCALV 81
           D+R     F+ +G    F+GP+ T++ F+DN L++ +L     G VLVIDG GS+  ALV
Sbjct: 44  DVRSCDLQFRQFGGRSQFAGPISTVRCFQDNALLKSVLSQPSAGGVLVIDGAGSLHTALV 103
Query: 82  GGNLGQLAHNNGWSGIVVNGCIRDVDEINGCGIGVRALGSHPLKSNKKGHGDKHVPVYIA 141
           G  + +LA + GW+G++V+G +RD   + G  IG++ALG++P KS K G G++ V + + 
Sbjct: 104 GDVIAELARSTGWTGLIVHGAVRDAAALRGIDIGIKALGTNPRKSTKTGAGERDVEITLG 163
Query: 142 GVYIAGSFIRDGEWLYADSDGILV 165
           GV    +F+  G+  Y+D DGI+V
Sbjct: 164 GV----TFV-PGDIAYSDDDGIIV 182

>pdb|1VI4|A Chain A, Crystal Structure Of Regulator Of Ribonuclease Acivity A Protein 1 Length = 174

Iteration: 1
 Score =  106 bits (264), Expect = 8e-24,   Method: Compositional matrix adjust.
 Identities = 59/166 (35%), Positives = 93/166 (56%), Gaps = 10/166 (6%)
Query: 7   TAEACDSNAALLASGDLRVLQPVFQIYGQCRSFSGPVVTLKVFEDNVLVRELLETRGEGK 66
           T + CD   +      + +L    Q +GQ  +F G +VT++ + DN  VR++L   G+GK
Sbjct: 8   TPDLCDKYES-----QVTLLNLPLQNFGQRSAFWGEIVTVRCYHDNSKVRDVLSQNGKGK 62
Query: 67  VLVIDGGGSMRCALVGGNLGQLAHNNGWSGIVVNGCIRDVDEINGCGIGVRALGSHPLKS 126
           VLV+DG GS   AL G  L  LA  N W G+++ G +RDV   +   +G++ALG+ P K+
Sbjct: 63  VLVVDGHGSCHKALXGDQLAILAIKNDWEGVIIYGAVRDVVAXSEXDLGIKALGTSPFKT 122
Query: 127 NKKGHGDKHVPVYIAGVYIAGSFIRDGEWLYADSDGILVSKSELSI 172
            K+G G  +V      +      +  G++LYAD +GIL S++ L +
Sbjct: 123 EKRGAGQVNVT-----LTXQNQIVEPGDYLYADWNGILXSETALDV 163

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	172
1vi4_A	174	Regulator of ribonuclease acivity A protein 1; str	3e-69
2pcn_A	161	S-adenosylmethionine:2-demethylmenaquinone methylt	4e-68
3c8o_A	162	Regulator of ribonuclease activity A; RRAA, PAO1,	4e-68
1j3l_A	164	Demethylmenaquinone methyltransferase; vitamine K2	1e-67
1nxj_A	183	Probable S-adenosylmethionine:2- demethylmenaquino	6e-66
1q5x_A	161	Regulator of RNAse E activity A; 3-layer sandwich,	1e-65
3noj_A	238	4-carboxy-4-hydroxy-2-oxoadipate aldolase/oxaloac	1e-36
3k4i_A	244	Uncharacterized protein; structural genomics, prot	2e-25
2c5q_A	240	RRAA-like protein YER010C; structural genomics,unk	2e-21

>1vi4_A Regulator of ribonuclease acivity A protein 1; structural genomics, unknown function; 1.87A {Vibrio cholerae} SCOP: c.8.7.1 Length = 174

 Score =  206 bits (527), Expect = 3e-69
 Identities = 59/168 (35%), Positives = 96/168 (57%), Gaps = 10/168 (5%)

Query: 5   VATAEACDSNAALLASGDLRVLQPVFQIYGQCRSFSGPVVTLKVFEDNVLVRELLETRGE 64
             T + CD          + +L    Q +GQ  +F G +VT++ + DN  VR++L   G+
Sbjct: 6   DITPDLCDKY-----ESQVTLLNLPLQNFGQRSAFWGEIVTVRCYHDNSKVRDVLSQNGK 60

Query: 65  GKVLVIDGGGSMRCALVGGNLGQLAHNNGWSGIVVNGCIRDVDEINGCGIGVRALGSHPL 124
           GKVLV+DG GS   AL+G  L  LA  N W G+++ G +RDV  ++   +G++ALG+ P 
Sbjct: 61  GKVLVVDGHGSCHKALMGDQLAILAIKNDWEGVIIYGAVRDVVAMSEMDLGIKALGTSPF 120

Query: 125 KSNKKGHGDKHVPVYIAGVYIAGSFIRDGEWLYADSDGILVSKSELSI 172
           K+ K+G G  +V + +         +  G++LYAD +GIL+S++ L +
Sbjct: 121 KTEKRGAGQVNVTLTMQNQ-----IVEPGDYLYADWNGILMSETALDV 163

>2pcn_A S-adenosylmethionine:2-demethylmenaquinone methyltransferase; beta, beta alpha domain; 1.90A {Geobacillus kaustophilus} Length = 161

 Score =  203 bits (519), Expect = 4e-68
 Identities = 75/166 (45%), Positives = 103/166 (62%), Gaps = 10/166 (6%)

Query: 5   VATAEACDSNAALLASGDLRVLQPVFQIYGQCRSFSGPVVTLKVFEDNVLVRELLETRGE 64
           + TA+ CD         +L+V +  FQ YG  R FSGP+ T+ VFEDNVLVRE LET   
Sbjct: 1   MKTADLCDQF-----LDELQVCELPFQSYGGKRMFSGPIATVDVFEDNVLVREALETVPP 55

Query: 65  GKVLVIDGGGSMRCALVGGNLGQLAHNNGWSGIVVNGCIRDVDEINGCGIGVRALGSHPL 124
           G VLV+DG GS R AL+G  L Q+A   G +G++++GCIRD  EI    IGV A+G+ P+
Sbjct: 56  GTVLVVDGKGSRRVALLGDRLAQIACERGLAGVIIHGCIRDSAEIGAMPIGVMAIGTCPV 115

Query: 125 KSNKKGHGDKHVPVYIAGVYIAGSFIRDGEWLYADSDGILVSKSEL 170
           KS K+G G + V +   GV         G ++YAD+DG++V+  +L
Sbjct: 116 KSKKEGKGARDVVLEFGGV-----RWEPGAYVYADADGVVVANKDL 156

>3c8o_A Regulator of ribonuclease activity A; RRAA, PAO1, RNAse E regulater, hydrolase regulator; HET: PGE PG4; 1.90A {Pseudomonas aeruginosa} Length = 162

 Score =  203 bits (518), Expect = 4e-68
 Identities = 81/168 (48%), Positives = 111/168 (66%), Gaps = 10/168 (5%)

Query: 5   VATAEACDSNAALLASGDLRVLQPVFQIYGQCRSFSGPVVTLKVFEDNVLVRELLETRGE 64
             T + CD+   L+     +V++P+F  +G   SF G +VT+K FEDN LV+E ++  G+
Sbjct: 3   YVTPDLCDAYPELV-----QVVEPMFSNFGGRDSFGGEIVTIKCFEDNSLVKEQVDKDGK 57

Query: 65  GKVLVIDGGGSMRCALVGGNLGQLAHNNGWSGIVVNGCIRDVDEINGCGIGVRALGSHPL 124
           GKVLV+DGGGS+R AL+G  L + A  NGW GIVV GCIRDVD I    +GV+AL SHPL
Sbjct: 58  GKVLVVDGGGSLRRALLGDMLAEKAAKNGWEGIVVYGCIRDVDVIAQTDLGVQALASHPL 117

Query: 125 KSNKKGHGDKHVPVYIAGVYIAGSFIRDGEWLYADSDGILVSKSELSI 172
           K++K+G GD +V V   GV       R GE++YAD++GI+VS   L +
Sbjct: 118 KTDKRGIGDLNVAVTFGGV-----TFRPGEFVYADNNGIIVSPQALKM 160

>1j3l_A Demethylmenaquinone methyltransferase; vitamine K2, structural genomics, riken structural genomics/proteomics initiative, RSGI; 2.30A {Thermus thermophilus} SCOP: c.8.7.1 Length = 164

 Score =  202 bits (516), Expect = 1e-67
 Identities = 69/167 (41%), Positives = 98/167 (58%), Gaps = 11/167 (6%)

Query: 5   VATAEACDSNAALLASGDLRVLQPVFQIYGQCRSFSGPVVTLKVFEDNVLVRELLETRGE 64
             T +  D         +   L  VF+ +G    F+G V TL+VFEDN LVR++LE  G 
Sbjct: 3   ARTTDLSDLY------PEGEALPMVFKSFGGRARFAGRVRTLRVFEDNALVRKVLEEEGA 56

Query: 65  GKVLVIDGGGSMRCALVGGNLGQLAHNNGWSGIVVNGCIRDVDEINGCGIGVRALGSHPL 124
           G+VL +DGGGS+R AL+GGNL + A   GW+G+VV+G +RD +E+    IG+ AL + P 
Sbjct: 57  GQVLFVDGGGSLRTALLGGNLARRAWEKGWAGVVVHGAVRDTEELREVPIGLLALAATPK 116

Query: 125 KSNKKGHGDKHVPVYIAGVYIAGSFIRDGEWLYADSDGILVSKSELS 171
           KS K+G G+  VP+ + GV      +  G +L AD DG+L+     S
Sbjct: 117 KSAKEGKGEVDVPLKVLGV-----EVLPGSFLLADEDGLLLLPEPPS 158

>1nxj_A Probable S-adenosylmethionine:2- demethylmenaquinone methyltransferase; beta/BETA/alpha domain, structural genomics, PSI; HET: TLA; 1.90A {Mycobacterium tuberculosis} SCOP: c.8.7.1 Length = 183

 Score =  198 bits (506), Expect = 6e-66
 Identities = 60/161 (37%), Positives = 93/161 (57%), Gaps = 10/161 (6%)

