Citrus Sinensis ID: 031066

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160------
Protein Sequence
MALVTTAEVCDANPQLIVSGELRALQPIFQIYGRRQVFSGPIVTLKVFEDNVLIREFLEEKGNGRVLVVDGGGSLRCAILGGNPVVQAQNNGWAGIVVNGCIRDVDEINGCDIGVRALASHPMKANKKGIGEKHVPITIGGTRISDGEWLYADTDGILISRAELSV
Secondary Structure (PSIPRED)
cccccccccccccccccccccEEEcccccccccccEEEEEEEEEEEEcccHHHHHHHHHccccccEEEEEcccccccccccHHHHHHHHHcccEEEEEEcccccHHHHccccccEEEEEEccccccccccccccccEEEccEEEccccEEEEccccEEEEcccccc
Secondary Structure Prediction (SSPRO)
ccccccHHHHHccHHHHHHHHcEEcccccEEccccccEEEEEEEEEcccEcHHHHHHHccccccEEEEEEcccccccEEEcHHHHHHHHHccccEEEEEEEEccHHHHcccccEEEEEEEcccEcEcccccEEcccEEEccEEEccccEEEEccccEEEEcccccc
Coil and Loop (DISEMBL)
MALVTTAevcdanpqlivsgelralqpifqiygrrqvfsgpivtlKVFEDNVLIREFLEekgngrvlvvdgggslrcailggnpvvqaqnngwagIVVNGcirdvdeingcdigvralashpmkankkgigekhvpitiggtrisdgewlyadtdgiliSRAELSV
Flexible Loop (DISEMBL)
malvttaevcdanpqlivsgELRALQPIFQIYGRRQVFSGPIVTLKVFEDNVLIREFleekgngrvLVVDGGGSLRCAILGGNPVVQAQNNGWAGIVVNGCIRDVDEINGCDIGVRALAShpmkankkgigekhvpitiggtrisdgewlyaDTDGILISRAELSV
Low Complexity Region (SEG)
MALVTTAEVCDANPQLIVSGELRALQPIFQIYGRRQVFSGPIVTLKVFEDNVLIREFLEEKGNGRVLVVDGGGSLRCAILGGNPVVQAQNNGWAGIVVNGCIRDVDEINGCDIGVRALASHPMKANKKGIGEKHVPITIGGTRISDGEWLYADTDGILISRAELSV
Disordered region (IsUnstruct)
****TTAEVCDANPQLIVSGELRALQPIFQIYGRRQVFSGPIVTLKVFEDNVLIREFLEEKGNGRVLVVDGGGSLRCAILGGNPVVQAQNNGWAGIVVNGCIRDVDEINGCDIGVRALASHPMKANKKGIGEKHVPITIGGTRISDGEWLYADTDGILIS******
Disordered Region (DISOPRED)
*ALVTTAEVCDANPQLIVSGELRALQPIFQIYGRRQVFSGPIVTLKVFEDNVLIREFLEEKGNGRVLVVDGGGSLRCAILGGNPVVQAQNNGWAGIVVNGCIRDVDEINGCDIGVRALASHPMKANKKGIGEKHVPITIGGTRISDGEWLYADTDGILISRAELSV
Disordered Region (DISEMBL)
MALVTTAEVCDANPQLIVSGELRALQPIFQIYGRRQVFSGPIVTLKVFEDNVLIREFLEEKGNGRVLVVDGGGSLRCAILGGNPVVQAQNNGWAGIVVNGCIRDVDEINGCDIGVRALASHPMKANKKGIGEKHVPITIGGTRISDGEWLYADTDGILISRAELSV
Disordered Region (DISPRO)
**LVTTAEVCDANPQLIVSGELRALQPIFQIYGRRQVFSGPIVTLKVFEDNVLIREFLEEKGNGRVLVVDGGGSLRCAILGGNPVVQAQNNGWAGIVVNGCIRDVDEINGCDIGVRALASHPMKANKKGIGEKHVPITIGGTRISDGEWLYADTDGILISRA****
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MALVTTAEVCDANPQLIVSGELRALQPIFQIYGRRQVFSGPIVTLKVFEDNVLIREFLEEKGNGRVLVVDGGGSLRCAILGGNPVVQAQNNGWAGIVVNGCIRDVDEINGCDIGVRALASHPMKANKKGIGEKHVPITIGGTRISDGEWLYADTDGILISRAELSV
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	166	2.2.26 [Sep-21-2011]
Q9FFE0	166	Regulator of ribonuclease	yes	no	1.0	1.0	0.855	9e-80
Q9M8R9	166	Regulator of ribonuclease	yes	no	1.0	1.0	0.843	4e-79
Q9FH13	166	Regulator of ribonuclease	no	no	1.0	1.0	0.716	8e-66
A9AHQ6	164	Putative regulator of rib	yes	no	0.963	0.975	0.562	6e-50
Q46ZV6	165	Putative regulator of rib	yes	no	0.957	0.963	0.534	3e-49
Q2SX33	165	Putative regulator of rib	yes	no	0.975	0.981	0.543	2e-48
Q63SX7	165	Putative regulator of rib	yes	no	0.951	0.957	0.544	1e-47
A3NAY8	165	Putative regulator of rib	yes	no	0.951	0.957	0.544	1e-47
Q3JQZ3	165	Putative regulator of rib	yes	no	0.951	0.957	0.544	1e-47
A3NWR9	165	Putative regulator of rib	yes	no	0.951	0.957	0.544	1e-47

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

 Score =  295 bits (755), Expect = 9e-80,   Method: Compositional matrix adjust.
 Identities = 142/166 (85%), Positives = 156/166 (93%)

Query: 1   MALVTTAEVCDANPQLIVSGELRALQPIFQIYGRRQVFSGPIVTLKVFEDNVLIREFLEE 60
           MA VTTAEVCDAN +LI SG+LRALQPIFQIYGRRQ+FSGP+VT+KVFEDN LIR+F+EE
Sbjct: 1   MAFVTTAEVCDANQELIRSGQLRALQPIFQIYGRRQIFSGPVVTVKVFEDNGLIRQFIEE 60

Query: 61  KGNGRVLVVDGGGSLRCAILGGNPVVQAQNNGWAGIVVNGCIRDVDEINGCDIGVRALAS 120
           KGNGRVLVVDGGGS RCAILGGNPVVQAQNNGWAGIVVNGCIRDVDEINGCDIGVRALAS
Sbjct: 61  KGNGRVLVVDGGGSQRCAILGGNPVVQAQNNGWAGIVVNGCIRDVDEINGCDIGVRALAS 120

Query: 121 HPMKANKKGIGEKHVPITIGGTRISDGEWLYADTDGILISRAELSV 166
           HP+KA+KKG+GE+ VP+ I GTRI DGEWLYADTDGIL+S+ ELSV
Sbjct: 121 HPIKASKKGLGEQRVPVNIAGTRICDGEWLYADTDGILVSQIELSV 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 =  293 bits (750), Expect = 4e-79,   Method: Compositional matrix adjust.
 Identities = 140/166 (84%), Positives = 155/166 (93%)

Query: 1   MALVTTAEVCDANPQLIVSGELRALQPIFQIYGRRQVFSGPIVTLKVFEDNVLIREFLEE 60
           MA VTTAEVCDAN ++I SG+LRALQP+FQIYGRRQ+FSGP+VT+KVFEDN LIR FLEE
Sbjct: 1   MAFVTTAEVCDANQEMIRSGQLRALQPVFQIYGRRQIFSGPVVTVKVFEDNGLIRHFLEE 60

Query: 61  KGNGRVLVVDGGGSLRCAILGGNPVVQAQNNGWAGIVVNGCIRDVDEINGCDIGVRALAS 120
           KGNGRVLVVDGGGSLRCAILGGNPVVQAQNNGWAGI+VNGCIRDVDEINGCDIGVRALAS
Sbjct: 61  KGNGRVLVVDGGGSLRCAILGGNPVVQAQNNGWAGIIVNGCIRDVDEINGCDIGVRALAS 120

Query: 121 HPMKANKKGIGEKHVPITIGGTRISDGEWLYADTDGILISRAELSV 166
           HP+KA+KKG+GE+ V + I GTRI DGEWLYADTDGIL+S+ ELSV
Sbjct: 121 HPIKASKKGLGEQRVSLNIAGTRICDGEWLYADTDGILVSQIELSV 166

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

Arabidopsis thaliana (taxid: 3702)

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

 Score =  249 bits (635), Expect = 8e-66,   Method: Compositional matrix adjust.
 Identities = 119/166 (71%), Positives = 141/166 (84%)

Query: 1   MALVTTAEVCDANPQLIVSGELRALQPIFQIYGRRQVFSGPIVTLKVFEDNVLIREFLEE 60
           MA   TAE CD+N +LI +G+LRAL PIF+IYG+R+ FSGPIVTLKVFEDNVL+R  LE 
Sbjct: 1   MAAFATAEACDSNAELISNGDLRALHPIFKIYGQRRCFSGPIVTLKVFEDNVLVRNQLET 60

Query: 61  KGNGRVLVVDGGGSLRCAILGGNPVVQAQNNGWAGIVVNGCIRDVDEINGCDIGVRALAS 120
           KG G VLV+DGGGS+RCA++GGN    AQNNGW+GIVVNGC+RDVDEIN CD+GVRAL S
Sbjct: 61  KGEGGVLVIDGGGSMRCALVGGNLGQLAQNNGWSGIVVNGCVRDVDEINDCDVGVRALGS 120

Query: 121 HPMKANKKGIGEKHVPITIGGTRISDGEWLYADTDGILISRAELSV 166
           +P+K+ KKG GEK+VP+ IGGT I DGEWLYAD+DGILIS+ ELSV
Sbjct: 121 NPLKSTKKGHGEKNVPVHIGGTLIRDGEWLYADSDGILISKTELSV 166

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

Arabidopsis thaliana (taxid: 3702)

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

 Score =  196 bits (498), Expect = 6e-50,   Method: Compositional matrix adjust.
 Identities = 90/160 (56%), Positives = 118/160 (73%)

Query: 6   TAEVCDANPQLIVSGELRALQPIFQIYGRRQVFSGPIVTLKVFEDNVLIREFLEEKGNGR 65
           T ++CDA+   + +G LR LQP  + YG    F+GP  TLKVFEDN L+R  LE+ G GR
Sbjct: 5   TTDLCDAHEDKLAAGTLRVLQPALRPYGGAARFAGPAATLKVFEDNTLVRAALEQDGGGR 64

Query: 66  VLVVDGGGSLRCAILGGNPVVQAQNNGWAGIVVNGCIRDVDEINGCDIGVRALASHPMKA 125
           VLVVDGG SLRCA++GGN    A+ NGWAGIVV+GC+RD  E+  C +GV ALA+HP K+
Sbjct: 65  VLVVDGGASLRCALVGGNLGALAEKNGWAGIVVHGCVRDAAELRECKVGVLALATHPRKS 124

Query: 126 NKKGIGEKHVPITIGGTRISDGEWLYADTDGILISRAELS 165
           +K+G GE+ VP+T+ GTRI+ GEW+YAD DG+L+S   L+
Sbjct: 125 DKRGAGERDVPVTVLGTRIAPGEWIYADDDGVLVSATSLT 164

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

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

 Score =  193 bits (491), Expect = 3e-49,   Method: Compositional matrix adjust.
 Identities = 85/159 (53%), Positives = 117/159 (73%)

Query: 6   TAEVCDANPQLIVSGELRALQPIFQIYGRRQVFSGPIVTLKVFEDNVLIREFLEEKGNGR 65
           T ++CDAN   +  G LR + P+F+ +G++Q F+GP  TLK+FEDN L+RE LE  G GR
Sbjct: 5   TTDLCDANEPRLADGTLRVMAPVFRAFGKQQAFAGPAATLKIFEDNSLVREALESPGQGR 64

Query: 66  VLVVDGGGSLRCAILGGNPVVQAQNNGWAGIVVNGCIRDVDEINGCDIGVRALASHPMKA 125
           VLVVDGGGSLRCA++GGN  + A+ NGW GI+VNGC+RD  E++ CDIG+RALA+HP K+
Sbjct: 65  VLVVDGGGSLRCALVGGNLGLLAEKNGWVGIIVNGCVRDTGELDVCDIGIRALAAHPQKS 124

Query: 126 NKKGIGEKHVPITIGGTRISDGEWLYADTDGILISRAEL 164
            K+G GE+ V + + G  +  G W+Y D DG+L+S  +L
Sbjct: 125 QKRGAGERDVAVQMPGAVVRPGNWIYVDADGVLVSEEKL 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 =  191 bits (484), Expect = 2e-48,   Method: Compositional matrix adjust.
 Identities = 88/162 (54%), Positives = 119/162 (73%)

Query: 3   LVTTAEVCDANPQLIVSGELRALQPIFQIYGRRQVFSGPIVTLKVFEDNVLIREFLEEKG 62
           +  T ++CDAN + + +G LR ++P+F+ +G  + F+GP  TLK+FEDN L+R  LE+ G
Sbjct: 2   MFATTDLCDANEERLAAGTLRVIEPVFRSFGGVRRFAGPAATLKLFEDNTLVRAALEQDG 61

Query: 63  NGRVLVVDGGGSLRCAILGGNPVVQAQNNGWAGIVVNGCIRDVDEINGCDIGVRALASHP 122
            GRVLVVDGGGSLRCA++GGN    A+ NGW GIVVNGC+RD  E+  C  GV ALA+HP
Sbjct: 62  AGRVLVVDGGGSLRCALVGGNLGKLAEKNGWVGIVVNGCVRDSAELAECRAGVLALAAHP 121

Query: 123 MKANKKGIGEKHVPITIGGTRISDGEWLYADTDGILISRAEL 164
            K++K+G G   VP+ + GTRI+ G+W+YAD DGIL+S A L
Sbjct: 122 RKSDKRGAGVSDVPVDVRGTRIAPGDWIYADADGILVSDAAL 163