Query: 5   VATAEACDSNAALLASGDLRVLQPVFQIYGQCRSFSGPVVTLKVFEDNVLVRELLETRGE 64
             TA+  D         D+R     F+ +G    F+GP+ T++ F+DN L++ +L     
Sbjct: 32  RPTADLVDD-----IGPDVRSCDLQFRQFGGRSQFAGPISTVRCFQDNALLKSVLSQPSA 86

Query: 65  GKVLVIDGGGSMRCALVGGNLGQLAHNNGWSGIVVNGCIRDVDEINGCGIGVRALGSHPL 124
           G VLVIDG GS+  ALVG  + +LA + GW+G++V+G +RD   + G  IG++ALG++P 
Sbjct: 87  GGVLVIDGAGSLHTALVGDVIAELARSTGWTGLIVHGAVRDAAALRGIDIGIKALGTNPR 146

Query: 125 KSNKKGHGDKHVPVYIAGVYIAGSFIRDGEWLYADSDGILV 165
           KS K G G++ V + + GV         G+  Y+D DGI+V
Sbjct: 147 KSTKTGAGERDVEITLGGV-----TFVPGDIAYSDDDGIIV 182

>1q5x_A Regulator of RNAse E activity A; 3-layer sandwich, alpha-beta structure, parallel beta sheet, antiparallel beta sheet, hydrolase inhibitor; 2.00A {Escherichia coli} SCOP: c.8.7.1 Length = 161

 Score =  197 bits (502), Expect = 1e-65
 Identities = 67/168 (39%), Positives = 100/168 (59%), Gaps = 10/168 (5%)

Query: 5   VATAEACDSNAALLASGDLRVLQPVFQIYGQCRSFSGPVVTLKVFEDNVLVRELLETRGE 64
             T+E CD         D+ V++P+F  +G   SF G ++T+K FEDN L+ +LLE  G 
Sbjct: 3   YDTSELCDIY-----QEDVNVVEPLFSNFGGRASFGGQIITVKCFEDNGLLYDLLEQNGR 57

Query: 65  GKVLVIDGGGSMRCALVGGNLGQLAHNNGWSGIVVNGCIRDVDEINGCGIGVRALGSHPL 124
           G+VLV+DGGGS+R ALV   L +LA  N W G+V+ G +R VD++    IG++A+ + P+
Sbjct: 58  GRVLVVDGGGSVRRALVDAELARLAVQNEWEGLVIYGAVRQVDDLEELDIGIQAMAAIPV 117

Query: 125 KSNKKGHGDKHVPVYIAGVYIAGSFIRDGEWLYADSDGILVSKSELSI 172
            +  +G G+  V V   GV         G+ LYAD+ GI++S+  L I
Sbjct: 118 GAAGEGIGESDVRVNFGGV-----TFFSGDHLYADNTGIILSEDPLDI 160

>3noj_A 4-carboxy-4-hydroxy-2-oxoadipate aldolase/oxaloac decarboxylase; class II aldolase, A-B-B-A sandwich, metalloprotein, lyase; HET: PG4; 1.82A {Pseudomonas putida} Length = 238

 Score =  125 bits (316), Expect = 1e-36
 Identities = 37/167 (22%), Positives = 62/167 (37%), Gaps = 12/167 (7%)

Query: 5   VATAEACDSNAALLASGDLRVLQPVFQIYGQCRSFSGPVVTLKVFE-DNVLVRELLETRG 63
           +  A   +      A     +L    +   Q  S +G  VT+ V   DN +    +E   
Sbjct: 29  LGVATVHE------AQNRKGLLSSKMRPIQQGTSLAGSAVTVLVAPGDNWMFHVAVEQCR 82

Query: 64  EGKVLVIDGGGSMRCALVGGNLGQLAHNNGWSGIVVNGCIRDVDEINGCGIGVRALGSHP 123
            G VLV+           G  L       G   ++V+  +RD   +   G  V A   + 
Sbjct: 83  PGDVLVVSPSSPCTDGYFGDLLATSLQARGVRALIVDAGVRDTQTLRDMGFAVWARAINA 142

Query: 124 LKSNKKGHGDKHVPVYIAGVYIAGSFIRDGEWLYADSDGILVSKSEL 170
             + K+  G  ++PV   G       I  G+ + AD DG++V + + 
Sbjct: 143 QGTVKETLGSVNLPVICGGQ-----LINPGDIVVADDDGVVVVRRDE 184

>3k4i_A Uncharacterized protein; structural genomics, protein structure INI NEW YORK structural genomix research consortium, nysgxrc; 1.69A {Pseudomonas syringae PV} Length = 244

 Score = 96.7 bits (241), Expect = 2e-25
 Identities = 37/167 (22%), Positives = 61/167 (36%), Gaps = 15/167 (8%)

Query: 5   VATAEACDSNAALLASGDLRVLQPVFQIYGQCRSFSGPVVTLKVF-----EDNVLVRELL 59
           + TA   D   AL + G    L  +       R   G   T++       E        +
Sbjct: 23  LDTASLSD---ALDSLGIDGGLPGIASQVPGTR-CVGIAFTVQYQPVDASEGFRGAANYI 78

Query: 60  ETRGEGKVLVIDGGGSMRCALVGGNLGQLAHNNGWSGIVVNGCIRDVDEINGCGIGVRAL 119
           +    G V+V    G   C + G  +   A  NG  G V++G  RD+D +  C   + + 
Sbjct: 79  DQVPSGSVIVSSNSGRHDCTVWGDIMTHFALANGIKGTVIDGVARDIDTVINCNYPLFSR 138

Query: 120 GSHPLKSNKKGH-GDKHVPVYIAGVYIAGSFIRDGEWLYADSDGILV 165
           G     +  +       VP+ I G+      I+ G+ +  D  G +V
Sbjct: 139 GRFMQSAKNRTQLKAVQVPLVIDGIT-----IQPGDLMVCDGSGCVV 180

>2c5q_A RRAA-like protein YER010C; structural genomics,unknown function, structural genomics, unknown function, pseudo-knot; HET: CME; 1.70A {Saccharomyces cerevisiae} Length = 240

 Score = 86.0 bits (213), Expect = 2e-21
 Identities = 32/171 (18%), Positives = 57/171 (33%), Gaps = 15/171 (8%)

Query: 8   AEACDSNAALLASGDLRVLQPVFQIYGQCRSFSGPVVTLKVF--EDNVLVRELLETRGEG 65
           ++   +   +   G    L  +        S  G   T+     +D       +++    
Sbjct: 16  SDGLLNVYNIPTGGYFPNLTAISPPQNS--SIVGTAYTVLFAPIDDPRPAVNYIDSVPPN 73

Query: 66  KVLVIDGGGSMR----------CALVGGNLGQLAHNNGWSGIVVNGCIRDVDEINGCGIG 115
            +LV+     ++           A+ GG +   A     +G VV G IRDVDE       
Sbjct: 74  SILVLALEPHLQSQFHPFIKITQAMYGGLMSTRAQYLKSNGTVVFGRIRDVDEHRTLNHP 133

Query: 116 VRALGSHPLKSNKKG-HGDKHVPVYIAGVYIAGSFIRDGEWLYADSDGILV 165
           V A G               +V + I         I  G+++  D++GI+ 
Sbjct: 134 VFAYGVGSCAPKAVVKAVGTNVQLKILTSDGVTQTICPGDYIAGDNNGIVR 184

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	172
1q5x_A	161	Regulator of RNAse E activity A; 3-layer sandwich,	100.0
3c8o_A	162	Regulator of ribonuclease activity A; RRAA, PAO1,	100.0
2pcn_A	161	S-adenosylmethionine:2-demethylmenaquinone methylt	100.0
1j3l_A	164	Demethylmenaquinone methyltransferase; vitamine K2	100.0
1vi4_A	174	Regulator of ribonuclease acivity A protein 1; str	100.0
1nxj_A	183	Probable S-adenosylmethionine:2- demethylmenaquino	100.0
3noj_A	238	4-carboxy-4-hydroxy-2-oxoadipate aldolase/oxaloac	100.0
3k4i_A	244	Uncharacterized protein; structural genomics, prot	100.0
2c5q_A	240	RRAA-like protein YER010C; structural genomics,unk	100.0

>1q5x_A Regulator of RNAse E activity A; 3-layer sandwich, alpha-beta structure, parallel beta sheet, antiparallel beta sheet, hydrolase inhibitor; 2.00A {Escherichia coli} SCOP: c.8.7.1

Probab=100.00  E-value=2.3e-53  Score=330.94  Aligned_cols=158  Identities=41%  Similarity=0.752  Sum_probs=149.2