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

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

 Score =  188 bits (478), Expect = 1e-47,   Method: Compositional matrix adjust.
 Identities = 86/158 (54%), Positives = 117/158 (74%)

Query: 3   LVTTAEVCDANPQLIVSGELRALQPIFQIYGRRQVFSGPIVTLKVFEDNVLIREFLEEKG 62
           +  T ++CDA+   + +G LR L+P+F+ +G  + F+GP  TLK+FEDN L+R  LE+ G
Sbjct: 2   MFATTDLCDAHEDRLAAGTLRVLEPVFRPFGGVRRFAGPAATLKLFEDNSLVRTALEQDG 61

Query: 63  NGRVLVVDGGGSLRCAILGGNPVVQAQNNGWAGIVVNGCIRDVDEINGCDIGVRALASHP 122
            GRVLVVDGGGSLRCA++GGN    A+ NGWAGIVVNGC+RD DE+  C +GV ALA+HP
Sbjct: 62  AGRVLVVDGGGSLRCALVGGNLGKLAEKNGWAGIVVNGCVRDSDELAECRVGVLALAAHP 121

Query: 123 MKANKKGIGEKHVPITIGGTRISDGEWLYADTDGILIS 160
            K++K+G G    P+ + GTRI  G+W+YAD DG+L+S
Sbjct: 122 RKSDKRGAGVSDAPVDVRGTRIVPGDWIYADADGVLVS 159

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 =  188 bits (478), Expect = 1e-47,   Method: Compositional matrix adjust.
 Identities = 86/158 (54%), Positives = 117/158 (74%)

Query: 3   LVTTAEVCDANPQLIVSGELRALQPIFQIYGRRQVFSGPIVTLKVFEDNVLIREFLEEKG 62
           +  T ++CDA+   + +G LR L+P+F+ +G  + F+GP  TLK+FEDN L+R  LE+ G
Sbjct: 2   MFATTDLCDAHEDRLAAGTLRVLEPVFRPFGGVRRFAGPAATLKLFEDNSLVRTALEQDG 61

Query: 63  NGRVLVVDGGGSLRCAILGGNPVVQAQNNGWAGIVVNGCIRDVDEINGCDIGVRALASHP 122
            GRVLVVDGGGSLRCA++GGN    A+ NGWAGIVVNGC+RD DE+  C +GV ALA+HP
Sbjct: 62  AGRVLVVDGGGSLRCALVGGNLGKLAEKNGWAGIVVNGCVRDSDELAECRVGVLALAAHP 121

Query: 123 MKANKKGIGEKHVPITIGGTRISDGEWLYADTDGILIS 160
            K++K+G G    P+ + GTRI  G+W+YAD DG+L+S
Sbjct: 122 RKSDKRGAGVSDAPVDVRGTRIVPGDWIYADADGVLVS 159

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 =  188 bits (478), Expect = 1e-47,   Method: Compositional matrix adjust.
 Identities = 86/158 (54%), Positives = 117/158 (74%)

Query: 3   LVTTAEVCDANPQLIVSGELRALQPIFQIYGRRQVFSGPIVTLKVFEDNVLIREFLEEKG 62
           +  T ++CDA+   + +G LR L+P+F+ +G  + F+GP  TLK+FEDN L+R  LE+ G
Sbjct: 2   MFATTDLCDAHEDRLAAGTLRVLEPVFRPFGGVRRFAGPAATLKLFEDNSLVRTALEQDG 61

Query: 63  NGRVLVVDGGGSLRCAILGGNPVVQAQNNGWAGIVVNGCIRDVDEINGCDIGVRALASHP 122
            GRVLVVDGGGSLRCA++GGN    A+ NGWAGIVVNGC+RD DE+  C +GV ALA+HP
Sbjct: 62  AGRVLVVDGGGSLRCALVGGNLGKLAEKNGWAGIVVNGCVRDSDELAECRVGVLALAAHP 121

Query: 123 MKANKKGIGEKHVPITIGGTRISDGEWLYADTDGILIS 160
            K++K+G G    P+ + GTRI  G+W+YAD DG+L+S
Sbjct: 122 RKSDKRGAGVSDAPVDVRGTRIVPGDWIYADADGVLVS 159

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 =  188 bits (478), Expect = 1e-47,   Method: Compositional matrix adjust.
 Identities = 86/158 (54%), Positives = 117/158 (74%)

Query: 3   LVTTAEVCDANPQLIVSGELRALQPIFQIYGRRQVFSGPIVTLKVFEDNVLIREFLEEKG 62
           +  T ++CDA+   + +G LR L+P+F+ +G  + F+GP  TLK+FEDN L+R  LE+ G
Sbjct: 2   MFATTDLCDAHEDRLAAGTLRVLEPVFRPFGGVRRFAGPAATLKLFEDNSLVRTALEQDG 61

Query: 63  NGRVLVVDGGGSLRCAILGGNPVVQAQNNGWAGIVVNGCIRDVDEINGCDIGVRALASHP 122
            GRVLVVDGGGSLRCA++GGN    A+ NGWAGIVVNGC+RD DE+  C +GV ALA+HP
Sbjct: 62  AGRVLVVDGGGSLRCALVGGNLGKLAEKNGWAGIVVNGCVRDSDELAECRVGVLALAAHP 121

Query: 123 MKANKKGIGEKHVPITIGGTRISDGEWLYADTDGILIS 160
            K++K+G G    P+ + GTRI  G+W+YAD DG+L+S
Sbjct: 122 RKSDKRGAGVSDAPVDVRGTRIVPGDWIYADADGVLVS 159

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	166
224144943	166	predicted protein [Populus trichocarpa]	1.0	1.0	0.975	3e-88
255547584	166	Regulator of ribonuclease activity A, pu	1.0	1.0	0.975	4e-88
388502142	166	unknown [Lotus japonicus]	1.0	1.0	0.945	4e-87
330318635	166	dimethylmenaquinone methyltransferase [C	1.0	1.0	0.951	8e-87
225430941	166	PREDICTED: regulator of ribonuclease-lik	1.0	1.0	0.957	1e-86
357507775	166	Regulator of ribonuclease-like protein [	1.0	1.0	0.945	2e-86
211906464	166	dimethylmenaquinone methyltransferase [G	1.0	1.0	0.951	3e-86
356531896	166	PREDICTED: regulator of ribonuclease-lik	1.0	1.0	0.933	4e-86
224128794	166	predicted protein [Populus trichocarpa]	1.0	1.0	0.951	4e-86
351723477	166	uncharacterized protein LOC100500691 [Gl	1.0	1.0	0.927	7e-85

>gi|224144943|ref|XP_002325470.1| predicted protein [Populus trichocarpa] gi|118486747|gb|ABK95209.1| unknown [Populus trichocarpa] gi|222862345|gb|EEE99851.1| predicted protein [Populus trichocarpa]

 Score =  328 bits (842), Expect = 3e-88,   Method: Compositional matrix adjust.
 Identities = 162/166 (97%), Positives = 164/166 (98%)

Query: 1   MALVTTAEVCDANPQLIVSGELRALQPIFQIYGRRQVFSGPIVTLKVFEDNVLIREFLEE 60
           MALVTTAEVCDANPQLIVSGELRALQPIFQIYGRRQVFSGP+VTLKVFEDNVLIREFLEE
Sbjct: 1   MALVTTAEVCDANPQLIVSGELRALQPIFQIYGRRQVFSGPVVTLKVFEDNVLIREFLEE 60

Query: 61  KGNGRVLVVDGGGSLRCAILGGNPVVQAQNNGWAGIVVNGCIRDVDEINGCDIGVRALAS 120
           KGNGRVLVVDGGGSLRCAILGGNPVVQAQNNGWAGIVVNGCIRDVDEI GCDIGVRALAS
Sbjct: 61  KGNGRVLVVDGGGSLRCAILGGNPVVQAQNNGWAGIVVNGCIRDVDEIMGCDIGVRALAS 120

Query: 121 HPMKANKKGIGEKHVPITIGGTRISDGEWLYADTDGILISRAELSV 166
           HPMKANKKGIGEKHVPITIGGTRISDGEWLYADTDGILISR EL+V
Sbjct: 121 HPMKANKKGIGEKHVPITIGGTRISDGEWLYADTDGILISRTELAV 166

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255547584|ref|XP_002514849.1| Regulator of ribonuclease activity A, putative [Ricinus communis] gi|223545900|gb|EEF47403.1| Regulator of ribonuclease activity A, putative [Ricinus communis]

 Score =  328 bits (842), Expect = 4e-88,   Method: Compositional matrix adjust.
 Identities = 162/166 (97%), Positives = 165/166 (99%)

Query: 1   MALVTTAEVCDANPQLIVSGELRALQPIFQIYGRRQVFSGPIVTLKVFEDNVLIREFLEE 60
           MALVTTAEVCDANPQLIVSGELRALQPIFQIYGRRQVFSGP+VTLKVFEDNVLIREFLEE
Sbjct: 1   MALVTTAEVCDANPQLIVSGELRALQPIFQIYGRRQVFSGPVVTLKVFEDNVLIREFLEE 60

Query: 61  KGNGRVLVVDGGGSLRCAILGGNPVVQAQNNGWAGIVVNGCIRDVDEINGCDIGVRALAS 120
           KGNGRVLVVDGGGSLRCAILGGNPVVQAQNNGWAGI+VNGCIRDVDEINGCDIGVRALAS
Sbjct: 61  KGNGRVLVVDGGGSLRCAILGGNPVVQAQNNGWAGILVNGCIRDVDEINGCDIGVRALAS 120

Query: 121 HPMKANKKGIGEKHVPITIGGTRISDGEWLYADTDGILISRAELSV 166
           HPMKANKKGIGEKHVPITIGGTRISDGE+LYADTDGILISR ELSV
Sbjct: 121 HPMKANKKGIGEKHVPITIGGTRISDGEFLYADTDGILISRNELSV 166

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388502142|gb|AFK39137.1| unknown [Lotus japonicus]

 Score =  325 bits (833), Expect = 4e-87,   Method: Compositional matrix adjust.
 Identities = 157/166 (94%), Positives = 163/166 (98%)

Query: 1   MALVTTAEVCDANPQLIVSGELRALQPIFQIYGRRQVFSGPIVTLKVFEDNVLIREFLEE 60
           MALVTTAEVCDANPQLI+SGE+RAL P+FQIYGRRQVFSGP+VTLKVFEDNVL+REFLEE
Sbjct: 1   MALVTTAEVCDANPQLILSGEVRALHPVFQIYGRRQVFSGPVVTLKVFEDNVLVREFLEE 60

Query: 61  KGNGRVLVVDGGGSLRCAILGGNPVVQAQNNGWAGIVVNGCIRDVDEINGCDIGVRALAS 120
           KGNGRVLVVDGGGSLRCAILGGNPVVQAQNNGWAGIVVNGCIRDVDEINGCDIGVRALAS
Sbjct: 61  KGNGRVLVVDGGGSLRCAILGGNPVVQAQNNGWAGIVVNGCIRDVDEINGCDIGVRALAS 120

Query: 121 HPMKANKKGIGEKHVPITIGGTRISDGEWLYADTDGILISRAELSV 166
           HPMKANKKG+GEKHVPITI GTRISDGEWLYADTDGILISR ELSV
Sbjct: 121 HPMKANKKGMGEKHVPITIAGTRISDGEWLYADTDGILISRTELSV 166

Source: Lotus japonicus

Species: Lotus japonicus

Genus: Lotus

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|330318635|gb|AEC10979.1| dimethylmenaquinone methyltransferase [Camellia sinensis]

 Score =  324 bits (830), Expect = 8e-87,   Method: Compositional matrix adjust.
 Identities = 158/166 (95%), Positives = 162/166 (97%)

Query: 1   MALVTTAEVCDANPQLIVSGELRALQPIFQIYGRRQVFSGPIVTLKVFEDNVLIREFLEE 60
           MALVTTAEVCDANPQLIVSGELRALQP+FQIYGRRQVFSGPIVTLKVFEDNVL+REFLEE
Sbjct: 1   MALVTTAEVCDANPQLIVSGELRALQPVFQIYGRRQVFSGPIVTLKVFEDNVLVREFLEE 60

Query: 61  KGNGRVLVVDGGGSLRCAILGGNPVVQAQNNGWAGIVVNGCIRDVDEINGCDIGVRALAS 120
           KGNGRVLVVDGG SLRCAILGGNPVVQAQNNGWAGIVVNGCIRDVDEINGCDIGVRAL S
Sbjct: 61  KGNGRVLVVDGGASLRCAILGGNPVVQAQNNGWAGIVVNGCIRDVDEINGCDIGVRALNS 120

Query: 121 HPMKANKKGIGEKHVPITIGGTRISDGEWLYADTDGILISRAELSV 166
           HPMKANKKGIGEKHVP+TIGGTRI DGEWLYADTDGILIS+ ELSV
Sbjct: 121 HPMKANKKGIGEKHVPVTIGGTRICDGEWLYADTDGILISKMELSV 166

Source: Camellia sinensis

Species: Camellia sinensis

Genus: Camellia

Family: Theaceae

Order: Ericales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225430941|ref|XP_002277981.1| PREDICTED: regulator of ribonuclease-like protein 2 [Vitis vinifera] gi|147863614|emb|CAN79757.1| hypothetical protein VITISV_009897 [Vitis vinifera]

 Score =  323 bits (828), Expect = 1e-86,   Method: Compositional matrix adjust.
 Identities = 159/166 (95%), Positives = 161/166 (96%)