Q ss_pred             CCChhhHhHhhh-ccccCCceecccccceecCCCceEEEEEEEEEeecCcHHHHHHHhhCCCCcEEEEEcCCCCCcceeh
Q 030761            4 VVATAEACDSNA-ALLASGDLRVLQPVFQIYGQCRSFSGPVVTLKVFEDNVLVRELLETRGEGKVLVIDGGGSMRCALVG   82 (172)
Q Consensus         4 ~~~t~~v~Dal~-~~~~~g~~~~l~p~~~~~~~~~~~~G~A~Tv~~~~d~~~~~~~~~~~~~G~VlVid~~g~~~~a~~G   82 (172)
                      +++|++|||+|+ +++      .+.|.++++++..+++|+|+|+|+.+||+.+++++++++||+|||||++++.++|+||
T Consensus         2 ~~~ta~l~Dal~~~~~------~~~~~i~~~~~~~~~~G~A~Tv~~~~dn~~~~~al~~~~~G~VlVvd~~g~~~~a~~G   75 (161)
T 1q5x_A            2 KYDTSELCDIYQEDVN------VVEPLFSNFGGRASFGGQIITVKCFEDNGLLYDLLEQNGRGRVLVVDGGGSVRRALVD   75 (161)
T ss_dssp             CCCHHHHHHHHGGGSE------ECCSCCEECSSCSSEEEEEEEEECSSBCHHHHHHHTSCCTTEEEEEECTTCSSSEEEC
T ss_pred             ccccccHhhhhhhccC------CccCcceECCCCCEEEEEEEEEEEeCCcHHHHHHHhhcCCCCEEEEECCCCCCceeeh
Confidence            589999999998 443      4667788888888999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHCCCcEEEecCccCCHHHHhcCCCcEEEcceecCCCCCCccceeceeEEEeeeccCCeEEccCCEEEEcCCc
Q 030761           83 GNLGQLAHNNGWSGIVVNGCIRDVDEINGCGIGVRALGSHPLKSNKKGHGDKHVPVYIAGVYIAGSFIRDGEWLYADSDG  162 (172)
Q Consensus        83 ~l~a~~a~~~G~~G~VidG~vRD~~~i~~~~~pvfa~g~~p~~~~~~~~~~~~vpV~ig~~~~~gv~V~pGD~v~aD~dG  162 (172)
                      |+|+++|++|||+|+|+||++||++||++++|||||+|++|.++.++.++++|+||+|+     |++|+|||+||||+||
T Consensus        76 ~~la~~a~~~G~~G~VidG~vRD~~~i~~~~~pv~a~g~~p~~~~~~~~g~~nvpV~~g-----Gv~V~PGD~i~aD~dG  150 (161)
T 1q5x_A           76 AELARLAVQNEWEGLVIYGAVRQVDDLEELDIGIQAMAAIPVGAAGEGIGESDVRVNFG-----GVTFFSGDHLYADNTG  150 (161)
T ss_dssp             HHHHHHHHHTTCCEEEEEEEECCHHHHTTSSSEEEEEEECSSBCBCSCCSEESCCEEET-----TEEECTTCEEEECSSC
T ss_pred             HHHHHHHHHCCCeEEEecCccCCHHHHhcCCCcEEEeEeccCCCCcCceeeeCCCEEEC-----CEEECCCCEEEEcCCe
Confidence            99999999999999999999999999999999999999999998888999999999999     9999999999999999


Q ss_pred             eEEecCCcCC
Q 030761          163 ILVSKSELSI  172 (172)
Q Consensus       163 VvviP~~l~~  172 (172)
                      |||||+++++
T Consensus       151 VvviP~~l~~  160 (161)
T 1q5x_A          151 IILSEDPLDI  160 (161)
T ss_dssp             EEEESSCSSC
T ss_pred             EEEEchHHcc
Confidence            9999999874

>3c8o_A Regulator of ribonuclease activity A; RRAA, PAO1, RNAse E regulater, hydrolase regulator; HET: PGE PG4; 1.90A {Pseudomonas aeruginosa}

Probab=100.00  E-value=3.2e-53  Score=330.40  Aligned_cols=158  Identities=50%  Similarity=0.873  Sum_probs=149.5

Q ss_pred             CCChhhHhHhhhccccCCceecccccceecCCCceEEEEEEEEEeecCcHHHHHHHhhCCCCcEEEEEcCCCCCcceehH
Q 030761            4 VVATAEACDSNAALLASGDLRVLQPVFQIYGQCRSFSGPVVTLKVFEDNVLVRELLETRGEGKVLVIDGGGSMRCALVGG   83 (172)
Q Consensus         4 ~~~t~~v~Dal~~~~~~g~~~~l~p~~~~~~~~~~~~G~A~Tv~~~~d~~~~~~~~~~~~~G~VlVid~~g~~~~a~~G~   83 (172)
                      +++|++|||+|..     +++.+.|.++++++.++++|+|+||++.+||+.+++++++.+||+|||||++++.++|+|||
T Consensus         2 ~~~t~~l~Da~~~-----~~~~~~~~~~~~~~~~~~~G~A~Tv~~~~dn~~~~~al~~~~~G~VlVvd~~g~~~~a~~G~   76 (162)
T 3c8o_A            2 HYVTPDLCDAYPE-----LVQVVEPMFSNFGGRDSFGGEIVTIKCFEDNSLVKEQVDKDGKGKVLVVDGGGSLRRALLGD   76 (162)
T ss_dssp             CCCHHHHHHHCTT-----TCEECCSCCEECSSCSCEEEEEEEEECSSCCHHHHHHHTSCCBTEEEEEECTTCSSSBSCCH
T ss_pred             cCChhhHHHhhhc-----ccCccCcccccCCCCCEEEEEEEEEEEeCCchHHHHHHhccCCCCEEEEECCCCCCccchHH
Confidence            5899999999962     23457788999988899999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHCCCcEEEecCccCCHHHHhcCCCcEEEcceecCCCCCCccceeceeEEEeeeccCCeEEccCCEEEEcCCce
Q 030761           84 NLGQLAHNNGWSGIVVNGCIRDVDEINGCGIGVRALGSHPLKSNKKGHGDKHVPVYIAGVYIAGSFIRDGEWLYADSDGI  163 (172)
Q Consensus        84 l~a~~a~~~G~~G~VidG~vRD~~~i~~~~~pvfa~g~~p~~~~~~~~~~~~vpV~ig~~~~~gv~V~pGD~v~aD~dGV  163 (172)
                      +|+++|++|||+|+|+||++||++||++++|||||+|++|.++.++.++++|+||+|+     |++|+|||+||||+|||
T Consensus        77 ~la~~a~~~G~~GiVidG~vRD~~~l~~~~~pv~a~g~~p~~~~~~~~g~~nvpV~~g-----Gv~V~PGD~i~aD~dGV  151 (162)
T 3c8o_A           77 MLAEKAAKNGWEGIVVYGCIRDVDVIAQTDLGVQALASHPLKTDKRGIGDLNVAVTFG-----GVTFRPGEFVYADNNGI  151 (162)
T ss_dssp             HHHHHHHHTTBCEEEEEEEECCHHHHTTSSSEEEEEEECCCBCCCCSCCEESCCEEET-----TEEECTTSEEEECSSCE
T ss_pred             HHHHHHHHCCCeEEEecCCCCCHHHHhcCCCcEEEeecCCCCCcceeeeeeCCCEEEC-----CEEECCCCEEEEcCCeE
Confidence            9999999999999999999999999999999999999999998888899999999999     99999999999999999


Q ss_pred             EEecCCcC
Q 030761          164 LVSKSELS  171 (172)
Q Consensus       164 vviP~~l~  171 (172)
                      ||||++|.
T Consensus       152 vviP~~l~  159 (162)
T 3c8o_A          152 IVSPQALK  159 (162)
T ss_dssp             EEESSCCC
T ss_pred             EEECcccc
Confidence            99999985

>2pcn_A S-adenosylmethionine:2-demethylmenaquinone methyltransferase; beta, beta alpha domain; 1.90A {Geobacillus kaustophilus}

Probab=100.00  E-value=5.1e-53  Score=329.01  Aligned_cols=157  Identities=47%  Similarity=0.796  Sum_probs=149.1

Q ss_pred             CChhhHhHhhhccccCCceecccccceecCCCceEEEEEEEEEeecCcHHHHHHHhhCCCCcEEEEEcCCCCCcceehHH
Q 030761            5 VATAEACDSNAALLASGDLRVLQPVFQIYGQCRSFSGPVVTLKVFEDNVLVRELLETRGEGKVLVIDGGGSMRCALVGGN   84 (172)
Q Consensus         5 ~~t~~v~Dal~~~~~~g~~~~l~p~~~~~~~~~~~~G~A~Tv~~~~d~~~~~~~~~~~~~G~VlVid~~g~~~~a~~G~l   84 (172)
                      ++|++|||+|..     ..+.+.|.|+++++.++++|+|+|+++.+||+.+++++++.+||+|||||+.++.++|+|||+
T Consensus         1 ~~t~dl~Da~~~-----~~~~~~~~~~~~~~~~~~~G~A~Tv~~~~dn~~~~~al~~~~~G~VlVvd~~g~~~~a~~G~~   75 (161)
T 2pcn_A            1 MKTADLCDQFLD-----ELQVCELPFQSYGGKRMFSGPIATVDVFEDNVLVREALETVPPGTVLVVDGKGSRRVALLGDR   75 (161)
T ss_dssp             CCHHHHHHHHGG-----GEEECCSCCEECSSCSCEEEEEEEEECSSBCHHHHHHHHHSCTTCEEEEECTTCCSSEEECHH
T ss_pred             CCHHHHhhcccc-----ccCccCccceeCCCCCEEEEEEEEEEEecCchHHHHHHHhcCCCCEEEEECCCCCCceeehHH
Confidence            589999999973     245677889999888999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHCCCcEEEecCccCCHHHHhcCCCcEEEcceecCCCCCCccceeceeEEEeeeccCCeEEccCCEEEEcCCceE
Q 030761           85 LGQLAHNNGWSGIVVNGCIRDVDEINGCGIGVRALGSHPLKSNKKGHGDKHVPVYIAGVYIAGSFIRDGEWLYADSDGIL  164 (172)
Q Consensus        85 ~a~~a~~~G~~G~VidG~vRD~~~i~~~~~pvfa~g~~p~~~~~~~~~~~~vpV~ig~~~~~gv~V~pGD~v~aD~dGVv  164 (172)
                      |+++|++|||+|+|+||++||++||++++|||||+|++|.++.++.++++|+||+|+     |++|+|||+||||+||||
T Consensus        76 la~~a~~~G~~GiVidG~vRD~~~i~~~~~pv~a~g~~p~~~~~~~~g~~nvpV~~g-----Gv~V~PGD~i~aD~dGVv  150 (161)
T 2pcn_A           76 LAQIACERGLAGVIIHGCIRDSAEIGAMPIGVMAIGTCPVKSKKEGKGARDVVLEFG-----GVRWEPGAYVYADADGVV  150 (161)
T ss_dssp             HHHHHHHTTCCEEEEEEEESCHHHHTTSSSEEEEEEECCSCCBCSCCSEESCCEEET-----TEEECTTCEEEEETTEEE
T ss_pred             HHHHHHHcCCcEEEecccccCHHHHhcCCCcEEEeecCCCCCccceeeeeCCCEEEC-----CEEECCCCEEEECCCeEE
Confidence            999999999999999999999999999999999999999988888899999999999     999999999999999999


Q ss_pred             EecCCcC
Q 030761          165 VSKSELS  171 (172)
Q Consensus       165 viP~~l~  171 (172)
                      |||++|+
T Consensus       151 viP~~l~  157 (161)
T 2pcn_A          151 VANKDLL  157 (161)
T ss_dssp             EESSCTT
T ss_pred             EEChHHh
Confidence            9999986

>1j3l_A Demethylmenaquinone methyltransferase; vitamine K2, structural genomics, riken structural genomics/proteomics initiative, RSGI; 2.30A {Thermus thermophilus} SCOP: c.8.7.1

Probab=100.00  E-value=5.5e-53  Score=329.63  Aligned_cols=157  Identities=43%  Similarity=0.738  Sum_probs=149.6

Q ss_pred             CCChhhHhHhhhccccCCceecccccceecCCCceEEEEEEEEEeecCcHHHHHHHhhCCCCcEEEEEcCCCCCcceehH
Q 030761            4 VVATAEACDSNAALLASGDLRVLQPVFQIYGQCRSFSGPVVTLKVFEDNVLVRELLETRGEGKVLVIDGGGSMRCALVGG   83 (172)
Q Consensus         4 ~~~t~~v~Dal~~~~~~g~~~~l~p~~~~~~~~~~~~G~A~Tv~~~~d~~~~~~~~~~~~~G~VlVid~~g~~~~a~~G~   83 (172)
                      +++|++|||+|++      ++.+.|.++++++.++++|+|+|+++.+||+.+++++++.+||+|||||+.++.++|+|||
T Consensus         2 ~~~t~~v~Da~~~------~~~~~~~~~~~~~~~~~~G~A~Tv~~~~dn~~~~~al~~~~~G~VlVvd~~g~~~~a~~G~   75 (164)
T 1j3l_A            2 EARTTDLSDLYPE------GEALPMVFKSFGGRARFAGRVRTLRVFEDNALVRKVLEEEGAGQVLFVDGGGSLRTALLGG   75 (164)
T ss_dssp             CCCHHHHHHHCTT------SEEECSCSEECSSBSSEEEEEEEEECSSBCHHHHHHHTSCCBTEEEEEECTTCCSSBSCCH
T ss_pred             cCCcccHhhcccc------cCCCCcceeeCCCCCEEEEEEEEEEeeCCchHHHHHHhccCCCcEEEEECCCCCCceeehH
Confidence            5899999999986      3457778888888899999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHCCCcEEEecCccCCHHHHhcCCCcEEEcceecCCCCCCccceeceeEEEeeeccCCeEEccCCEEEEcCCce
Q 030761           84 NLGQLAHNNGWSGIVVNGCIRDVDEINGCGIGVRALGSHPLKSNKKGHGDKHVPVYIAGVYIAGSFIRDGEWLYADSDGI  163 (172)
Q Consensus        84 l~a~~a~~~G~~G~VidG~vRD~~~i~~~~~pvfa~g~~p~~~~~~~~~~~~vpV~ig~~~~~gv~V~pGD~v~aD~dGV  163 (172)
                      +|+++|++|||+|+|+||++||++||++++|||||+|++|.++.++.++++|+||+|+     |++|+|||+||||+|||
T Consensus        76 ~la~~a~~~G~~GiVidG~vRD~~~i~~~~~pV~a~g~~p~~~~~~~~g~~nvpV~~g-----Gv~V~PGD~i~aD~dGV  150 (164)
T 1j3l_A           76 NLARRAWEKGWAGVVVHGAVRDTEELREVPIGLLALAATPKKSAKEGKGEVDVPLKVL-----GVEVLPGSFLLADEDGL  150 (164)
T ss_dssp             HHHHHHHHTTBCEEEEESEECCHHHHTTSSSEEEESEECSSBCBCSCCCEESCCEEET-----TEEECTTCEEEEETTEE
T ss_pred             HHHHHHHHCCCeEEEecCcccCHHHHhcCCCcEEEeecCCCCCccceeeeeCCCEEEC-----CEEECCCCEEEECCCeE
Confidence            9999999999999999999999999999999999999999988888899999999999     99999999999999999


Q ss_pred             EEecCCcC
Q 030761          164 LVSKSELS  171 (172)
Q Consensus       164 vviP~~l~  171 (172)
                      ||||++|.
T Consensus       151 vviP~~l~  158 (164)
T 1j3l_A          151 LLLPEPPS  158 (164)
T ss_dssp             EEESSSCC
T ss_pred             EEEChhhc
Confidence            99999985

>1vi4_A Regulator of ribonuclease acivity A protein 1; structural genomics, unknown function; 1.87A {Vibrio cholerae} SCOP: c.8.7.1

Probab=100.00  E-value=8e-53  Score=331.40  Aligned_cols=159  Identities=37%  Similarity=0.702  Sum_probs=151.3

Q ss_pred             CCCChhhHhHhhhccccCCceecccccceecCCCceEEEEEEEEEeecCcHHHHHHHhhCCCCcEEEEEcCCCCCcceeh
Q 030761            3 GVVATAEACDSNAALLASGDLRVLQPVFQIYGQCRSFSGPVVTLKVFEDNVLVRELLETRGEGKVLVIDGGGSMRCALVG   82 (172)
Q Consensus         3 ~~~~t~~v~Dal~~~~~~g~~~~l~p~~~~~~~~~~~~G~A~Tv~~~~d~~~~~~~~~~~~~G~VlVid~~g~~~~a~~G   82 (172)
                      .+++|++|||+|.+ +    ++.+.|.++++++..+++|+|+|||+.+||+.+++++++.+||+|||||+.++.++|+||
T Consensus         4 ~~~~tadl~D~l~~-~----~~v~~~~~~~~~~~~~~~G~A~Tv~~~~dn~~~~~al~~~~~G~VlVvd~~g~~~~A~~G   78 (174)
T 1vi4_A            4 MRDITPDLCDKYES-Q----VTLLNLPLQNFGQRSAFWGEIVTVRCYHDNSKVRDVLSQNGKGKVLVVDGHGSCHKALMG   78 (174)
T ss_dssp             CCCCHHHHHHHSGG-G----CEECCCCCEECSSCSCEEEEEEEEECSSCCHHHHHHHTSCCTTEEEEEECTTCCSSEEEC
T ss_pred             ccccHHHHHHHhhc-c----cccccccceECCCCCEEEEEEEEEEEeCccHHHHHHHhccCCCEEEEEECCCCCCceehH
Confidence            46899999999987 2    356788899999889999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHCCCcEEEecCccCCHHHHhcCCCcEEEcceecCCCCCCccceeceeEEEeeeccCCeEEccCCEEEEcCCc
Q 030761           83 GNLGQLAHNNGWSGIVVNGCIRDVDEINGCGIGVRALGSHPLKSNKKGHGDKHVPVYIAGVYIAGSFIRDGEWLYADSDG  162 (172)
Q Consensus        83 ~l~a~~a~~~G~~G~VidG~vRD~~~i~~~~~pvfa~g~~p~~~~~~~~~~~~vpV~ig~~~~~gv~V~pGD~v~aD~dG  162 (172)
                      |+|+++|++|||+|+|+||++||++||++++|||||+|++|.++.++.++++|+||+|+     |++|+|||+||||+||
T Consensus        79 ~~la~~a~~~G~aGiVidG~vRD~~~l~~~~~pV~a~g~~p~~~~~~~~g~~nvpV~ig-----Gv~V~PGD~I~aD~dG  153 (174)
T 1vi4_A           79 DQLAILAIKNDWEGVIIYGAVRDVVAMSEMDLGIKALGTSPFKTEKRGAGQVNVTLTMQ-----NQIVEPGDYLYADWNG  153 (174)
T ss_dssp             HHHHHHHHHTTCCEEEEEEEECCHHHHTTSSSEEEEEEECSCCCCCCSCCEESCCEEET-----TEEECTTSEEEEETTE
T ss_pred             HHHHHHHHHCCCeEEEeccccCCHHHHHhCCCCeEEeecCCCCCCCCCcceeCCCEEEC-----CEEECCCCEEEEcCCe
Confidence            99999999999999999999999999999999999999999988887899999999999     9999999999999999


Q ss_pred             eEEecCCcC
Q 030761          163 ILVSKSELS  171 (172)
Q Consensus       163 VvviP~~l~  171 (172)
                      |||||++|+
T Consensus       154 VvviP~~l~  162 (174)
T 1vi4_A          154 ILMSETALD  162 (174)
T ss_dssp             EEEESSCCC
T ss_pred             EEEEChHHc
Confidence            999999986

>1nxj_A Probable S-adenosylmethionine:2- demethylmenaquinone methyltransferase; beta/BETA/alpha domain, structural genomics, PSI; HET: TLA; 1.90A {Mycobacterium tuberculosis} SCOP: c.8.7.1

Probab=100.00  E-value=4.4e-51  Score=323.69  Aligned_cols=156  Identities=38%  Similarity=0.736  Sum_probs=146.7

Q ss_pred             CCCCCChhhHhHhhhccccCCceecccccceecCCCceEEEEEEEEEeecCcHHHHHHHhhCCCCcEEEEEcCCCCCcce
Q 030761            1 MAGVVATAEACDSNAALLASGDLRVLQPVFQIYGQCRSFSGPVVTLKVFEDNVLVRELLETRGEGKVLVIDGGGSMRCAL   80 (172)
Q Consensus         1 ~l~~~~t~~v~Dal~~~~~~g~~~~l~p~~~~~~~~~~~~G~A~Tv~~~~d~~~~~~~~~~~~~G~VlVid~~g~~~~a~   80 (172)
                      .|++++|++|||+|..     +++.+.|.++++++..+++|+|+||++.+||+.+++++++++||+|||||++++.++|+
T Consensus        28 ~L~~~~t~dv~Dal~~-----~~~~~~~~i~~~~~~~~~~G~A~TV~~~~dn~~~~~al~~~~~G~VlVvd~~g~~~~A~  102 (183)
T 1nxj_A           28 AISFRPTADLVDDIGP-----DVRSCDLQFRQFGGRSQFAGPISTVRCFQDNALLKSVLSQPSAGGVLVIDGAGSLHTAL  102 (183)
T ss_dssp             CCCCCCHHHHHHHHCT-----TCEECCCCCEECSSBSCEEEEEEEEECSSBCHHHHHHHHSCCSSCEEEEECTTCCSSEE
T ss_pred             HhcCCCHHHHHhhhhc-----ccCccCcceeECCCCCEEEEEEEEEEEeCCchHHHHHHHhcCCCCEEEEECCCCCCcee
Confidence            3778999999999962     23457778888888899999999999999999999999999999999999999999999