Query: 1   MALVTTAEVCDANPQLIVSGELRALQPIFQIYGRRQVFSGPIVTLKVFEDNVLIREFLEE 60
           MALVTTAEVCDANPQLIVSGELRALQP+FQIYGRR VFSGPIVTLKVFEDNVLIREFLEE
Sbjct: 1   MALVTTAEVCDANPQLIVSGELRALQPVFQIYGRRPVFSGPIVTLKVFEDNVLIREFLEE 60

Query: 61  KGNGRVLVVDGGGSLRCAILGGNPVVQAQNNGWAGIVVNGCIRDVDEINGCDIGVRALAS 120
           KGNGRVLVVDGGGS+RCAILGGNPVVQAQNNGWAGIVVNGCIRDVDEINGCDIGVRAL S
Sbjct: 61  KGNGRVLVVDGGGSMRCAILGGNPVVQAQNNGWAGIVVNGCIRDVDEINGCDIGVRALNS 120

Query: 121 HPMKANKKGIGEKHVPITIGGTRISDGEWLYADTDGILISRAELSV 166
           HPMKANKKGIGEKHVPI I GTRISDGEWLYADTDGILISR ELSV
Sbjct: 121 HPMKANKKGIGEKHVPIAIAGTRISDGEWLYADTDGILISRTELSV 166

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357507775|ref|XP_003624176.1| Regulator of ribonuclease-like protein [Medicago truncatula] gi|217071150|gb|ACJ83935.1| unknown [Medicago truncatula] gi|355499191|gb|AES80394.1| Regulator of ribonuclease-like protein [Medicago truncatula]

 Score =  323 bits (827), Expect = 2e-86,   Method: Compositional matrix adjust.
 Identities = 157/166 (94%), Positives = 161/166 (96%)

Query: 1   MALVTTAEVCDANPQLIVSGELRALQPIFQIYGRRQVFSGPIVTLKVFEDNVLIREFLEE 60
           MALVTTAEVCDANPQLI+SGELRALQPIFQIYGRRQVFSGPIVTLKVFEDNVL+REFLEE
Sbjct: 1   MALVTTAEVCDANPQLILSGELRALQPIFQIYGRRQVFSGPIVTLKVFEDNVLVREFLEE 60

Query: 61  KGNGRVLVVDGGGSLRCAILGGNPVVQAQNNGWAGIVVNGCIRDVDEINGCDIGVRALAS 120
           KGNGRVLVVDGG SLRCAILGGNPVVQAQNNGWAGI+VNGCIRDVDEINGCDIGVRAL S
Sbjct: 61  KGNGRVLVVDGGASLRCAILGGNPVVQAQNNGWAGIIVNGCIRDVDEINGCDIGVRALGS 120

Query: 121 HPMKANKKGIGEKHVPITIGGTRISDGEWLYADTDGILISRAELSV 166
           HPMKANKKG+GEKHVPITI GTRI DGEWLYADTDGILISR ELSV
Sbjct: 121 HPMKANKKGMGEKHVPITIAGTRIGDGEWLYADTDGILISRTELSV 166

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|211906464|gb|ACJ11725.1| dimethylmenaquinone methyltransferase [Gossypium hirsutum]

 Score =  322 bits (825), Expect = 3e-86,   Method: Compositional matrix adjust.
 Identities = 158/166 (95%), Positives = 161/166 (96%)

Query: 1   MALVTTAEVCDANPQLIVSGELRALQPIFQIYGRRQVFSGPIVTLKVFEDNVLIREFLEE 60
           MALVTTAEVCDANPQLIVSGELRALQPIFQIYGRR VFSGPIVTLKVFEDNVLIREFLEE
Sbjct: 1   MALVTTAEVCDANPQLIVSGELRALQPIFQIYGRRPVFSGPIVTLKVFEDNVLIREFLEE 60

Query: 61  KGNGRVLVVDGGGSLRCAILGGNPVVQAQNNGWAGIVVNGCIRDVDEINGCDIGVRALAS 120
           KGNGRVLVVDGGGSLRCAILGGNPVVQAQNNGWAGIVVNGC+RDVDEINGCDIGVRAL S
Sbjct: 61  KGNGRVLVVDGGGSLRCAILGGNPVVQAQNNGWAGIVVNGCVRDVDEINGCDIGVRALHS 120

Query: 121 HPMKANKKGIGEKHVPITIGGTRISDGEWLYADTDGILISRAELSV 166
           HPMKANKKGIGEKHVPITI GTRI DGEWLYADTDGIL+S+ ELSV
Sbjct: 121 HPMKANKKGIGEKHVPITIAGTRICDGEWLYADTDGILVSKTELSV 166

Source: Gossypium hirsutum

Species: Gossypium hirsutum

Genus: Gossypium

Family: Malvaceae

Order: Malvales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356531896|ref|XP_003534512.1| PREDICTED: regulator of ribonuclease-like protein 2-like [Glycine max]

 Score =  322 bits (825), Expect = 4e-86,   Method: Compositional matrix adjust.
 Identities = 155/166 (93%), Positives = 161/166 (96%)

Query: 1   MALVTTAEVCDANPQLIVSGELRALQPIFQIYGRRQVFSGPIVTLKVFEDNVLIREFLEE 60
           MA VTTAEVCDANPQLI+SGELRALQP+FQIYGRRQVFSGPIVTLKVFEDNVL+REFLEE
Sbjct: 1   MAFVTTAEVCDANPQLILSGELRALQPVFQIYGRRQVFSGPIVTLKVFEDNVLVREFLEE 60

Query: 61  KGNGRVLVVDGGGSLRCAILGGNPVVQAQNNGWAGIVVNGCIRDVDEINGCDIGVRALAS 120
           KGNGRVLVVDGG SLRCAILGGNPVVQAQNNGWAGIVVNGCIRDVDEINGCDIGVRALAS
Sbjct: 61  KGNGRVLVVDGGASLRCAILGGNPVVQAQNNGWAGIVVNGCIRDVDEINGCDIGVRALAS 120

Query: 121 HPMKANKKGIGEKHVPITIGGTRISDGEWLYADTDGILISRAELSV 166
           HPMKANKKG+GEKHVP+ I GTRISDG+WLYADTDGILISR ELSV
Sbjct: 121 HPMKANKKGMGEKHVPVNIAGTRISDGDWLYADTDGILISRTELSV 166

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224128794|ref|XP_002328968.1| predicted protein [Populus trichocarpa] gi|222839202|gb|EEE77553.1| predicted protein [Populus trichocarpa]

 Score =  322 bits (824), Expect = 4e-86,   Method: Compositional matrix adjust.
 Identities = 158/166 (95%), Positives = 161/166 (96%)

Query: 1   MALVTTAEVCDANPQLIVSGELRALQPIFQIYGRRQVFSGPIVTLKVFEDNVLIREFLEE 60
           MALVTTAEVCD NPQ IVSGELRALQPIFQIYGRRQVFSGP+VTLK FEDNVLIREFLEE
Sbjct: 1   MALVTTAEVCDTNPQQIVSGELRALQPIFQIYGRRQVFSGPVVTLKAFEDNVLIREFLEE 60

Query: 61  KGNGRVLVVDGGGSLRCAILGGNPVVQAQNNGWAGIVVNGCIRDVDEINGCDIGVRALAS 120
           +G+GRVLVVDGGGSLRCAILGGNPVVQAQNNGWAGIVVNGCIRDVDEINGCDIGVRAL S
Sbjct: 61  RGSGRVLVVDGGGSLRCAILGGNPVVQAQNNGWAGIVVNGCIRDVDEINGCDIGVRALGS 120

Query: 121 HPMKANKKGIGEKHVPITIGGTRISDGEWLYADTDGILISRAELSV 166
           HPMKANKKGIGEKHVPITIGGTRISDGEWLYADTDGILISRAEL V
Sbjct: 121 HPMKANKKGIGEKHVPITIGGTRISDGEWLYADTDGILISRAELCV 166

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|351723477|ref|NP_001238048.1| uncharacterized protein LOC100500691 [Glycine max] gi|255630950|gb|ACU15838.1| unknown [Glycine max]

 Score =  318 bits (814), Expect = 7e-85,   Method: Compositional matrix adjust.
 Identities = 154/166 (92%), Positives = 159/166 (95%)

Query: 1   MALVTTAEVCDANPQLIVSGELRALQPIFQIYGRRQVFSGPIVTLKVFEDNVLIREFLEE 60
           MA VTTAEVCDANPQLI+SGE RALQP+FQIYGRRQVFSGPIVTLKVFEDNVL+REFLEE
Sbjct: 1   MAFVTTAEVCDANPQLILSGEPRALQPVFQIYGRRQVFSGPIVTLKVFEDNVLVREFLEE 60

Query: 61  KGNGRVLVVDGGGSLRCAILGGNPVVQAQNNGWAGIVVNGCIRDVDEINGCDIGVRALAS 120
           KGNGRVLVVDGG SLRCAILGGNPVVQAQNNGWAGI+VNGCIRDVDEINGCDIGVRALAS
Sbjct: 61  KGNGRVLVVDGGASLRCAILGGNPVVQAQNNGWAGIIVNGCIRDVDEINGCDIGVRALAS 120

Query: 121 HPMKANKKGIGEKHVPITIGGTRISDGEWLYADTDGILISRAELSV 166
           HPMKANKKG+GEK VPI I GTRISDGEWLYADTDGILISR ELSV
Sbjct: 121 HPMKANKKGMGEKQVPINIAGTRISDGEWLYADTDGILISRTELSV 166

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

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	166
TAIR|locus:2171397	166	AT5G16450 [Arabidopsis thalian	1.0	1.0	0.855	3.5e-75
TAIR|locus:2075432	166	AT3G02770 [Arabidopsis thalian	1.0	1.0	0.843	1.9e-74
TAIR|locus:2156430	166	AT5G56260 [Arabidopsis thalian	1.0	1.0	0.716	2.3e-62
UNIPROTKB|P0A8R0	161	rraA "ribonuclease E inhibitor	0.939	0.968	0.416	1.8e-30
TIGR_CMR|SO_4197	161	SO_4197 "S-adenosylmethionine:	0.939	0.968	0.422	2.3e-30
UNIPROTKB|Q47VZ9	165	rraA "Regulator of ribonucleas	0.939	0.945	0.422	2.4e-28
TIGR_CMR|CPS_4374	165	CPS_4374 "protein of unknown f	0.939	0.945	0.422	2.4e-28
UNIPROTKB|P0A666	157	rraA "Putative regulator of ri	0.855	0.904	0.394	1.3e-27
TIGR_CMR|SO_2567	164	SO_2567 "S-adenosylmethionine:	0.849	0.859	0.415	4.5e-27
UNIPROTKB|Q489G8	163	CPS_0538 "Putative uncharacter	0.879	0.895	0.376	5.2e-26

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

 Score = 758 (271.9 bits), Expect = 3.5e-75, P = 3.5e-75
 Identities = 142/166 (85%), Positives = 156/166 (93%)

Query:     1 MALVTTAEVCDANPQLIVSGELRALQPIFQIYGRRQVFSGPIVTLKVFEDNVLIREFLEE 60
             MA VTTAEVCDAN +LI SG+LRALQPIFQIYGRRQ+FSGP+VT+KVFEDN LIR+F+EE
Sbjct:     1 MAFVTTAEVCDANQELIRSGQLRALQPIFQIYGRRQIFSGPVVTVKVFEDNGLIRQFIEE 60

Query:    61 KGNGRVLVVDGGGSLRCAILGGNPVVQAQNNGWAGIVVNGCIRDVDEINGCDIGVRALAS 120
             KGNGRVLVVDGGGS RCAILGGNPVVQAQNNGWAGIVVNGCIRDVDEINGCDIGVRALAS
Sbjct:    61 KGNGRVLVVDGGGSQRCAILGGNPVVQAQNNGWAGIVVNGCIRDVDEINGCDIGVRALAS 120

Query:   121 HPMKANKKGIGEKHVPITIGGTRISDGEWLYADTDGILISRAELSV 166
             HP+KA+KKG+GE+ VP+ I GTRI DGEWLYADTDGIL+S+ ELSV
Sbjct:   121 HPIKASKKGLGEQRVPVNIAGTRICDGEWLYADTDGILVSQIELSV 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 = 751 (269.4 bits), Expect = 1.9e-74, P = 1.9e-74
 Identities = 140/166 (84%), Positives = 155/166 (93%)

Query:     1 MALVTTAEVCDANPQLIVSGELRALQPIFQIYGRRQVFSGPIVTLKVFEDNVLIREFLEE 60
             MA VTTAEVCDAN ++I SG+LRALQP+FQIYGRRQ+FSGP+VT+KVFEDN LIR FLEE
Sbjct:     1 MAFVTTAEVCDANQEMIRSGQLRALQPVFQIYGRRQIFSGPVVTVKVFEDNGLIRHFLEE 60

Query:    61 KGNGRVLVVDGGGSLRCAILGGNPVVQAQNNGWAGIVVNGCIRDVDEINGCDIGVRALAS 120
             KGNGRVLVVDGGGSLRCAILGGNPVVQAQNNGWAGI+VNGCIRDVDEINGCDIGVRALAS
Sbjct:    61 KGNGRVLVVDGGGSLRCAILGGNPVVQAQNNGWAGIIVNGCIRDVDEINGCDIGVRALAS 120

Query:   121 HPMKANKKGIGEKHVPITIGGTRISDGEWLYADTDGILISRAELSV 166
             HP+KA+KKG+GE+ V + I GTRI DGEWLYADTDGIL+S+ ELSV
Sbjct:   121 HPIKASKKGLGEQRVSLNIAGTRICDGEWLYADTDGILVSQIELSV 166

GO:0005737 "cytoplasm" evidence=ISM

GO:0008428 "ribonuclease inhibitor activity" evidence=IEA

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

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

 Score = 637 (229.3 bits), Expect = 2.3e-62, P = 2.3e-62
 Identities = 119/166 (71%), Positives = 141/166 (84%)