Q ss_pred             ehHHHHHHHHHCCCcEEEecCccCCHHHHhcCCCcEEEcceecCCCCCCccceeceeEEEeeeccCCeEEccCCEEEEcC
Q 030761           81 VGGNLGQLAHNNGWSGIVVNGCIRDVDEINGCGIGVRALGSHPLKSNKKGHGDKHVPVYIAGVYIAGSFIRDGEWLYADS  160 (172)
Q Consensus        81 ~G~l~a~~a~~~G~~G~VidG~vRD~~~i~~~~~pvfa~g~~p~~~~~~~~~~~~vpV~ig~~~~~gv~V~pGD~v~aD~  160 (172)
                      |||+|+++|++|||+|+|+||++||++||++++|||||+|++|.++.++.++++|+||+||     |++|+|||+|+||+
T Consensus       103 ~G~~la~~a~~~G~aGiVidG~vRD~~ei~~l~fPV~a~g~~p~~~~~~~~g~~nvPV~ig-----Gv~V~PGD~I~aD~  177 (183)
T 1nxj_A          103 VGDVIAELARSTGWTGLIVHGAVRDAAALRGIDIGIKALGTNPRKSTKTGAGERDVEITLG-----GVTFVPGDIAYSDD  177 (183)
T ss_dssp             ECHHHHHHHHHHTCCEEEEEEEESCHHHHTTSSSEEEEEEECCSBCBCSCCSEESCCEEET-----TEEECTTSEEEECS
T ss_pred             eHHHHHHHHHHCCCcEEEeccccCCHHHHhcCCCcEEEeeeCCCCCCCCccceeCCCEEEC-----CEEECCCCEEEECC
Confidence            9999999999999999999999999999999999999999999988888899999999999     99999999999999


Q ss_pred             CceEEe
Q 030761          161 DGILVS  166 (172)
Q Consensus       161 dGVvvi  166 (172)
                      ||||||
T Consensus       178 dGVVvI  183 (183)
T 1nxj_A          178 DGIIVV  183 (183)
T ss_dssp             SCEEEC
T ss_pred             CeEEEC
Confidence            999996

>3noj_A 4-carboxy-4-hydroxy-2-oxoadipate aldolase/oxaloac decarboxylase; class II aldolase, A-B-B-A sandwich, metalloprotein, lyase; HET: PG4; 1.82A {Pseudomonas putida}

Probab=100.00  E-value=5.7e-51  Score=334.85  Aligned_cols=160  Identities=23%  Similarity=0.335  Sum_probs=149.0

Q ss_pred             CCCCCChhhHhHhhhccccCCceecccccceecCCCceEEEEEEEEEeec-CcHHHHHHHhhCCCCcEEEEEcCCCCCcc
Q 030761            1 MAGVVATAEACDSNAALLASGDLRVLQPVFQIYGQCRSFSGPVVTLKVFE-DNVLVRELLETRGEGKVLVIDGGGSMRCA   79 (172)
Q Consensus         1 ~l~~~~t~~v~Dal~~~~~~g~~~~l~p~~~~~~~~~~~~G~A~Tv~~~~-d~~~~~~~~~~~~~G~VlVid~~g~~~~a   79 (172)
                      +|++++|++|||+|.++++      +.|.++++.+..+++|+|+||++.+ ||+.+++++++++||+|||||++++.++|
T Consensus        25 ~l~~~~tatv~dal~r~g~------~~~~i~p~~~~~~~~G~A~TV~~~p~dn~~~~~ai~~~~~G~VlVvd~~g~~~~A   98 (238)
T 3noj_A           25 ALGRLGVATVHEAQNRKGL------LSSKMRPIQQGTSLAGSAVTVLVAPGDNWMFHVAVEQCRPGDVLVVSPSSPCTDG   98 (238)
T ss_dssp             HHHHHCHHHHHHHTTSCCB------CCTTCEESSSSCCEEEEEEEEEECTTBCHHHHHHHTTCCTTEEEEEEESSCCCSB
T ss_pred             HhhCCChhHHHHHhhccCC------CchhceECCCCCeEEEEEEEEEEECCCcHHHHHHHHhcCCCCEEEEECCCCCCeE
Confidence            3678999999999987543      4466777877889999999999985 89999999999999999999999999999


Q ss_pred             eehHHHHHHHHHCCCcEEEecCccCCHHHHhcCCCcEEEcceecCCCCCCccceeceeEEEeeeccCCeEEccCCEEEEc
Q 030761           80 LVGGNLGQLAHNNGWSGIVVNGCIRDVDEINGCGIGVRALGSHPLKSNKKGHGDKHVPVYIAGVYIAGSFIRDGEWLYAD  159 (172)
Q Consensus        80 ~~G~l~a~~a~~~G~~G~VidG~vRD~~~i~~~~~pvfa~g~~p~~~~~~~~~~~~vpV~ig~~~~~gv~V~pGD~v~aD  159 (172)
                      +|||+|+++|+++||+|+|+||+|||+++|++++|||||+|++|.++.+..++++|+||+||     |++|+|||+||||
T Consensus        99 ~~G~~la~~a~~~G~aGiVidG~vRD~~~l~~~~fPV~a~g~~p~~~~k~~~g~invPV~ig-----Gv~V~PGD~V~aD  173 (238)
T 3noj_A           99 YFGDLLATSLQARGVRALIVDAGVRDTQTLRDMGFAVWARAINAQGTVKETLGSVNLPVICG-----GQLINPGDIVVAD  173 (238)
T ss_dssp             CCCHHHHHHHHHTTCCEEEEEEEECCHHHHHHHTCEEEEEEECCCCCBCCSCCEESSCEEET-----TEEECTTCEEEEE
T ss_pred             ehHHHHHHHHHHCCCcEEEeecccCCHHHHHhCCCCEEEeecCCCCCCCCCeeeeCCCEEEC-----CEEECCCCEEEEc
Confidence            99999999999999999999999999999999999999999999988777899999999999     9999999999999


Q ss_pred             CCceEEecCCcC
Q 030761          160 SDGILVSKSELS  171 (172)
Q Consensus       160 ~dGVvviP~~l~  171 (172)
                      +|||||||++++
T Consensus       174 ~dGVvviP~~~a  185 (238)
T 3noj_A          174 DDGVVVVRRDEC  185 (238)
T ss_dssp             TTEEEEECGGGH
T ss_pred             CCeEEEEcHHHH
Confidence            999999999864

>3k4i_A Uncharacterized protein; structural genomics, protein structure INI NEW YORK structural genomix research consortium, nysgxrc; 1.69A {Pseudomonas syringae PV}

Probab=100.00  E-value=2.9e-50  Score=331.77  Aligned_cols=162  Identities=23%  Similarity=0.335  Sum_probs=142.5

Q ss_pred             CCCCCChhhHhHhhhccccCCceecccccceecCCCceEEEEEEEEEeec-CcHHHH----HHHhhCCCCcEEEEEcCCC
Q 030761            1 MAGVVATAEACDSNAALLASGDLRVLQPVFQIYGQCRSFSGPVVTLKVFE-DNVLVR----ELLETRGEGKVLVIDGGGS   75 (172)
Q Consensus         1 ~l~~~~t~~v~Dal~~~~~~g~~~~l~p~~~~~~~~~~~~G~A~Tv~~~~-d~~~~~----~~~~~~~~G~VlVid~~g~   75 (172)
                      +|++++|++|||+|+++++.+..    |.++++.+..+++|+|+||++.+ |++..+    +++++++||||||||++++
T Consensus        19 ~l~~~~ta~v~Dal~~~g~~~~~----~~i~p~~~~~~~~G~A~TV~~~p~d~~~~~~~~~~~id~~~~GdVlVvd~~g~   94 (244)
T 3k4i_A           19 ECEHLDTASLSDALDSLGIDGGL----PGIASQVPGTRCVGIAFTVQYQPVDASEGFRGAANYIDQVPSGSVIVSSNSGR   94 (244)
T ss_dssp             HHTTCCHHHHHHHHHHTTCCCBC----TTCEECSTTCCEEEEEEEEEEEEC----------CGGGGCCTTEEEEEECTTC
T ss_pred             HhcCCChHHHHHHHHhcCCcccC----ccceECCCCCeEEEEEEEEEEecCCCchhhhhhHHHHHcCCCCeEEEEECCCC
Confidence            47899999999999998875543    55666677889999999999997 444444    3599999999999999999


Q ss_pred             CCcceehHHHHHHHHHCCCcEEEecCccCCHHHHhcCCCcEEEcceecCCCCC-CccceeceeEEEeeeccCCeEEccCC
Q 030761           76 MRCALVGGNLGQLAHNNGWSGIVVNGCIRDVDEINGCGIGVRALGSHPLKSNK-KGHGDKHVPVYIAGVYIAGSFIRDGE  154 (172)
Q Consensus        76 ~~~a~~G~l~a~~a~~~G~~G~VidG~vRD~~~i~~~~~pvfa~g~~p~~~~~-~~~~~~~vpV~ig~~~~~gv~V~pGD  154 (172)
                      .++|+|||+|+++|+++||+|+||||+|||+++|++++|||||+|++|..+.. ..++++|+||+||     |++|+|||
T Consensus        95 ~~~A~~G~lla~~a~~~G~aGvVidG~vRD~~ei~~~~fPV~a~g~~p~~~~~~~~~g~~nvPV~ig-----Gv~V~PGD  169 (244)
T 3k4i_A           95 HDCTVWGDIMTHFALANGIKGTVIDGVARDIDTVINCNYPLFSRGRFMQSAKNRTQLKAVQVPLVID-----GITIQPGD  169 (244)
T ss_dssp             SSSBSCCHHHHHHHHHHTCCEEEEESBBSCHHHHHHTTCCEEESCBCCCCSTTTEEEEEESSCEEET-----TEEECTTC
T ss_pred             CCeEehHHHHHHHHHHCCCeEEEeCCccCCHHHHHhCCCCEEEeecCCCCCCCccccceecccEEEC-----CEEECCCC
Confidence            99999999999999999999999999999999999999999999999975543 4789999999999     99999999


Q ss_pred             EEEEcCCceEEecCCcC
Q 030761          155 WLYADSDGILVSKSELS  171 (172)
Q Consensus       155 ~v~aD~dGVvviP~~l~  171 (172)
                      +||||+|||||||++++
T Consensus       170 ~V~aD~dGVVviP~~~a  186 (244)
T 3k4i_A          170 LMVCDGSGCVVVPQQLA  186 (244)
T ss_dssp             EEEEETTEEEEECGGGH
T ss_pred             EEEEcCCeEEEEcHHHH
Confidence            99999999999999874

>2c5q_A RRAA-like protein YER010C; structural genomics,unknown function, structural genomics, unknown function, pseudo-knot; HET: CME; 1.70A {Saccharomyces cerevisiae}

Probab=100.00  E-value=3.4e-49  Score=324.76  Aligned_cols=163  Identities=20%  Similarity=0.160  Sum_probs=143.1

Q ss_pred             CCCCCChhhHhHhhhc-cccCCceecccccceec--CCCceEEEEEEEEEeecCcHH--HHHHHhhCCCCcEEEEEcCCC
Q 030761            1 MAGVVATAEACDSNAA-LLASGDLRVLQPVFQIY--GQCRSFSGPVVTLKVFEDNVL--VRELLETRGEGKVLVIDGGGS   75 (172)
Q Consensus         1 ~l~~~~t~~v~Dal~~-~~~~g~~~~l~p~~~~~--~~~~~~~G~A~Tv~~~~d~~~--~~~~~~~~~~G~VlVid~~g~   75 (172)
                      +|++++||+|||+|++ +++..  ..+.|.++++  ++..+++|+|+||++.+++..  .++++++++||+|||||++++
T Consensus         6 ~l~~~~t~~v~Dal~~~~g~~~--~~~~~~~~~~~~g~~~~~~G~A~TV~~~~~~~~~~~~~aid~~~~G~VlVvd~~g~   83 (240)
T 2c5q_A            6 KLQRFSTCDISDGLLNVYNIPT--GGYFPNLTAISPPQNSSIVGTAYTVLFAPIDDPRPAVNYIDSVPPNSILVLALEPH   83 (240)
T ss_dssp             HHTTSCHHHHHHHHHHHHCCTT--TTEECSCEEEECCSSSCEEEEEEEEEEEETTSSSCCCCCGGGCCTTEEEEEEECGG
T ss_pred             HhcCCCHHHHHHHHHHhhCcCc--cccCcceeECccCCCCEEEEEEEEEEEECCCCcHHHHHHHhcCCCCEEEEEECCCC
Confidence            4789999999999998 77631  1223344444  346799999999999975532  457999999999999999888


Q ss_pred             CC----------cceehHHHHHHHHHCCCcEEEecCccCCHHHHhcCCCcEEEcceecCCCCCC-ccceeceeEEEeeec
Q 030761           76 MR----------CALVGGNLGQLAHNNGWSGIVVNGCIRDVDEINGCGIGVRALGSHPLKSNKK-GHGDKHVPVYIAGVY  144 (172)
Q Consensus        76 ~~----------~a~~G~l~a~~a~~~G~~G~VidG~vRD~~~i~~~~~pvfa~g~~p~~~~~~-~~~~~~vpV~ig~~~  144 (172)
                      .+          +|+|||+|+++|++|||+|+|+||+|||+++|++++|||||+|++|..+.+. +++++|+||+|+   
T Consensus        84 ~~~~~~~~~~~~~A~~G~l~a~~a~~~G~aGiVidG~vRD~~el~~l~~PV~a~g~~p~~~~~~~~~g~~nvPV~ig---  160 (240)
T 2c5q_A           84 LQSQFHPFIKITQAMYGGLMSTRAQYLKSNGTVVFGRIRDVDEHRTLNHPVFAYGVGSCAPKAVVKAVGTNVQLKIL---  160 (240)
T ss_dssp             GBCSSTTCBSCCSCSCCHHHHHHHHHTTCCEEEEEEEECCHHHHHHHTCCEEEEEECSSCSTTTEEEEEESCCEEEE---
T ss_pred             cccccccccccceeeehHHHHHHHHHcCCeEEEecCCcCCHHHHhcCCCcEEEeecCCCCCCCcccccccCccEEEC---
Confidence            88          9999999999999999999999999999999999999999999999887776 699999999999   


Q ss_pred             cCC-----eEEccCCEEEEcCCceEEecC--Cc
Q 030761          145 IAG-----SFIRDGEWLYADSDGILVSKS--EL  170 (172)
Q Consensus       145 ~~g-----v~V~pGD~v~aD~dGVvviP~--~l  170 (172)
                        |     ++|+|||+||||+|||||||+  ++
T Consensus       161 --G~~~~~v~V~PGD~I~aD~dGVVviP~~~~~  191 (240)
T 2c5q_A          161 --TSDGVTQTICPGDYIAGDNNGIVRIPVQETD  191 (240)
T ss_dssp             --CTTSCEEEECTTCEEEEETTEEEEECTTTSC
T ss_pred             --CcCcceEEECCCCEEEEcCCcEEEeCCcHHH
Confidence              9     999999999999999999999  65

---

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	172
d1q5xa_	160	c.8.7.1 (A:) Regulator of RNase E activity RraA (M	3e-47
d1vi4a_	162	c.8.7.1 (A:) Hypothetical protein VC2366 {Vibrio c	3e-45
d1nxja_	156	c.8.7.1 (A:) Hypothetical protein Rv3853 {Mycobact	1e-44
d1j3la_	164	c.8.7.1 (A:) Demethylmenaquinone methyltransferase	8e-43

>d1q5xa_ c.8.7.1 (A:) Regulator of RNase E activity RraA (MenG) {Escherichia coli [TaxId: 562]} Length = 160

class: Alpha and beta proteins (a/b)
fold: The "swivelling" beta/beta/alpha domain
superfamily: RraA-like
family: RraA-like
domain: Regulator of RNase E activity RraA (MenG)
species: Escherichia coli [TaxId: 562]

 Score =  149 bits (377), Expect = 3e-47
 Identities = 67/166 (40%), Positives = 100/166 (60%), Gaps = 10/166 (6%)

Query: 7   TAEACDSNAALLASGDLRVLQPVFQIYGQCRSFSGPVVTLKVFEDNVLVRELLETRGEGK 66
           T+E CD         D+ V++P+F  +G   SF G ++T+K FEDN L+ +LLE  G G+
Sbjct: 4   TSELCDIY-----QEDVNVVEPLFSNFGGRASFGGQIITVKCFEDNGLLYDLLEQNGRGR 58

Query: 67  VLVIDGGGSMRCALVGGNLGQLAHNNGWSGIVVNGCIRDVDEINGCGIGVRALGSHPLKS 126
           VLV+DGGGS+R ALV   L +LA  N W G+V+ G +R VD++    IG++A+ + P+ +
Sbjct: 59  VLVVDGGGSVRRALVDAELARLAVQNEWEGLVIYGAVRQVDDLEELDIGIQAMAAIPVGA 118

Query: 127 NKKGHGDKHVPVYIAGVYIAGSFIRDGEWLYADSDGILVSKSELSI 172
             +G G+  V V   GV         G+ LYAD+ GI++S+  L I
Sbjct: 119 AGEGIGESDVRVNFGGVT-----FFSGDHLYADNTGIILSEDPLDI 159

>d1vi4a_ c.8.7.1 (A:) Hypothetical protein VC2366 {Vibrio cholerae [TaxId: 666]} Length = 162

class: Alpha and beta proteins (a/b)
fold: The "swivelling" beta/beta/alpha domain
superfamily: RraA-like
family: RraA-like
domain: Hypothetical protein VC2366
species: Vibrio cholerae [TaxId: 666]

 Score =  144 bits (364), Expect = 3e-45
 Identities = 59/166 (35%), Positives = 96/166 (57%), Gaps = 10/166 (6%)

Query: 7   TAEACDSNAALLASGDLRVLQPVFQIYGQCRSFSGPVVTLKVFEDNVLVRELLETRGEGK 66
           T + CD          + +L    Q +GQ  +F G +VT++ + DN  VR++L   G+GK
Sbjct: 5   TPDLCDKY-----ESQVTLLNLPLQNFGQRSAFWGEIVTVRCYHDNSKVRDVLSQNGKGK 59

Query: 67  VLVIDGGGSMRCALVGGNLGQLAHNNGWSGIVVNGCIRDVDEINGCGIGVRALGSHPLKS 126
           VLV+DG GS   AL+G  L  LA  N W G+++ G +RDV  ++   +G++ALG+ P K+
Sbjct: 60  VLVVDGHGSCHKALMGDQLAILAIKNDWEGVIIYGAVRDVVAMSEMDLGIKALGTSPFKT 119

Query: 127 NKKGHGDKHVPVYIAGVYIAGSFIRDGEWLYADSDGILVSKSELSI 172
            K+G G  +V + +         +  G++LYAD +GIL+S++ L +
Sbjct: 120 EKRGAGQVNVTLTMQNQI-----VEPGDYLYADWNGILMSETALDV 160

>d1nxja_ c.8.7.1 (A:) Hypothetical protein Rv3853 {Mycobacterium tuberculosis [TaxId: 1773]} Length = 156

class: Alpha and beta proteins (a/b)
fold: The "swivelling" beta/beta/alpha domain
superfamily: RraA-like
family: RraA-like
domain: Hypothetical protein Rv3853
species: Mycobacterium tuberculosis [TaxId: 1773]

 Score =  142 bits (359), Expect = 1e-44
 Identities = 60/160 (37%), Positives = 93/160 (58%), Gaps = 10/160 (6%)