Query:     1 MALVTTAEVCDANPQLIVSGELRALQPIFQIYGRRQVFSGPIVTLKVFEDNVLIREFLEE 60
             MA   TAE CD+N +LI +G+LRAL PIF+IYG+R+ FSGPIVTLKVFEDNVL+R  LE 
Sbjct:     1 MAAFATAEACDSNAELISNGDLRALHPIFKIYGQRRCFSGPIVTLKVFEDNVLVRNQLET 60

Query:    61 KGNGRVLVVDGGGSLRCAILGGNPVVQAQNNGWAGIVVNGCIRDVDEINGCDIGVRALAS 120
             KG G VLV+DGGGS+RCA++GGN    AQNNGW+GIVVNGC+RDVDEIN CD+GVRAL S
Sbjct:    61 KGEGGVLVIDGGGSMRCALVGGNLGQLAQNNGWSGIVVNGCVRDVDEINDCDVGVRALGS 120

Query:   121 HPMKANKKGIGEKHVPITIGGTRISDGEWLYADTDGILISRAELSV 166
             +P+K+ KKG GEK+VP+ IGGT I DGEWLYAD+DGILIS+ ELSV
Sbjct:   121 NPLKSTKKGHGEKNVPVHIGGTLIRDGEWLYADSDGILISKTELSV 166

GO:0005737 "cytoplasm" evidence=ISM

GO:0008428 "ribonuclease inhibitor activity" evidence=IEA

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

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

 Score = 336 (123.3 bits), Expect = 1.8e-30, P = 1.8e-30
 Identities = 67/161 (41%), Positives = 99/161 (61%)

Query:     6 TAEVCDANPQLIVSGELRALQPIFQIYGRRQVFSGPIVTLKVFEDNVLIREFLEEKGNGR 65
             T+E+CD     I   ++  ++P+F  +G R  F G I+T+K FEDN L+ + LE+ G GR
Sbjct:     5 TSELCD-----IYQEDVNVVEPLFSNFGGRASFGGQIITVKCFEDNGLLYDLLEQNGRGR 59

Query:    66 VLVVDGGGSLRCAILGGNPVVQAQNNGWAGIVVNGCIRDVDEINGCDIGVRALASHPMKA 125
             VLVVDGGGS+R A++       A  N W G+V+ G +R VD++   DIG++A+A+ P+ A
Sbjct:    60 VLVVDGGGSVRRALVDAELARLAVQNEWEGLVIYGAVRQVDDLEELDIGIQAMAAIPVGA 119

Query:   126 NKKGIGEKHVPITIGGTRISDGEWLYADTDGILISRAELSV 166
               +GIGE  V +  GG     G+ LYAD  GI++S   L +
Sbjct:   120 AGEGIGESDVRVNFGGVTFFSGDHLYADNTGIILSEDPLDI 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

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

 Score = 335 (123.0 bits), Expect = 2.3e-30, P = 2.3e-30
 Identities = 68/161 (42%), Positives = 98/161 (60%)

Query:     6 TAEVCDANPQLIVSGELRALQPIFQIYGRRQVFSGPIVTLKVFEDNVLIREFLEEKGNGR 65
             T+E+CD    ++       ++P+F  YG    F G I T+K FEDN LI + L+E G G+
Sbjct:     5 TSELCDMYLDVV-----DVVEPMFSNYGGCSSFGGSISTIKCFEDNGLITDVLQEDGQGK 59

Query:    66 VLVVDGGGSLRCAILGGNPVVQAQNNGWAGIVVNGCIRDVDEINGCDIGVRALASHPMKA 125
             VL+VDGGGSLR A++ G     A +N W GI+V G +RDVD +   DIG++ALAS P+ A
Sbjct:    60 VLLVDGGGSLRRALIDGTIAELAVSNNWEGIIVYGSVRDVDALEELDIGIQALASIPVGA 119

Query:   126 NKKGIGEKHVPITIGGTRISDGEWLYADTDGILISRAELSV 166
             +   +GE  +P+  GG     G+ +YAD  GI++S   L +
Sbjct:   120 DGNSVGEVDIPVNFGGVTFLPGDHIYADNTGIILSPEPLDI 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 = 316 (116.3 bits), Expect = 2.4e-28, P = 2.4e-28
 Identities = 68/161 (42%), Positives = 96/161 (59%)

Query:     6 TAEVCDANPQLIVSGELRALQPIFQIYGRRQVFSGPIVTLKVFEDNVLIREFLEEKGNGR 65
             T+E+CD    LI       + PIF  YG R  F+G +VTLK FE   LI E +   G G+
Sbjct:     5 TSELCDFYADLI-----DVVDPIFCNYGGRSSFAGKVVTLKCFEHLGLINELVATYGTGK 59

Query:    66 VLVVDGGGSLRCAILGGNPVVQAQNNGWAGIVVNGCIRDVDEINGCDIGVRALASHPMKA 125
             VLV+DGGGS R A++       A NNGW GIV  G +RDVD ++G DIG++AL + P+ A
Sbjct:    60 VLVIDGGGSTRRALIDLGIAQCAANNGWEGIVCYGSVRDVDALDGVDIGIQALGAIPVGA 119

Query:   126 NKKGIGEKHVPITIGGTRISDGEWLYADTDGILISRAELSV 166
             +++ IGE  + I   G  +   +++YAD  GI++S   L +
Sbjct:   120 SEQNIGETDMAINFAGVTLLPDDYIYADNTGIILSPEALEI 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 = 316 (116.3 bits), Expect = 2.4e-28, P = 2.4e-28
 Identities = 68/161 (42%), Positives = 96/161 (59%)

Query:     6 TAEVCDANPQLIVSGELRALQPIFQIYGRRQVFSGPIVTLKVFEDNVLIREFLEEKGNGR 65
             T+E+CD    LI       + PIF  YG R  F+G +VTLK FE   LI E +   G G+
Sbjct:     5 TSELCDFYADLI-----DVVDPIFCNYGGRSSFAGKVVTLKCFEHLGLINELVATYGTGK 59

Query:    66 VLVVDGGGSLRCAILGGNPVVQAQNNGWAGIVVNGCIRDVDEINGCDIGVRALASHPMKA 125
             VLV+DGGGS R A++       A NNGW GIV  G +RDVD ++G DIG++AL + P+ A
Sbjct:    60 VLVIDGGGSTRRALIDLGIAQCAANNGWEGIVCYGSVRDVDALDGVDIGIQALGAIPVGA 119

Query:   126 NKKGIGEKHVPITIGGTRISDGEWLYADTDGILISRAELSV 166
             +++ IGE  + I   G  +   +++YAD  GI++S   L +
Sbjct:   120 SEQNIGETDMAINFAGVTLLPDDYIYADNTGIILSPEALEI 160

GO:0003674 "molecular_function" evidence=ND

GO:0008150 "biological_process" evidence=ND

UNIPROTKB|P0A666 rraA "Putative regulator of ribonuclease activity" [Mycobacterium tuberculosis (taxid:1773)]

 Score = 309 (113.8 bits), Expect = 1.3e-27, P = 1.3e-27
 Identities = 56/142 (39%), Positives = 90/142 (63%)

Query:    18 VSGELRALQPIFQIYGRRQVFSGPIVTLKVFEDNVLIREFLEEKGNGRVLVVDGGGSLRC 77
             +  ++R+    F+ +G R  F+GPI T++ F+DN L++  L +   G VLV+DG GSL  
Sbjct:    15 IGPDVRSCDLQFRQFGGRSQFAGPISTVRCFQDNALLKSVLSQPSAGGVLVIDGAGSLHT 74

Query:    78 AILGGNPVVQAQNNGWAGIVVNGCIRDVDEINGCDIGVRALASHPMKANKKGIGEKHVPI 137
             A++G      A++ GW G++V+G +RD   + G DIG++AL ++P K+ K G GE+ V I
Sbjct:    75 ALVGDVIAELARSTGWTGLIVHGAVRDAAALRGIDIGIKALGTNPRKSTKTGAGERDVEI 134

Query:   138 TIGGTRISDGEWLYADTDGILI 159
             T+GG     G+  Y+D DGI++
Sbjct:   135 TLGGVTFVPGDIAYSDDDGIIV 156

GO:0070207 "protein homotrimerization" evidence=IPI

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

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

 Score = 304 (112.1 bits), Expect = 4.5e-27, P = 4.5e-27
 Identities = 59/142 (41%), Positives = 91/142 (64%)

Query:    25 LQPI-FQIYGRRQVFSGPIVTLKVFEDNVLIREFLEEKGNGRVLVVDGGGSLRCAILGGN 83
             L P+ F+ +G +++F G +VT+K FEDN  ++E L + G+G+VL+VDGGGS R A+LG  
Sbjct:    18 LLPLAFRAFGGKRLFWGEVVTVKCFEDNSKVKEVLAQPGHGKVLIVDGGGSSRRALLGDL 77

Query:    84 PVVQAQNNGWAGIVVNGCIRDVDEINGCDIGVRALASHPMKANKKGIGEKHVPITIGGTR 143
                 A +NGW G+++NG +RD   ++  ++GV AL + PMK  K   G+ +VPI +G   
Sbjct:    78 IAQSAMDNGWQGVIINGYVRDAARLSSFNLGVYALGAMPMKTEKLDQGQINVPIELGCVT 137

Query:   144 ISDGEWLYADTDGILISRAELS 165
             +  G  +Y D +GI IS   L+
Sbjct:   138 VKPGMMVYVDENGIAISEESLN 159

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

GO:0009234 "menaquinone biosynthetic process" evidence=ISS

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

 Score = 294 (108.6 bits), Expect = 5.2e-26, P = 5.2e-26
 Identities = 55/146 (37%), Positives = 85/146 (58%)

Query:    21 ELRALQPIFQIYGRRQVFSGPIVTLKVFEDNVLIREFLEEKGNGRVLVVDGGGSLRCAIL 80
             +L      F  YG+  +F G IVT+  FEDN  ++E L   G+G+VLVVDG GS+  A+L
Sbjct:    15 QLSLANQAFTDYGKNTIFYGEIVTVSCFEDNSKVKEILATDGSGKVLVVDGKGSMNRALL 74

Query:    81 GGNPVVQAQNNGWAGIVVNGCIRDVDEINGCDIGVRALASHPMKANKKGIGEKHVPITIG 140
             G      A  N W  +V+NGCIRD   I   +I V+A+  +P+K  K G+G+ ++ +   
Sbjct:    75 GDMIAENAVKNNWQAVVINGCIRDAGTIRTLEIAVKAIGCNPIKTEKLGVGDTNIVVNFA 134

Query:   141 GTRISDGEWLYADTDGILISRAELSV 166
                   G ++Y D +G+ +S+++LSV
Sbjct:   135 NVEFIPGWYVYGDENGLAVSKSKLSV 160