Query: 6   ATAEACDSNAALLASGDLRVLQPVFQIYGQCRSFSGPVVTLKVFEDNVLVRELLETRGEG 65
            TA+  D         D+R     F+ +G    F+GP+ T++ F+DN L++ +L     G
Sbjct: 6   PTADLVDDI-----GPDVRSCDLQFRQFGGRSQFAGPISTVRCFQDNALLKSVLSQPSAG 60

Query: 66  KVLVIDGGGSMRCALVGGNLGQLAHNNGWSGIVVNGCIRDVDEINGCGIGVRALGSHPLK 125
            VLVIDG GS+  ALVG  + +LA + GW+G++V+G +RD   + G  IG++ALG++P K
Sbjct: 61  GVLVIDGAGSLHTALVGDVIAELARSTGWTGLIVHGAVRDAAALRGIDIGIKALGTNPRK 120

Query: 126 SNKKGHGDKHVPVYIAGVYIAGSFIRDGEWLYADSDGILV 165
           S K G G++ V + + GV         G+  Y+D DGI+V
Sbjct: 121 STKTGAGERDVEITLGGVT-----FVPGDIAYSDDDGIIV 155

>d1j3la_ c.8.7.1 (A:) Demethylmenaquinone methyltransferase {Thermus thermophilus [TaxId: 274]} Length = 164

class: Alpha and beta proteins (a/b)
fold: The "swivelling" beta/beta/alpha domain
superfamily: RraA-like
family: RraA-like
domain: Demethylmenaquinone methyltransferase
species: Thermus thermophilus [TaxId: 274]

 Score =  138 bits (348), Expect = 8e-43
 Identities = 69/167 (41%), Positives = 98/167 (58%), Gaps = 11/167 (6%)

Query: 5   VATAEACDSNAALLASGDLRVLQPVFQIYGQCRSFSGPVVTLKVFEDNVLVRELLETRGE 64
             T +  D         +   L  VF+ +G    F+G V TL+VFEDN LVR++LE  G 
Sbjct: 3   ARTTDLSDLY------PEGEALPMVFKSFGGRARFAGRVRTLRVFEDNALVRKVLEEEGA 56

Query: 65  GKVLVIDGGGSMRCALVGGNLGQLAHNNGWSGIVVNGCIRDVDEINGCGIGVRALGSHPL 124
           G+VL +DGGGS+R AL+GGNL + A   GW+G+VV+G +RD +E+    IG+ AL + P 
Sbjct: 57  GQVLFVDGGGSLRTALLGGNLARRAWEKGWAGVVVHGAVRDTEELREVPIGLLALAATPK 116

Query: 125 KSNKKGHGDKHVPVYIAGVYIAGSFIRDGEWLYADSDGILVSKSELS 171
           KS K+G G+  VP+ + GV      +  G +L AD DG+L+     S
Sbjct: 117 KSAKEGKGEVDVPLKVLGVE-----VLPGSFLLADEDGLLLLPEPPS 158

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	172
d1q5xa_	160	Regulator of RNase E activity RraA (MenG) {Escheri	100.0
d1vi4a_	162	Hypothetical protein VC2366 {Vibrio cholerae [TaxI	100.0
d1j3la_	164	Demethylmenaquinone methyltransferase {Thermus the	100.0
d1nxja_	156	Hypothetical protein Rv3853 {Mycobacterium tubercu	100.0

>d1q5xa_ c.8.7.1 (A:) Regulator of RNase E activity RraA (MenG) {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: The "swivelling" beta/beta/alpha domain
superfamily: RraA-like
family: RraA-like
domain: Regulator of RNase E activity RraA (MenG)
species: Escherichia coli [TaxId: 562]

Probab=100.00  E-value=5.3e-53  Score=326.76  Aligned_cols=159  Identities=42%  Similarity=0.765  Sum_probs=152.1

Q ss_pred             CCChhhHhHhhhccccCCceecccccceecCCCceEEEEEEEEEeecCcHHHHHHHhhCCCCcEEEEEcCCCCCcceehH
Q 030761            4 VVATAEACDSNAALLASGDLRVLQPVFQIYGQCRSFSGPVVTLKVFEDNVLVRELLETRGEGKVLVIDGGGSMRCALVGG   83 (172)
Q Consensus         4 ~~~t~~v~Dal~~~~~~g~~~~l~p~~~~~~~~~~~~G~A~Tv~~~~d~~~~~~~~~~~~~G~VlVid~~g~~~~a~~G~   83 (172)
                      +++|++|||+|..     .++.+.|.|++|++..+|+|+|+|+++.+||..+++++++++||+|||+|+.++.++|+|||
T Consensus         1 kf~T~dicD~~~~-----~~~~~~p~~~~~g~~~~~~G~a~Tv~~~~d~~~~~~al~~~~~G~VlVid~~g~~~~A~~G~   75 (160)
T d1q5xa_           1 KYDTSELCDIYQE-----DVNVVEPLFSNFGGRASFGGQIITVKCFEDNGLLYDLLEQNGRGRVLVVDGGGSVRRALVDA   75 (160)
T ss_dssp             CCCHHHHHHHHGG-----GSEECCSCCEECSSCSSEEEEEEEEECSSBCHHHHHHHTSCCTTEEEEEECTTCSSSEEECH
T ss_pred             Ccchhhhhhcccc-----cceEeChhhhccCCCCEEEEEEEEEEEeCcHHHHHHHHhccCCCcEEEEECCCCccccchHH
Confidence            6899999999864     46789999999999999999999999999999999999999999999999999899999999


Q ss_pred             HHHHHHHHCCCcEEEecCccCCHHHHhcCCCcEEEcceecCCCCCCccceeceeEEEeeeccCCeEEccCCEEEEcCCce
Q 030761           84 NLGQLAHNNGWSGIVVNGCIRDVDEINGCGIGVRALGSHPLKSNKKGHGDKHVPVYIAGVYIAGSFIRDGEWLYADSDGI  163 (172)
Q Consensus        84 l~a~~a~~~G~~G~VidG~vRD~~~i~~~~~pvfa~g~~p~~~~~~~~~~~~vpV~ig~~~~~gv~V~pGD~v~aD~dGV  163 (172)
                      +++++|+++||+|+|+||++||+++|++++||+||+|++|.++.+..++++|+||+||     |++|+|||+||||+|||
T Consensus        76 ~~a~~a~~~G~~G~VidG~vRD~~~i~~~~~pv~a~g~~p~~~~~~~~~~~nvpi~ig-----Gv~V~pGD~I~aD~dGv  150 (160)
T d1q5xa_          76 ELARLAVQNEWEGLVIYGAVRQVDDLEELDIGIQAMAAIPVGAAGEGIGESDVRVNFG-----GVTFFSGDHLYADNTGI  150 (160)
T ss_dssp             HHHHHHHHTTCCEEEEEEEECCHHHHTTSSSEEEEEEECSSBCBCSCCSEESCCEEET-----TEEECTTCEEEECSSCE
T ss_pred             HHHHHHHHcCcCEEeCccccCCHHHHhhCCCCeeeeeeeecCCccccccEECCeEEEC-----CEEECCCCEEEEeCCcE
Confidence            9999999999999999999999999999999999999999988777889999999999     99999999999999999


Q ss_pred             EEecCCcCC
Q 030761          164 LVSKSELSI  172 (172)
Q Consensus       164 vviP~~l~~  172 (172)
                      ||||+||.|
T Consensus       151 vVip~~l~~  159 (160)
T d1q5xa_         151 ILSEDPLDI  159 (160)
T ss_dssp             EEESSCSSC
T ss_pred             EEEchhcCC
Confidence            999999975

>d1vi4a_ c.8.7.1 (A:) Hypothetical protein VC2366 {Vibrio cholerae [TaxId: 666]}

class: Alpha and beta proteins (a/b)
fold: The "swivelling" beta/beta/alpha domain
superfamily: RraA-like
family: RraA-like
domain: Hypothetical protein VC2366
species: Vibrio cholerae [TaxId: 666]

Probab=100.00  E-value=3.5e-52  Score=322.68  Aligned_cols=159  Identities=37%  Similarity=0.721  Sum_probs=151.6

Q ss_pred             CCChhhHhHhhhccccCCceecccccceecCCCceEEEEEEEEEeecCcHHHHHHHhhCCCCcEEEEEcCCCCCcceehH
Q 030761            4 VVATAEACDSNAALLASGDLRVLQPVFQIYGQCRSFSGPVVTLKVFEDNVLVRELLETRGEGKVLVIDGGGSMRCALVGG   83 (172)
Q Consensus         4 ~~~t~~v~Dal~~~~~~g~~~~l~p~~~~~~~~~~~~G~A~Tv~~~~d~~~~~~~~~~~~~G~VlVid~~g~~~~a~~G~   83 (172)
                      ++.|++|||++..     .++.+.|.|++|++..+|+|+|+||++.+||+.++++|++.+||+|||||+.++.++|+|||
T Consensus         2 ~~~TpdlcD~~~~-----~i~~l~~~~~~~g~~~~~~G~a~Tv~~~~d~~~~~~~i~~~~~G~VlVid~~g~~~~a~~G~   76 (162)
T d1vi4a_           2 RDITPDLCDKYES-----QVTLLNLPLQNFGQRSAFWGEIVTVRCYHDNSKVRDVLSQNGKGKVLVVDGHGSCHKALMGD   76 (162)
T ss_dssp             CCCHHHHHHHSGG-----GCEECCCCCEECSSCSCEEEEEEEEECSSCCHHHHHHHTSCCTTEEEEEECTTCCSSEEECH
T ss_pred             CCCCchhhhcccc-----hhcCcChhhhCCCCCCEEEEEEEEEEEcCchHHHHHHHhcCCCCCEEEEECCCCccceehHH
Confidence            5689999999865     46789999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHCCCcEEEecCccCCHHHHhcCCCcEEEcceecCCCCCCccceeceeEEEeeeccCCeEEccCCEEEEcCCce
Q 030761           84 NLGQLAHNNGWSGIVVNGCIRDVDEINGCGIGVRALGSHPLKSNKKGHGDKHVPVYIAGVYIAGSFIRDGEWLYADSDGI  163 (172)
Q Consensus        84 l~a~~a~~~G~~G~VidG~vRD~~~i~~~~~pvfa~g~~p~~~~~~~~~~~~vpV~ig~~~~~gv~V~pGD~v~aD~dGV  163 (172)
                      +++++|+++||+|+|+||++||+++|++++|||||+|++|.++.+...+++|+||+|+     |++|+||||||||.|||
T Consensus        77 ~~a~~a~~~G~~G~VidG~vRD~~~i~~~~~pv~a~g~~p~~~~~~~~~~~n~pv~ig-----gv~V~PGD~i~aD~dGv  151 (162)
T d1vi4a_          77 QLAILAIKNDWEGVIIYGAVRDVVAMSEMDLGIKALGTSPFKTEKRGAGQVNVTLTMQ-----NQIVEPGDYLYADWNGI  151 (162)
T ss_dssp             HHHHHHHHTTCCEEEEEEEECCHHHHTTSSSEEEEEEECSCCCCCCSCCEESCCEEET-----TEEECTTSEEEEETTEE
T ss_pred             HHHHHHHHhCCCEEecccccCCHHHHhhCCCCeeeecccccCCcccccceeCCeEEEC-----CEEECCCCEEEEeCCcE
Confidence            9999999999999999999999999999999999999999988887889999999999     99999999999999999