GO:0003674 "molecular_function" evidence=ND

GO:0008150 "biological_process" evidence=ND

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q02KR3	RRAAH_PSEAB	No assigned EC number	0.5031	0.9397	0.9629	yes	no
Q48JZ3	RRAAH_PSE14	No assigned EC number	0.5030	0.9397	0.9512	yes	no
Q4ZUN7	RRAAH_PSEU2	No assigned EC number	0.5279	0.9397	0.9629	yes	no
A4XU32	RRAAH_PSEMY	No assigned EC number	0.5341	0.9397	0.9629	yes	no
Q8DCP6	RRAA_VIBVU	No assigned EC number	0.4812	0.9337	0.8959	yes	no
Q47BF5	RRAAH_DECAR	No assigned EC number	0.5375	0.9578	0.9754	yes	no
Q7MH54	RRAA_VIBVY	No assigned EC number	0.4812	0.9337	0.8959	yes	no
B7VBA7	RRAAH_PSEA8	No assigned EC number	0.5031	0.9397	0.9629	yes	no
Q88L51	RRAAH_PSEPK	No assigned EC number	0.4819	0.9698	0.9877	yes	no
Q13X79	RRAAH_BURXL	No assigned EC number	0.5375	0.9638	0.9756	yes	no
Q0A9G6	RRAAH_ALHEH	No assigned EC number	0.5217	0.9397	0.9689	yes	no
A3NWR9	RRAAH_BURP0	No assigned EC number	0.5443	0.9518	0.9575	yes	no
A1V5A8	RRAAH_BURMS	No assigned EC number	0.5443	0.9518	0.9575	yes	no
A1WU91	RRAAH_HALHL	No assigned EC number	0.4879	0.9879	1.0	yes	no
A3NAY8	RRAAH_BURP6	No assigned EC number	0.5443	0.9518	0.9575	yes	no
Q3KFE1	RRAAH_PSEPF	No assigned EC number	0.5	0.9698	0.9877	yes	no
A9AHQ6	RRAAH_BURM1	No assigned EC number	0.5625	0.9638	0.9756	yes	no
A2SB35	RRAAH_BURM9	No assigned EC number	0.5443	0.9518	0.9575	yes	no
A4VL60	RRAAH_PSEU5	No assigned EC number	0.4658	0.9397	0.9629	yes	no
Q46ZV6	RRAA_CUPPJ	No assigned EC number	0.5345	0.9578	0.9636	yes	no
Q63SX7	RRAAH_BURPS	No assigned EC number	0.5443	0.9518	0.9575	yes	no
Q1ICM4	RRAAH_PSEE4	No assigned EC number	0.4698	0.9698	0.9877	yes	no
C1DHC2	RRAAH_AZOVD	No assigned EC number	0.5031	0.9397	0.9629	yes	no
B1J596	RRAAH_PSEPW	No assigned EC number	0.4698	0.9698	0.9877	yes	no
B0KG79	RRAAH_PSEPG	No assigned EC number	0.4759	0.9698	0.9877	yes	no
B2JIG2	RRAAH_BURP8	No assigned EC number	0.5471	0.9578	0.9695	yes	no
B2SXN2	RRAAH_BURPP	No assigned EC number	0.5217	0.9698	0.9817	yes	no
Q7NXI6	RRAAH_CHRVO	No assigned EC number	0.4937	0.9277	0.9685	yes	no
A6V753	RRAAH_PSEA7	No assigned EC number	0.5031	0.9397	0.9629	yes	no
C1D7M1	RRAAH_LARHH	No assigned EC number	0.5032	0.9036	0.9433	yes	no
Q9M8R9	RRAA1_ARATH	No assigned EC number	0.8433	1.0	1.0	yes	no
Q3JQZ3	RRAAH_BURP1	No assigned EC number	0.5443	0.9518	0.9575	yes	no
A3MKY3	RRAAH_BURM7	No assigned EC number	0.5443	0.9518	0.9575	yes	no
Q2SX33	RRAAH_BURTA	No assigned EC number	0.5432	0.9759	0.9818	yes	no
Q0K9J4	RRAA_CUPNH	No assigned EC number	0.5220	0.9578	0.9636	yes	no
Q2SK70	RRAAH_HAHCH	No assigned EC number	0.4596	0.9397	0.9512	yes	no
Q883Q6	RRAAH_PSESM	No assigned EC number	0.4720	0.9397	0.9629	yes	no
Q62J86	RRAAH_BURMA	No assigned EC number	0.5443	0.9518	0.9575	yes	no
Q607E7	RRAAH_METCA	No assigned EC number	0.4687	0.9457	0.9751	yes	no
Q9FH13	RRAA3_ARATH	No assigned EC number	0.7168	1.0	1.0	no	no
Q9I2W7	RRAAH_PSEAE	No assigned EC number	0.5031	0.9397	0.9629	yes	no
B3R2J3	RRAAH_CUPTR	No assigned EC number	0.5187	0.9638	0.9696	yes	no
C3K0T6	RRAAH_PSEFS	No assigned EC number	0.4879	0.9698	0.9877	yes	no
Q4KFJ3	RRAAH_PSEF5	No assigned EC number	0.4879	0.9698	0.9877	yes	no
Q5P203	RRAAH_AROAE	No assigned EC number	0.4716	0.9277	0.9685	yes	no
A5W6M0	RRAAH_PSEP1	No assigned EC number	0.4819	0.9698	0.9877	yes	no
Q9FFE0	RRAA2_ARATH	No assigned EC number	0.8554	1.0	1.0	yes	no
Q21X23	RRAAH_RHOFD	No assigned EC number	0.4464	0.9578	0.9190	yes	no
Q8XZP1	RRAAH_RALSO	No assigned EC number	0.5092	0.9819	0.9878	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	166
TIGR01935	150	TIGR01935, NOT-MenG, RraA famliy	1e-80
PRK09372	159	PRK09372, PRK09372, ribonuclease activity regulato	3e-80
PRK12487	163	PRK12487, PRK12487, ribonuclease activity regulato	4e-51
COG0684	210	COG0684, MenG, Demethylmenaquinone methyltransfera	3e-50
pfam03737	154	pfam03737, Methyltransf_6, Demethylmenaquinone met	5e-46
TIGR02998	161	TIGR02998, RraA_entero, regulator of ribonuclease	4e-44
PRK06201	221	PRK06201, PRK06201, hypothetical protein; Validate	2e-21
PRK07028	430	PRK07028, PRK07028, bifunctional hexulose-6-phosph	1e-13
PRK12764	500	PRK12764, PRK12764, hypothetical protein; Provisio	3e-08
PRK08245	240	PRK08245, PRK08245, hypothetical protein; Validate	3e-06
TIGR02798	222	TIGR02798, ligK_PcmE, 4-carboxy-4-hydroxy-2-oxoadi	0.001

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

 Score =  234 bits (600), Expect = 1e-80
 Identities = 88/155 (56%), Positives = 113/155 (72%), Gaps = 5/155 (3%)

Query: 6   TAEVCDANPQLIVSGELRALQPIFQIYGRRQVFSGPIVTLKVFEDNVLIREFLEEKGNGR 65
           T ++CDA P  +     R L+P+F+ +G R  F+GPIVT+K FEDN L+RE LE+ G GR
Sbjct: 1   TPDLCDAYPDKV-----RVLEPMFRNFGGRAAFAGPIVTVKCFEDNSLVREVLEQPGAGR 55

Query: 66  VLVVDGGGSLRCAILGGNPVVQAQNNGWAGIVVNGCIRDVDEINGCDIGVRALASHPMKA 125
           VLVVDGGGSLRCA+LG N  V A+ NGW G++VNGC+RDV E+ G D+GV+ALA+HP K 
Sbjct: 56  VLVVDGGGSLRCALLGDNLAVLAEENGWEGVIVNGCVRDVAELAGMDLGVKALAAHPRKT 115

Query: 126 NKKGIGEKHVPITIGGTRISDGEWLYADTDGILIS 160
            K+G GE  VP+T  G     G++LYAD DGIL+S
Sbjct: 116 EKRGAGEVDVPVTFAGVTFVPGDYLYADEDGILVS 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|236487 PRK09372, PRK09372, ribonuclease activity regulator protein RraA; Provisional

 Score =  234 bits (599), Expect = 3e-80
 Identities = 83/160 (51%), Positives = 113/160 (70%), Gaps = 5/160 (3%)

Query: 6   TAEVCDANPQLIVSGELRALQPIFQIYGRRQVFSGPIVTLKVFEDNVLIREFLEEKGNGR 65
           T+++CD  P      ++R ++P+F  +G R  F GPI T+K FEDN L++E LEE G GR
Sbjct: 5   TSDLCDIYPD-----DVRVVEPLFSSFGGRSSFGGPITTVKCFEDNGLVKELLEEPGEGR 59

Query: 66  VLVVDGGGSLRCAILGGNPVVQAQNNGWAGIVVNGCIRDVDEINGCDIGVRALASHPMKA 125
           VLVVDGGGSLR A++G N    A +NGW GIVV GC+RDVDE+   DIG++ALA+ P+K+
Sbjct: 60  VLVVDGGGSLRRALVGDNLAELAVDNGWEGIVVYGCVRDVDELAELDIGIQALAAIPVKS 119

Query: 126 NKKGIGEKHVPITIGGTRISDGEWLYADTDGILISRAELS 165
           +K+GIGE+ VP+  GG     G++LYAD DGI++S   L 
Sbjct: 120 DKEGIGERDVPVNFGGVTFFPGDYLYADNDGIIVSPEPLD 159

Length = 159

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

 Score =  160 bits (407), Expect = 4e-51
 Identities = 68/162 (41%), Positives = 100/162 (61%), Gaps = 5/162 (3%)

Query: 5   TTAEVCDANPQLIVSGELRALQPIFQIYGRRQVFSGPIVTLKVFEDNVLIREFLEEKGNG 64
              ++ D         +L  L   F+ +G +++F G IVT++ FEDN  ++E L + G G
Sbjct: 4   LLPDLFDHYED-----KLTLLNLPFKNFGGKRIFWGEIVTVRCFEDNSKVKEVLAQDGKG 58

Query: 65  RVLVVDGGGSLRCAILGGNPVVQAQNNGWAGIVVNGCIRDVDEINGCDIGVRALASHPMK 124
           +VLVVDGGGS R A+LG      A +NGW GIV+NGC+RDV  ++  D+GV+AL + P+K
Sbjct: 59  KVLVVDGGGSCRRALLGDQIAQSALDNGWEGIVINGCVRDVGALSTMDLGVKALGASPIK 118

Query: 125 ANKKGIGEKHVPITIGGTRISDGEWLYADTDGILISRAELSV 166
             K+G GE +V +T+G   I  G+ LYAD +GI +S+  L  
Sbjct: 119 TEKRGQGEVNVTLTMGNVIIEPGDMLYADENGIAVSKEALDF 160

Length = 163

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

 Score =  160 bits (406), Expect = 3e-50
 Identities = 66/159 (41%), Positives = 95/159 (59%)

Query: 6   TAEVCDANPQLIVSGELRALQPIFQIYGRRQVFSGPIVTLKVFEDNVLIREFLEEKGNGR 65
           T ++CDA       G +  + P  + +G R  F GP VT++ F D+ L+   LE+ G G 
Sbjct: 13  TLDLCDAATVSDALGRVGVVDPGIRPFGGRSSFVGPAVTVRCFPDDWLLHVALEQAGPGD 72

Query: 66  VLVVDGGGSLRCAILGGNPVVQAQNNGWAGIVVNGCIRDVDEINGCDIGVRALASHPMKA 125
           VLV+DGGG LR A+ G      A+  GWAG+V++G +RDVDE+   D  V A    P  A
Sbjct: 73  VLVIDGGGDLRRALWGDLLATLAKVRGWAGVVIDGAVRDVDELRELDFPVFARGVTPRGA 132

Query: 126 NKKGIGEKHVPITIGGTRISDGEWLYADTDGILISRAEL 164
            K+GIGE +VP+T GG  ++ G+ + AD DG+++  AEL
Sbjct: 133 TKRGIGEVNVPVTCGGVTVNPGDIVVADADGVVVVPAEL 171

Length = 210

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

 Score =  147 bits (373), Expect = 5e-46
 Identities = 70/155 (45%), Positives = 98/155 (63%), Gaps = 6/155 (3%)

Query: 6   TAEVCDANPQLIVSGELRALQPIFQIYGRRQVFSGPIVTLKVFE-DNVLIREFLEEKGNG 64
           T ++CDA         +  ++PI   +G R  F GP VT++  E DN L+RE L++ G G
Sbjct: 5   TPDLCDAYGSQ-----VGVVEPILSNFGGRSSFVGPAVTVRCSEIDNGLVREVLDQAGPG 59

Query: 65  RVLVVDGGGSLRCAILGGNPVVQAQNNGWAGIVVNGCIRDVDEINGCDIGVRALASHPMK 124
           RVLVVDGGGSLR A+ G      A+ NGW G+VV GC+RDVD +   D+ + AL + P  
Sbjct: 60  RVLVVDGGGSLRRALWGDLLSTLAKKNGWEGVVVYGCVRDVDALRELDLPIFALGTTPCA 119

Query: 125 ANKKGIGEKHVPITIGGTRISDGEWLYADTDGILI 159
           A K GIGE +VP+T GG  +  G+++YAD +GI++
Sbjct: 120 AVKTGIGEVNVPVTCGGVTVRPGDYIYADNNGIVV 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|132043 TIGR02998, RraA_entero, regulator of ribonuclease activity A

 Score =  142 bits (360), Expect = 4e-44
 Identities = 68/161 (42%), Positives = 98/161 (60%), Gaps = 5/161 (3%)

Query: 6   TAEVCDANPQLIVSGELRALQPIFQIYGRRQVFSGPIVTLKVFEDNVLIREFLEEKGNGR 65
           T+E+CD       +  +  ++PIF  +G R  F G +VT+K FE N LI E LE+ G GR
Sbjct: 5   TSELCD-----FYADLVDVVEPIFSNFGGRSSFGGKVVTVKCFEHNGLINELLEQNGTGR 59

Query: 66  VLVVDGGGSLRCAILGGNPVVQAQNNGWAGIVVNGCIRDVDEINGCDIGVRALASHPMKA 125
           VLV+DGGGS R A++       A NNGW GIVV G +R VD +   DIG++ALA+ P+ A
Sbjct: 60  VLVIDGGGSTRRALIDAELAQLAANNGWEGIVVYGAVRQVDALEELDIGIQALAAIPVGA 119

Query: 126 NKKGIGEKHVPITIGGTRISDGEWLYADTDGILISRAELSV 166
           +++GIGE  + +   G      +++YAD  GI++S   L +
Sbjct: 120 DEQGIGESDIAVNFAGVTFFPDDYIYADNTGIILSPEPLEI 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|180465 PRK06201, PRK06201, hypothetical protein; Validated

 Score = 86.5 bits (215), Expect = 2e-21
 Identities = 44/135 (32%), Positives = 68/135 (50%), Gaps = 2/135 (1%)

Query: 32  YGRRQVFSGPIVTLKVFE-DNVLIREFLEEKGNGRVLVVDGGGSLRCAILGGNPVVQAQN 90
             R    +G  +T++    DN++I   L+    G V+VVDGGG L  A++G   +  A  
Sbjct: 47  MHRGGRLAGTALTVRTRPGDNLMIHRALDLARPGDVIVVDGGGDLTNALVGEIMLAIAAR 106

Query: 91  NGWAGIVVNGCIRDVDEINGCDIGVRALASHPMKANKKGIGEKHVPITIGGTRISDGEWL 150
            G AG+V++G +RDV  +      V A         K G GE +VP+ IGG  I  G+ +
Sbjct: 107 RGVAGVVIDGAVRDVAALREMGFPVFARGVTHRGPYKDGPGEINVPVAIGGMVIEPGDLI 166

Query: 151 YADTDGIL-ISRAEL 164
             D DG++ +  A+ 
Sbjct: 167 VGDDDGLVAVPPADA 181

Length = 221

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

 Score = 67.0 bits (164), Expect = 1e-13
 Identities = 46/161 (28%), Positives = 73/161 (45%), Gaps = 9/161 (5%)

Query: 4   VTTAEVCDANPQLIVSGELRALQPIFQIYGRRQVFSGPIVTLKVFE-DNVLIREFLEEKG 62
           V+T  + DA   +   G ++ ++P+     R     G  VT++ F  D     E ++   
Sbjct: 236 VSTPNISDA---MHRKGAMKGIKPL----VRGTKMVGKAVTVQTFAGDWAKPVEAIDVAK 288

Query: 63  NGRVLVVDGGGSLRCAILGGNPVVQAQNNGWAGIVVNGCIRDVDEINGCDIGVRALASHP 122
            G V+V+        A  G    +   N G AG+V++G +RDVDEI      V A A  P
Sbjct: 289 PGDVIVIYNSSK-DIAPWGELATLSCLNKGIAGVVIDGAVRDVDEIRKLGFPVFARAIVP 347

Query: 123 MKANKKGIGEKHVPITIGGTRISDGEWLYADTDGILISRAE 163
                KG GE +  I  GG  +  G+W+  D +G+++   E
Sbjct: 348 NAGEPKGFGEINAEIVCGGQTVRPGDWIIGDENGVVVVPKE 388

Length = 430

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

 Score = 51.7 bits (124), Expect = 3e-08
 Identities = 31/108 (28%), Positives = 50/108 (46%), Gaps = 11/108 (10%)

Query: 58  LEEKGNGRVLVVDGGGSLRCAILGGNPVVQAQNNGWAGIVVNGCIRDVDEINGCDIGVRA 117
            +    G VLV++  G      LG    ++AQ  G AG+V +G +RD   +    + V  
Sbjct: 340 FDSVNPGEVLVIEARGEKGTGTLGDILALRAQVRGAAGVVTDGGVRDYAAVAELGLPVFF 399

Query: 118 LASHPMKANKKGIGEKHVP----ITI--GGTRISDGEWLYADTDGILI 159
              HP       +G +HVP    IT+  GG  +  G+ +  D DG+++
Sbjct: 400 AGPHPAV-----LGRRHVPWDVDITVACGGATVQPGDVIVGDDDGVVV 442

Length = 500

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

 Score = 45.3 bits (108), Expect = 3e-06
 Identities = 35/118 (29%), Positives = 48/118 (40%), Gaps = 18/118 (15%)

Query: 55  REFLEEKGNGRVLVVDGGGSLRCAILGGNPVVQAQNNGWAGIVVNGCIRDVDEINGCDI- 113
           R  +E    G VLVVD  G  R    G     + +  G AG+V +G +RD   I    + 
Sbjct: 79  RAAIETCPPGCVLVVDARGDARAGSFGDILCTRLKKRGVAGLVTDGGVRDSPGIAALGLP 138

Query: 114 ----GVRA---LASH-PMKANKKGIGEKHVPITIGGTRISDGEWLYADTDG-ILISRA 162
               G  A   L     +  N        VPI  GG  +  G+ + AD DG ++I  A
Sbjct: 139 VWCAGPSAPTNLTGLTAVDIN--------VPIGCGGVAVFPGDIIVADDDGVVVIPAA 188

Length = 240

>gnl|CDD|131845 TIGR02798, ligK_PcmE, 4-carboxy-4-hydroxy-2-oxoadipate aldolase/oxaloacetate decarboxylase

 Score = 37.5 bits (87), Expect = 0.001
 Identities = 31/143 (21%), Positives = 61/143 (42%), Gaps = 5/143 (3%)

Query: 25  LQPIFQIYGRRQVFSGPIVTLKVFE-DNVLIREFLEEKGNGRVLVVDGGGSLRCAILGGN 83
           ++PI+   G R    G  VT+ +   DN ++    E+   G V+V            G  
Sbjct: 40  MRPIYT--GAR--VCGTAVTVLLQPGDNWMMHVAAEQIQEGDVVVAACTAECEDGYFGDL 95

Query: 84  PVVQAQNNGWAGIVVNGCIRDVDEINGCDIGVRALASHPMKANKKGIGEKHVPITIGGTR 143
                Q  G  G++++  +RDV ++   +  V + A H     K  +G  ++P+      
Sbjct: 96  LATSFQARGCRGLIIDAGVRDVRDLTEMNFPVWSKAIHAKGTVKATLGSVNIPVVCANAL 155

Query: 144 ISDGEWLYADTDGILISRAELSV 166
           ++ G+ + AD DG+++     + 
Sbjct: 156 VNPGDVVVADDDGVVVVPRANAG 178

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. Length = 222

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	166
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
TIGR01935	150	NOT-MenG RraA famliy. This model was initially cla	100.0
PRK06201	221	hypothetical protein; Validated	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=1.2e-53  Score=331.14  Aligned_cols=158  Identities=43%  Similarity=0.791  Sum_probs=152.8

Q ss_pred             CCchhhHhhhccCCccCCeeeeccccccccCCCeeEEEEEEEEEeecCcHHHHHHHhhcCCCcEEEEeCCCCCccceech
Q 031066            3 LVTTAEVCDANPQLIVSGELRALQPIFQIYGRRQVFSGPIVTLKVFEDNVLIREFLEEKGNGRVLVVDGGGSLRCAILGG   82 (166)
Q Consensus         3 ~~~t~~v~Da~~~~~~~g~~~~l~p~~~~~~~~~~~~G~A~Tv~~~~d~~~~~~~i~~~~~G~VlVvd~~g~~~~a~~G~   82 (166)
                      ++.|++|||++.+     .++.++|.|++||+.++++|+|+||++.+||..++++|++++||||||||++++.++|+|||
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            5899999999988     47899999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHcCCcEEEeeCccCCHHHHhcCCccEEEeeeecCCCCCccceeeeeeEEECCEEEccCCEEEEeCCceEEecC
Q 031066           83 NPVVQAQNNGWAGIVVNGCIRDVDEINGCDIGVRALASHPMKANKKGIGEKHVPITIGGTRISDGEWLYADTDGILISRA  162 (166)
Q Consensus        83 ~~a~~a~~~G~~G~VidG~vRD~~~i~~~~~pv~a~g~~p~~~~~~~~~~~~~pV~igGv~V~pGD~i~aD~dGVvviP~  162 (166)
                      +++++|++||++|+|+||++||++||++++|||||++++|.++.+...+++|+||+|+|++|+|||+|+||.|||+|||+
T Consensus        77 ~la~~a~~~G~aGvVidG~vRD~~~i~~l~~PVfa~g~~p~~~~~~~~g~~nvpV~iggv~V~PGD~IvaD~DGVvVip~  156 (161)
T TIGR02998        77 ELAQLAANNGWEGIVVYGAVRQVDALEELDIGIQALAAIPVGADEQGIGESDIAVNFAGVTFFPDDYIYADNTGIILSPE  156 (161)
T ss_pred             HHHHHHHHCCCeEEEEeecccCHHHHhhCCCCcEEeeccCCCCCCCCcceeCCCEEECCEEECCCCEEEEcCCcEEEECc
Confidence            99999999999999999999999999999999999999999888888999999999999999999999999999999999


Q ss_pred             ccC
Q 031066          163 ELS  165 (166)
Q Consensus       163 ~l~  165 (166)
                      +|+
T Consensus       157 ~~~  159 (161)
T TIGR02998       157 PLE  159 (161)
T ss_pred             ccc
Confidence            985

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=3.8e-51  Score=316.86  Aligned_cols=158  Identities=53%  Similarity=0.982  Sum_probs=148.3

Q ss_pred             CCchhhHhhhccCCccCCeeeeccccccccCCCeeEEEEEEEEEeecCcHHHHHHHhhcCCCcEEEEeCCCCCccceech
Q 031066            3 LVTTAEVCDANPQLIVSGELRALQPIFQIYGRRQVFSGPIVTLKVFEDNVLIREFLEEKGNGRVLVVDGGGSLRCAILGG   82 (166)
Q Consensus         3 ~~~t~~v~Da~~~~~~~g~~~~l~p~~~~~~~~~~~~G~A~Tv~~~~d~~~~~~~i~~~~~G~VlVvd~~g~~~~a~~G~   82 (166)
                      +++|++|||++..     .++.+.|.++++++.++++|+|+||++.+||...++++++++||||||||+.++.+.|+|||
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            6899999999775     24567777877888899999999999999999999999999999999999999889999999


Q ss_pred             HHHHHHHHcCCcEEEeeCccCCHHHHhcCCccEEEeeeecCCCCCccceeeeeeEEECCEEEccCCEEEEeCCceEEecC
Q 031066           83 NPVVQAQNNGWAGIVVNGCIRDVDEINGCDIGVRALASHPMKANKKGIGEKHVPITIGGTRISDGEWLYADTDGILISRA  162 (166)
Q Consensus        83 ~~a~~a~~~G~~G~VidG~vRD~~~i~~~~~pv~a~g~~p~~~~~~~~~~~~~pV~igGv~V~pGD~i~aD~dGVvviP~  162 (166)
                      +++++|+++|++|+|+||++||++||++++|||||++++|.++.+...+++|+||+|+|++|+|||+|+||.|||+|||+
T Consensus        77 ~~~~~a~~~G~~G~VidG~vRD~~~i~~~~~Pvfa~g~~p~~~~~~~~~~~n~pV~iggv~V~PGD~I~aD~dGVvviP~  156 (159)
T PRK09372         77 NLAELAVDNGWEGIVVYGCVRDVDELAELDIGIQALAAIPVKSDKEGIGERDVPVNFGGVTFFPGDYLYADNDGIIVSPE  156 (159)
T ss_pred             HHHHHHHHcCCeEEEecccccCHHHHhhCCCCeEEeeecCCCCCCCCccEecccEEECCEEECCCCEEEEcCCCEEEECC
Confidence            99999999999999999999999999999999999999999887778999999999999999999999999999999999


Q ss_pred             ccC
Q 031066          163 ELS  165 (166)
Q Consensus       163 ~l~  165 (166)
                      +|.
T Consensus       157 ~l~  159 (159)
T PRK09372        157 PLD  159 (159)
T ss_pred             cCC
Confidence            984

>PRK12487 ribonuclease activity regulator protein RraA; Reviewed

Probab=100.00  E-value=3.6e-51  Score=317.75  Aligned_cols=158  Identities=44%  Similarity=0.797  Sum_probs=150.1

Q ss_pred             CCchhhHhhhccCCccCCeeeeccccccccCCCeeEEEEEEEEEeecCcHHHHHHHhhcCCCcEEEEeCCCCCccceech
Q 031066            3 LVTTAEVCDANPQLIVSGELRALQPIFQIYGRRQVFSGPIVTLKVFEDNVLIREFLEEKGNGRVLVVDGGGSLRCAILGG   82 (166)
Q Consensus         3 ~~~t~~v~Da~~~~~~~g~~~~l~p~~~~~~~~~~~~G~A~Tv~~~~d~~~~~~~i~~~~~G~VlVvd~~g~~~~a~~G~   82 (166)
                      .+.|++|||.+.+     .++.+.|.++++++.++++|+|+||++.+|+..+++++++++||||||||++++.++|+|||
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     46778888999988899999999999998999999999999999999999999899999999


Q ss_pred             HHHHHHHHcCCcEEEeeCccCCHHHHhcCCccEEEeeeecCCCCCccceeeeeeEEECCEEEccCCEEEEeCCceEEecC
Q 031066           83 NPVVQAQNNGWAGIVVNGCIRDVDEINGCDIGVRALASHPMKANKKGIGEKHVPITIGGTRISDGEWLYADTDGILISRA  162 (166)
Q Consensus        83 ~~a~~a~~~G~~G~VidG~vRD~~~i~~~~~pv~a~g~~p~~~~~~~~~~~~~pV~igGv~V~pGD~i~aD~dGVvviP~  162 (166)
                      +++++|+++|++|+|+||++||++||++++|||||++++|.++.+...+++|+||+|+|++|+|||+|+||+|||+|||+
T Consensus        77 ~~a~~a~~~G~aG~VidG~vRD~~~i~~l~fPVfa~g~~p~~~~~~~~~~~nvPV~iggv~V~PGDiI~aD~dGVvvip~  156 (163)
T PRK12487         77 QIAQSALDNGWEGIVINGCVRDVGALSTMDLGVKALGASPIKTEKRGQGEVNVTLTMGNVIIEPGDMLYADENGIAVSKE  156 (163)
T ss_pred             HHHHHHHHCCCeEEEEeecccCHHHHhhCCCCeEEeecCCCCCCCCCcceecccEEECCEEECCCCEEEEcCCCEEEECc
Confidence            99999999999999999999999999999999999999999887778899999999999999999999999999999999


Q ss_pred             ccC
Q 031066          163 ELS  165 (166)
Q Consensus       163 ~l~  165 (166)
                      +|+
T Consensus       157 ~l~  159 (163)
T PRK12487        157 ALD  159 (163)
T ss_pred             hhh
Confidence            985

>TIGR01935 NOT-MenG RraA famliy

Probab=100.00  E-value=6.7e-50  Score=307.21  Aligned_cols=150  Identities=59%  Similarity=1.106  Sum_probs=144.3

Q ss_pred             hhhHhhhccCCccCCeeeeccccccccCCCeeEEEEEEEEEeecCcHHHHHHHhhcCCCcEEEEeCCCCCccceechHHH
Q 031066            6 TAEVCDANPQLIVSGELRALQPIFQIYGRRQVFSGPIVTLKVFEDNVLIREFLEEKGNGRVLVVDGGGSLRCAILGGNPV   85 (166)
Q Consensus         6 t~~v~Da~~~~~~~g~~~~l~p~~~~~~~~~~~~G~A~Tv~~~~d~~~~~~~i~~~~~G~VlVvd~~g~~~~a~~G~~~a   85 (166)
                      |++|||.+.+     .++.++|.|++|++.++++|+|+||++.+|+..++++|++++||||||||+.++.+.|+|||+++
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            7899999987     47889999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHcCCcEEEeeCccCCHHHHhcCCccEEEeeeecCCCCCccceeeeeeEEECCEEEccCCEEEEeCCceEEe
Q 031066           86 VQAQNNGWAGIVVNGCIRDVDEINGCDIGVRALASHPMKANKKGIGEKHVPITIGGTRISDGEWLYADTDGILIS  160 (166)
Q Consensus        86 ~~a~~~G~~G~VidG~vRD~~~i~~~~~pv~a~g~~p~~~~~~~~~~~~~pV~igGv~V~pGD~i~aD~dGVvvi  160 (166)
                      ++|+++|++|+|+||++||++||++++|||||++++|.++.+...+++|+||+|+|++|+|||+|+||.|||+|.
T Consensus        76 ~~a~~~G~~G~VidG~vRD~~~i~~~~~Pvfa~g~~p~~~~~~~~~~~nvPV~igGv~V~PGD~IvaD~dGVvv~  150 (150)
T TIGR01935        76 VLAEENGWEGVIVNGCVRDVAELAGMDLGVKALAAHPRKTEKRGAGEVDVPVTFAGVTFVPGDYLYADEDGILVS  150 (150)
T ss_pred             HHHHHCCCEEEEEeecccCHHHHhhCCCCEEEeeecCCCCCCCcceEecceEEECCEEECCCCEEEEcCCCEEEC
Confidence            999999999999999999999999999999999999998888889999999999999999999999999999984

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.