Q ss_pred             EEecCCcCC
Q 030761          164 LVSKSELSI  172 (172)
Q Consensus       164 vviP~~l~~  172 (172)
                      ||||++|.+
T Consensus       152 vvip~~Le~  160 (162)
T d1vi4a_         152 LMSETALDV  160 (162)
T ss_dssp             EEESSCCCC
T ss_pred             EEECccccc
Confidence            999998764

>d1j3la_ c.8.7.1 (A:) Demethylmenaquinone methyltransferase {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: The "swivelling" beta/beta/alpha domain
superfamily: RraA-like
family: RraA-like
domain: Demethylmenaquinone methyltransferase
species: Thermus thermophilus [TaxId: 274]

Probab=100.00  E-value=3.1e-52  Score=323.41  Aligned_cols=157  Identities=43%  Similarity=0.738  Sum_probs=150.1

Q ss_pred             CCChhhHhHhhhccccCCceecccccceecCCCceEEEEEEEEEeecCcHHHHHHHhhCCCCcEEEEEcCCCCCcceehH
Q 030761            4 VVATAEACDSNAALLASGDLRVLQPVFQIYGQCRSFSGPVVTLKVFEDNVLVRELLETRGEGKVLVIDGGGSMRCALVGG   83 (172)
Q Consensus         4 ~~~t~~v~Dal~~~~~~g~~~~l~p~~~~~~~~~~~~G~A~Tv~~~~d~~~~~~~~~~~~~G~VlVid~~g~~~~a~~G~   83 (172)
                      .++|++|||++++      .+.|.|.|++|++..+|+|+|+||++.+||+.++++|++.+||+|||||++++.++|+|||
T Consensus         2 ~~~T~dl~D~~~~------~~~l~~~~~~~g~~~~~~G~a~Tv~~~~Dn~~v~~~l~~~~~G~VlVid~~g~~~~A~~Gd   75 (164)
T d1j3la_           2 EARTTDLSDLYPE------GEALPMVFKSFGGRARFAGRVRTLRVFEDNALVRKVLEEEGAGQVLFVDGGGSLRTALLGG   75 (164)
T ss_dssp             CCCHHHHHHHCTT------SEEECSCSEECSSBSSEEEEEEEEECSSBCHHHHHHHTSCCBTEEEEEECTTCCSSBSCCH
T ss_pred             CcCcchHhhcCCC------cCccchhhhccCCCceEEeeeEEEEEcCCcHHHHHHHHhCCCCCEEEEECCCCchhhhhhH
Confidence            5789999999975      3568889999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHCCCcEEEecCccCCHHHHhcCCCcEEEcceecCCCCCCccceeceeEEEeeeccCCeEEccCCEEEEcCCce
Q 030761           84 NLGQLAHNNGWSGIVVNGCIRDVDEINGCGIGVRALGSHPLKSNKKGHGDKHVPVYIAGVYIAGSFIRDGEWLYADSDGI  163 (172)
Q Consensus        84 l~a~~a~~~G~~G~VidG~vRD~~~i~~~~~pvfa~g~~p~~~~~~~~~~~~vpV~ig~~~~~gv~V~pGD~v~aD~dGV  163 (172)
                      +++++|+++||+|+|+||++||+++|++++|||||+|++|.++.++..+++|+||+|+     |++|+||||||||+|||
T Consensus        76 ~~a~~a~~~G~~G~VidG~vRD~~~i~~~~~pv~a~g~~p~~~~~~~~~~~n~pi~ig-----gv~I~PGD~i~aD~dGV  150 (164)
T d1j3la_          76 NLARRAWEKGWAGVVVHGAVRDTEELREVPIGLLALAATPKKSAKEGKGEVDVPLKVL-----GVEVLPGSFLLADEDGL  150 (164)
T ss_dssp             HHHHHHHHTTBCEEEEESEECCHHHHTTSSSEEEESEECSSBCBCSCCCEESCCEEET-----TEEECTTCEEEEETTEE
T ss_pred             HHHHHHHHhCCCEEeCccccCCHHHHhhCCCCceeEeeeccCCcccccceECCcEEEC-----CEEEcCCCEEEEcCCcE
Confidence            9999999999999999999999999999999999999999988887789999999999     99999999999999999


Q ss_pred             EEecCCcC
Q 030761          164 LVSKSELS  171 (172)
Q Consensus       164 vviP~~l~  171 (172)
                      ||||++++
T Consensus       151 vviP~~~~  158 (164)
T d1j3la_         151 LLLPEPPS  158 (164)
T ss_dssp             EEESSSCC
T ss_pred             EEEccccc
Confidence            99999875

>d1nxja_ c.8.7.1 (A:) Hypothetical protein Rv3853 {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: The "swivelling" beta/beta/alpha domain
superfamily: RraA-like
family: RraA-like
domain: Hypothetical protein Rv3853
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=100.00  E-value=5.3e-50  Score=308.65  Aligned_cols=155  Identities=38%  Similarity=0.743  Sum_probs=147.4

Q ss_pred             CCCCChhhHhHhhhccccCCceecccccceecCCCceEEEEEEEEEeecCcHHHHHHHhhCCCCcEEEEEcCCCCCccee
Q 030761            2 AGVVATAEACDSNAALLASGDLRVLQPVFQIYGQCRSFSGPVVTLKVFEDNVLVRELLETRGEGKVLVIDGGGSMRCALV   81 (172)
Q Consensus         2 l~~~~t~~v~Dal~~~~~~g~~~~l~p~~~~~~~~~~~~G~A~Tv~~~~d~~~~~~~~~~~~~G~VlVid~~g~~~~a~~   81 (172)
                      ++-.+|++|||+|..     .++.+.|.|++|++..+|+|+|+||++.+||..+++++++.+||+|||||+.++.++|+|
T Consensus         2 ~~~~pTadl~D~~~~-----~~~~~~~~~~~~g~~~~~~G~a~TV~~~~dn~~v~~~l~~~~~G~VlVid~~g~~~~a~~   76 (156)
T d1nxja_           2 ISFRPTADLVDDIGP-----DVRSCDLQFRQFGGRSQFAGPISTVRCFQDNALLKSVLSQPSAGGVLVIDGAGSLHTALV   76 (156)
T ss_dssp             CCCCCHHHHHHHHCT-----TCEECCCCCEECSSBSCEEEEEEEEECSSBCHHHHHHHHSCCSSCEEEEECTTCCSSEEE
T ss_pred             CcccchHHHhhcccc-----hheEecccccCCCCCcEEEEEEEEEEEeCChHHHHHHHhccCCCcEEEEECCCCccceee
Confidence            455789999999964     467889999999999999999999999999999999999999999999999999999999


Q ss_pred             hHHHHHHHHHCCCcEEEecCccCCHHHHhcCCCcEEEcceecCCCCCCccceeceeEEEeeeccCCeEEccCCEEEEcCC
Q 030761           82 GGNLGQLAHNNGWSGIVVNGCIRDVDEINGCGIGVRALGSHPLKSNKKGHGDKHVPVYIAGVYIAGSFIRDGEWLYADSD  161 (172)
Q Consensus        82 G~l~a~~a~~~G~~G~VidG~vRD~~~i~~~~~pvfa~g~~p~~~~~~~~~~~~vpV~ig~~~~~gv~V~pGD~v~aD~d  161 (172)
                      ||+++++|++|||+|+|+||++||+++|++++||+||+|++|.++.+...+++|+||+|+     |++|+||||||||.|
T Consensus        77 G~~~a~~a~~~G~~GiVidG~vRD~~~i~~~~~pv~a~g~~p~~~~~~~~~~~n~pv~ig-----gv~V~pGD~I~aD~d  151 (156)
T d1nxja_          77 GDVIAELARSTGWTGLIVHGAVRDAAALRGIDIGIKALGTNPRKSTKTGAGERDVEITLG-----GVTFVPGDIAYSDDD  151 (156)
T ss_dssp             CHHHHHHHHHHTCCEEEEEEEESCHHHHTTSSSEEEEEEECCSBCBCSCCSEESCCEEET-----TEEECTTSEEEECSS
T ss_pred             chHHHHHHHHcCCCEEECcccccCHHHHhcCCceEEEeecccCCCcccccceECCeEEEC-----CEEECCCCEEEEcCC
Confidence            999999999999999999999999999999999999999999988888889999999999     999999999999999


Q ss_pred             ceEEe
Q 030761          162 GILVS  166 (172)
Q Consensus       162 GVvvi  166 (172)
                      |||||
T Consensus       152 GvvvI  156 (156)
T d1nxja_         152 GIIVV  156 (156)
T ss_dssp             CEEEC
T ss_pred             eEEEC
Confidence            99996