>PRK06201 hypothetical protein; Validated

Probab=100.00  E-value=6.9e-49  Score=318.65  Aligned_cols=157  Identities=30%  Similarity=0.488  Sum_probs=143.0

Q ss_pred             CCCchhhHhhhccCCccCCeeeeccccccccCCCeeEEEEEEEEEeec-CcHHHHHHHhhcCCCcEEEEeCCCCCcccee
Q 031066            2 ALVTTAEVCDANPQLIVSGELRALQPIFQIYGRRQVFSGPIVTLKVFE-DNVLIREFLEEKGNGRVLVVDGGGSLRCAIL   80 (166)
Q Consensus         2 ~~~~t~~v~Da~~~~~~~g~~~~l~p~~~~~~~~~~~~G~A~Tv~~~~-d~~~~~~~i~~~~~G~VlVvd~~g~~~~a~~   80 (166)
                      ++++|++|||+|++++..  ...++|++    +.++++|+|+|+++.+ |+..+++++++++||||||||+.++.++|+|
T Consensus        23 ~~l~t~~v~Dal~~~g~~--~~~i~p~~----~~~~~~G~A~Tv~~~~~d~~~~~~ai~~~~pG~VlVid~~g~~~~a~~   96 (221)
T PRK06201         23 RELPVANISDSMNRMTAG--GAGLRPMH----RGGRLAGTALTVRTRPGDNLMIHRALDLARPGDVIVVDGGGDLTNALV   96 (221)
T ss_pred             hcCCchHHHHHHcccCCC--cccceecC----CCCEEEEEEEEEEeeCCCcHHHHHHHhccCCCcEEEEECCCCCCccch
Confidence            578999999999986421  23455544    4579999999999996 7889999999999999999999999999999


Q ss_pred             chHHHHHHHHcCCcEEEeeCccCCHHHHhcCCccEEEeeeecCCCCCccceeeeeeEEECCEEEccCCEEEEeCCceEEe
Q 031066           81 GGNPVVQAQNNGWAGIVVNGCIRDVDEINGCDIGVRALASHPMKANKKGIGEKHVPITIGGTRISDGEWLYADTDGILIS  160 (166)
Q Consensus        81 G~~~a~~a~~~G~~G~VidG~vRD~~~i~~~~~pv~a~g~~p~~~~~~~~~~~~~pV~igGv~V~pGD~i~aD~dGVvvi  160 (166)
                      ||+++++|+++|++|+|+||++||++||++++|||||+|++|.++.+...+++|+||+|||++|+|||+|+||.|||+||
T Consensus        97 G~~~a~~a~~~G~~G~VidG~vRD~~~i~~~~fPvfa~g~~p~~~~~~~~~~~n~pV~igGv~V~PGD~I~aD~dGVvvi  176 (221)
T PRK06201         97 GEIMLAIAARRGVAGVVIDGAVRDVAALREMGFPVFARGVTHRGPYKDGPGEINVPVAIGGMVIEPGDLIVGDDDGLVAV  176 (221)
T ss_pred             hHHHHHHHHHCCCeEEEEeeccCCHHHHhhCCCCeEEeccCCCCCCCCCccccCccEEECCEEEcCCCEEEEcCCceEEE
Confidence            99999999999999999999999999999999999999999998766778999999999999999999999999999999


Q ss_pred             cCcc
Q 031066          161 RAEL  164 (166)
Q Consensus       161 P~~l  164 (166)
                      |+++
T Consensus       177 P~~~  180 (221)
T PRK06201        177 PPAD  180 (221)
T ss_pred             cHHH
Confidence            9876

>PRK09262 hypothetical protein; Provisional

Probab=100.00  E-value=2.7e-48  Score=315.84  Aligned_cols=157  Identities=24%  Similarity=0.324  Sum_probs=142.7

Q ss_pred             CCCchhhHhhhccCCccCCeeeeccccccccCCCeeEEEEEEEEEee-cCcHHHHHHHhhcCCCcEEEEeCCCCCcccee
Q 031066            2 ALVTTAEVCDANPQLIVSGELRALQPIFQIYGRRQVFSGPIVTLKVF-EDNVLIREFLEEKGNGRVLVVDGGGSLRCAIL   80 (166)
Q Consensus         2 ~~~~t~~v~Da~~~~~~~g~~~~l~p~~~~~~~~~~~~G~A~Tv~~~-~d~~~~~~~i~~~~~G~VlVvd~~g~~~~a~~   80 (166)
                      ++++|++|||+|++++.-.  ..++|+    .++++++|+|+||++. .|++.++++++.++||||||||+.++.++|+|
T Consensus        21 ~~~~ta~v~Dal~~~g~~~--~~i~p~----~~~~~~~G~A~TV~~~~~d~~~~~~ai~~~~pGdVlVid~~g~~~~a~~   94 (225)
T PRK09262         21 AEFGVATVHEAQGRVGLLK--PYMRPI----YQGARIAGTAVTVLVQPGDNWMMHVAVEQCQPGDVLVVAPTSPCTDGFF   94 (225)
T ss_pred             cCCCCccHHHHhcccCCCC--cceEEC----CCCCeEEEEEEEEEeecCCcHHHHHHHHccCCCCEEEEECCCCCceeee
Confidence            5789999999999864211  234554    3457999999999999 48899999999999999999999999999999


Q ss_pred             chHHHHHHHHcCCcEEEeeCccCCHHHHhcCCccEEEeeeecCCCCCccceeeeeeEEECCEEEccCCEEEEeCCceEEe
Q 031066           81 GGNPVVQAQNNGWAGIVVNGCIRDVDEINGCDIGVRALASHPMKANKKGIGEKHVPITIGGTRISDGEWLYADTDGILIS  160 (166)
Q Consensus        81 G~~~a~~a~~~G~~G~VidG~vRD~~~i~~~~~pv~a~g~~p~~~~~~~~~~~~~pV~igGv~V~pGD~i~aD~dGVvvi  160 (166)
                      ||+++++|+++|++|+|+||++||+++|++++|||||+|++|.++.+...+++|+||+|||++|+|||+|+||.|||+||
T Consensus        95 Ge~~a~~a~~~G~~GiVidG~vRD~~~i~~l~~Pvfa~g~~p~~~~~~~~~~~nvpV~iggv~V~PGD~IvaD~dGVvvI  174 (225)
T PRK09262         95 GDLLATSLQARGVRGLVIDAGVRDVRTLTEMGFPVWSRAISAQGTVKATLGSVNVPVVCAGALVNPGDVVVADDDGVVVV  174 (225)
T ss_pred             hHHHHHHHHHCCCeEEEEeceeCCHHHHhhCCCceEEeecCCCCCCCCCcceecccEEECCEEECCCCEEEEECCcEEEE
Confidence            99999999999999999999999999999999999999999988777778999999999999999999999999999999


Q ss_pred             cCcc
Q 031066          161 RAEL  164 (166)
Q Consensus       161 P~~l  164 (166)
                      |+++
T Consensus       175 P~~~  178 (225)
T PRK09262        175 PRAQ  178 (225)
T ss_pred             CHHH
Confidence            9875

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

Probab=100.00  E-value=2.6e-48  Score=315.31  Aligned_cols=157  Identities=21%  Similarity=0.301  Sum_probs=142.9

Q ss_pred             CCCchhhHhhhccCCccCCeeeeccccccccCCCeeEEEEEEEEEeec-CcHHHHHHHhhcCCCcEEEEeCCCCCcccee
Q 031066            2 ALVTTAEVCDANPQLIVSGELRALQPIFQIYGRRQVFSGPIVTLKVFE-DNVLIREFLEEKGNGRVLVVDGGGSLRCAIL   80 (166)
Q Consensus         2 ~~~~t~~v~Da~~~~~~~g~~~~l~p~~~~~~~~~~~~G~A~Tv~~~~-d~~~~~~~i~~~~~G~VlVvd~~g~~~~a~~   80 (166)
                      ++++|++|||+|++++.-  ...++|+    .++++++|+|+||++.+ ||..+++++++++||||||||+.++.++|+|
T Consensus        19 ~~~~ta~v~Dal~~~g~~--~~~I~p~----~~~~ki~G~A~TV~~~~~d~~~~~~ai~~~~pGdVlVid~~g~~~~a~~   92 (222)
T TIGR02798        19 AAFGVATVHEAMGRVGLL--APYMRPI----YTGARVCGTAVTVLLQPGDNWMMHVAAEQIQEGDVVVAACTAECEDGYF   92 (222)
T ss_pred             hCCCCccHHHHhcccCCC--CccceEc----CCCCEEEEEEEEEEeecCCchHHHHHHHhCCCCeEEEEECCCCcceEee
Confidence            578999999999986531  1234554    34579999999999995 8899999999999999999999998899999


Q ss_pred             chHHHHHHHHcCCcEEEeeCccCCHHHHhcCCccEEEeeeecCCCCCccceeeeeeEEECCEEEccCCEEEEeCCceEEe
Q 031066           81 GGNPVVQAQNNGWAGIVVNGCIRDVDEINGCDIGVRALASHPMKANKKGIGEKHVPITIGGTRISDGEWLYADTDGILIS  160 (166)
Q Consensus        81 G~~~a~~a~~~G~~G~VidG~vRD~~~i~~~~~pv~a~g~~p~~~~~~~~~~~~~pV~igGv~V~pGD~i~aD~dGVvvi  160 (166)
                      ||+++++|+++|++|+|+||++||+++|++++|||||++++|.++.+...+++|+||.|+|++|+|||+|+||.||||||
T Consensus        93 G~~~a~~a~~~G~~GiVidG~vRD~~~i~~l~~Pvfa~g~~p~~~~~~~~~~~nvpv~iggv~V~PGD~i~aD~dGVvvi  172 (222)
T TIGR02798        93 GDLLATSFQARGCRGLIIDAGVRDVRDLTEMNFPVWSKAIHAKGTVKATLGSVNIPVVCANALVNPGDVVVADDDGVVVV  172 (222)
T ss_pred             hHHHHHHHHHCCCeEEEEecccCCHHHHhhCCCceEEeecCCCCCCCCCccccCCCEEECCEEECCCCEEEEcCCcEEEE
Confidence            99999999999999999999999999999999999999999988777788999999999999999999999999999999


Q ss_pred             cCcc
Q 031066          161 RAEL  164 (166)
Q Consensus       161 P~~l  164 (166)
                      |+++
T Consensus       173 P~~~  176 (222)
T TIGR02798       173 PRAN  176 (222)
T ss_pred             cHHH
Confidence            9875

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=1.7e-48  Score=312.66  Aligned_cols=159  Identities=42%  Similarity=0.725  Sum_probs=143.3

Q ss_pred             hhhHhhhccCCccCCeeeeccccccccCCCeeEEEEEEEEEeecCcHHHHHHHhhcCCCcEEEEeCCCCCccceechHHH
Q 031066            6 TAEVCDANPQLIVSGELRALQPIFQIYGRRQVFSGPIVTLKVFEDNVLIREFLEEKGNGRVLVVDGGGSLRCAILGGNPV   85 (166)
Q Consensus         6 t~~v~Da~~~~~~~g~~~~l~p~~~~~~~~~~~~G~A~Tv~~~~d~~~~~~~i~~~~~G~VlVvd~~g~~~~a~~G~~~a   85 (166)
                      |.++||++....-.+....+.|.++++++.++|+|+|+||||.++|+..+.+|++++||||||||+.++.++|+||++++
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            55666665543222233445567777787889999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHcCCcEEEeeCccCCHHHHhcCCccEEEeeeecCCCCCccceeeeeeEEECCEEEccCCEEEEeCCceEEecCcc
Q 031066           86 VQAQNNGWAGIVVNGCIRDVDEINGCDIGVRALASHPMKANKKGIGEKHVPITIGGTRISDGEWLYADTDGILISRAEL  164 (166)
Q Consensus        86 ~~a~~~G~~G~VidG~vRD~~~i~~~~~pv~a~g~~p~~~~~~~~~~~~~pV~igGv~V~pGD~i~aD~dGVvviP~~l  164 (166)
                      +.|+.|||+|+|+||+|||++++++|+||+||++++|.++.+...+++|+||+|||++|+|||||+||+|||||+|+++
T Consensus        93 ~~a~~~G~~GvVidG~vRDv~~l~el~~pv~a~~~~p~~~~k~~~geinvpV~~gGv~v~PGD~vvgD~dGvVVvp~~~  171 (210)
T COG0684          93 TLAKVRGWAGVVIDGAVRDVDELRELDFPVFARGVTPRGATKRGIGEVNVPVTCGGVTVNPGDIVVADADGVVVVPAEL  171 (210)
T ss_pred             HHHHHcCccEEEEeceeechHHHhhcCCCeEeccccCCCCCcCCcceecccEEECCEEECCCCEEEEcCCceEEeccch
Confidence            9999999999999999999999999999999999999999999999999999999999999999999999999999876

>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=5.6e-48  Score=297.82  Aligned_cols=152  Identities=38%  Similarity=0.682  Sum_probs=135.4

Q ss_pred             CCchhhHhhhccCCccCCeeeeccccccccCCCeeEEEEEEEEEeec-CcHHHHHHHhhcCCCcEEEEeCCCCCccceec
Q 031066            3 LVTTAEVCDANPQLIVSGELRALQPIFQIYGRRQVFSGPIVTLKVFE-DNVLIREFLEEKGNGRVLVVDGGGSLRCAILG   81 (166)
Q Consensus         3 ~~~t~~v~Da~~~~~~~g~~~~l~p~~~~~~~~~~~~G~A~Tv~~~~-d~~~~~~~i~~~~~G~VlVvd~~g~~~~a~~G   81 (166)
                      .++|++|||+|++.     ++.+.|.++++.+.++++|||+|+++.+ ++...+++++.++||+|||+|+.++.+.|+||
T Consensus         2 ~i~ta~l~Dal~~~-----~~~~~~~~~~~~~~~~~~G~A~Tv~~~~~~~~~~~~~i~~~~~G~VlVid~~~~~~~a~~G   76 (154)
T PF03737_consen    2 NISTADLCDALGKR-----LGGMNPIIRPLPPGMKIVGPAVTVRFAPGDNLLVREAIDAAPPGDVLVIDGGGDTDCAVWG   76 (154)
T ss_dssp             HCHHHHHHHHHGGT-----SEEEESTSEESSSCSSEEEEEEEEEESSTBSHHHHHHHTSS-TTEEEEEEETTGSSSEEE-
T ss_pred             ccchhhHhHCcccc-----cCEeccccccCCCCCEEEEEEEEEEEECCCCHHHHHHHhcCCCCeEEEEECCCCcceeeEC
Confidence            37899999999852     3445565555677899999999999998 88999999999999999999999988999999


Q ss_pred             hHHHHHHHHcCCcEEEeeCccCCHHHHhcCCccEEEeeeecCCCCCccceeeeeeEEECCEEEccCCEEEEeCCceEE
Q 031066           82 GNPVVQAQNNGWAGIVVNGCIRDVDEINGCDIGVRALASHPMKANKKGIGEKHVPITIGGTRISDGEWLYADTDGILI  159 (166)
Q Consensus        82 ~~~a~~a~~~G~~G~VidG~vRD~~~i~~~~~pv~a~g~~p~~~~~~~~~~~~~pV~igGv~V~pGD~i~aD~dGVvv  159 (166)
                      |+++++|+++|++|+|+||++||++||++++||+||+|++|.++.+...+++|+||+|+|++|+|||+|+||.|||||
T Consensus        77 ~~~a~~a~~~G~~G~VidG~vRD~~~i~~~~~Pvfa~g~~p~~~~~~~~~~~~~pv~~gGv~V~pGD~I~aD~dGVvV  154 (154)
T PF03737_consen   77 ELMATAAKARGVAGVVIDGAVRDVDEIRELGFPVFARGTTPRGGKKRGVGEINVPVTIGGVTVNPGDIIVADDDGVVV  154 (154)
T ss_dssp             HHHHHHHHHTTBSEEEEEEEES-HHHHTTSSSEEEEEEE-SSBTBCSSESEESSEEEETTEEE-TTSEEEEETTEEEE
T ss_pred             HHHHHHHHHCCCeEEECCCcccCHHHHhhcCCCeEecccCcccCcceeeeeeCCeEEECCEEECCCCEEEECCCcEEC
Confidence            999999999999999999999999999999999999999999888888999999999999999999999999999997

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=1.7e-47  Score=313.89  Aligned_cols=161  Identities=26%  Similarity=0.350  Sum_probs=142.7

Q ss_pred             CCCCchhhHhhhccCCcc-CCeeeeccccccccCCCeeEEEEEEEEEeec-Cc------------HHHHHHHhhcCCCcE
Q 031066            1 MALVTTAEVCDANPQLIV-SGELRALQPIFQIYGRRQVFSGPIVTLKVFE-DN------------VLIREFLEEKGNGRV   66 (166)
Q Consensus         1 ~~~~~t~~v~Da~~~~~~-~g~~~~l~p~~~~~~~~~~~~G~A~Tv~~~~-d~------------~~~~~~i~~~~~G~V   66 (166)
                      +++++|++|||+|++++. .+++..++|+++   +..+++|+|+||++.+ ++            ..++++|+.++||||
T Consensus        14 l~~l~t~~v~Dal~~~g~~~~~~~~i~pl~p---~~~~~~G~A~TV~~~p~~~~~~~~~~~~~~~~~~~~aid~~~~GdV   90 (240)
T PRK08245         14 LKRVSTATLTTALFKRGLRNQFIRGVRPLRP---GGPRMVGPAFTLRFVPAREDLNTPESFADPESPQRAAIETCPPGCV   90 (240)
T ss_pred             HhcCChhHHHHHHHhcCCccccCCCceecCC---CCCeEEEEEEEEEeecCCCcccccccccccchhHHHHHhccCCCeE
Confidence            357999999999999874 445566777654   1248999999999985 21            237899999999999


Q ss_pred             EEEeCCCCCccceechHHHHHHHHcCCcEEEeeCccCCHHHHhcCCccEEEeeeecCCCC-CccceeeeeeEEECCEEEc
Q 031066           67 LVVDGGGSLRCAILGGNPVVQAQNNGWAGIVVNGCIRDVDEINGCDIGVRALASHPMKAN-KKGIGEKHVPITIGGTRIS  145 (166)
Q Consensus        67 lVvd~~g~~~~a~~G~~~a~~a~~~G~~G~VidG~vRD~~~i~~~~~pv~a~g~~p~~~~-~~~~~~~~~pV~igGv~V~  145 (166)
                      ||||+.+..+.|+|||+++++|+++|++|+|+||++||++||++++|||||+|++|.++. +...+++|+||+|||++|+
T Consensus        91 lVid~~g~~~~a~~G~~~~~~a~~~G~~G~VidG~vRD~~ei~~~gfPvfarg~~p~~~~~~~~~~~~nvPV~igGv~V~  170 (240)
T PRK08245         91 LVVDARGDARAGSFGDILCTRLKKRGVAGLVTDGGVRDSPGIAALGLPVWCAGPSAPTNLTGLTAVDINVPIGCGGVAVF  170 (240)
T ss_pred             EEEECCCCCCccccHHHHHHHHHHCCCeEEEEeeccCCHHHHhhCCCceEecccCCCCCCCCCceEeecCCEEECCEEEc
Confidence            999999988999999999999999999999999999999999999999999999997665 5678999999999999999


Q ss_pred             cCCEEEEeCCceEEecCcc
Q 031066          146 DGEWLYADTDGILISRAEL  164 (166)
Q Consensus       146 pGD~i~aD~dGVvviP~~l  164 (166)
                      |||+|+||.|||+|||+++
T Consensus       171 PGD~I~aD~dGVvvIP~~~  189 (240)
T PRK08245        171 PGDIIVADDDGVVVIPAAL  189 (240)
T ss_pred             CCCEEEEcCCceEEEcHHH
Confidence            9999999999999999875

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

Probab=100.00  E-value=2e-44  Score=316.10  Aligned_cols=155  Identities=29%  Similarity=0.469  Sum_probs=142.1

Q ss_pred             CCCchhhHhhhccCCccCCeeeeccccccccCCCeeEEEEEEEEEeec-CcHHHHHHHhhcCCCcEEEEeCCCCCcccee
Q 031066            2 ALVTTAEVCDANPQLIVSGELRALQPIFQIYGRRQVFSGPIVTLKVFE-DNVLIREFLEEKGNGRVLVVDGGGSLRCAIL   80 (166)
Q Consensus         2 ~~~~t~~v~Da~~~~~~~g~~~~l~p~~~~~~~~~~~~G~A~Tv~~~~-d~~~~~~~i~~~~~G~VlVvd~~g~~~~a~~   80 (166)
                      ++++|++|||+|++++   .+..++|+++    +.+++|+|+|+++.+ |+...+++++.++||||||||+ ++.++|+|
T Consensus       234 ~~~~t~~i~d~l~~~g---~~~~i~p~~~----~~~~~G~A~Tv~~~~~d~~~~~~~~~~~~~G~VlVi~~-~~~~~a~~  305 (430)
T PRK07028        234 MQVSTPNISDAMHRKG---AMKGIKPLVR----GTKMVGKAVTVQTFAGDWAKPVEAIDVAKPGDVIVIYN-SSKDIAPW  305 (430)
T ss_pred             cCCCCCcHHhhhhccC---CCceeeecCC----CCeEEEEEEEEEeeCCCcHHHHHHHhcCCCCeEEEEEC-CCCCceee
Confidence            5799999999999864   3456777653    468999999999996 7788899999999999999999 67899999


Q ss_pred             chHHHHHHHHcCCcEEEeeCccCCHHHHhcCCccEEEeeeecCCCCCccceeeeeeEEECCEEEccCCEEEEeCCceEEe
Q 031066           81 GGNPVVQAQNNGWAGIVVNGCIRDVDEINGCDIGVRALASHPMKANKKGIGEKHVPITIGGTRISDGEWLYADTDGILIS  160 (166)
Q Consensus        81 G~~~a~~a~~~G~~G~VidG~vRD~~~i~~~~~pv~a~g~~p~~~~~~~~~~~~~pV~igGv~V~pGD~i~aD~dGVvvi  160 (166)
                      ||+++++|+++|++|+|+||++||+++++++||||||+|++|.++.+...+++|+||+|+|++|+|||+|+||.||||||
T Consensus       306 G~~~~~~a~~~G~~G~VidG~vRD~~~i~~~~~pv~~~g~~p~~~~~~~~~~~nvpv~~ggv~V~pGD~i~aD~dGvvvi  385 (430)
T PRK07028        306 GELATLSCLNKGIAGVVIDGAVRDVDEIRKLGFPVFARAIVPNAGEPKGFGEINAEIVCGGQTVRPGDWIIGDENGVVVV  385 (430)
T ss_pred             cHHHHHHHHHCCCeEEEEeeccCCHHHHhhCCCCeEeeecCCCCCCCCCccccCCCEEECCEEECCCCEEEEcCCceEEE
Confidence            99999999999999999999999999999999999999999987766678999999999999999999999999999999


Q ss_pred             cCcc
Q 031066          161 RAEL  164 (166)
Q Consensus       161 P~~l  164 (166)
                      |+++
T Consensus       386 p~~~  389 (430)
T PRK07028        386 PKER  389 (430)
T ss_pred             cHHH
Confidence            9875

>PRK12764 hypothetical protein; Provisional

Probab=100.00  E-value=1.9e-43  Score=315.25  Aligned_cols=159  Identities=22%  Similarity=0.341  Sum_probs=142.4

Q ss_pred             CCCchhhHhhhccCCccCC-eeeeccccccccCCCeeEEEEEEEEEeec-Cc----------HHHHHHHhhcCCCcEEEE
Q 031066            2 ALVTTAEVCDANPQLIVSG-ELRALQPIFQIYGRRQVFSGPIVTLKVFE-DN----------VLIREFLEEKGNGRVLVV   69 (166)
Q Consensus         2 ~~~~t~~v~Da~~~~~~~g-~~~~l~p~~~~~~~~~~~~G~A~Tv~~~~-d~----------~~~~~~i~~~~~G~VlVv   69 (166)
                      ++++|++|||+|+++++.+ .+.+++|+.+    .++++|+|+|+++.+ ++          ...+++++.++|||||||
T Consensus       276 ~~l~ta~vsdal~~~g~~~~~~~~i~p~~p----~~k~vG~A~Tv~~~p~~~~~~~~~~~~~~~~~~aid~~~pGdVlVI  351 (500)
T PRK12764        276 ASVATATLSAQLRKRGLNNVSIDGLTPTRP----GRRMVGRARTLRYVPNREDLFKEHGGGFNAQKRAFDSVNPGEVLVI  351 (500)
T ss_pred             hcCCcchHHHHHhhcCCCcccccCceecCC----CCeEEEEEEEEEeecCCcccccccccchhHHHHHHhcCCCCeEEEE
Confidence            5789999999999987543 4567777653    479999999999985 22          346799999999999999


Q ss_pred             eCCCCCccceechHHHHHHHHcCCcEEEeeCccCCHHHHhcCCccEEEeeeecCCCCCc-cceeeeeeEEECCEEEccCC
Q 031066           70 DGGGSLRCAILGGNPVVQAQNNGWAGIVVNGCIRDVDEINGCDIGVRALASHPMKANKK-GIGEKHVPITIGGTRISDGE  148 (166)
Q Consensus        70 d~~g~~~~a~~G~~~a~~a~~~G~~G~VidG~vRD~~~i~~~~~pv~a~g~~p~~~~~~-~~~~~~~pV~igGv~V~pGD  148 (166)
                      |+.+..+.|+|||+++++|+++|++|+|+||+|||+++|++++|||||+|++|..+.+. ..+++|+||+|||++|+|||
T Consensus       352 d~~g~~~~a~~Gel~a~~a~~~G~~G~ViDG~vRD~~ei~~lg~PVfarg~~p~~~~~~~~~~~~nvpV~~gGv~V~PGD  431 (500)
T PRK12764        352 EARGEKGTGTLGDILALRAQVRGAAGVVTDGGVRDYAAVAELGLPVFFAGPHPAVLGRRHVPWDVDITVACGGATVQPGD  431 (500)
T ss_pred             ECCCCCCeEchHHHHHHHHHHCCCeEEEEeecccCHHHHHhCCCCeEEeecCCCCCCcCcccceeCCcEEECCEEEcCCC
Confidence            99998899999999999999999999999999999999999999999999999876644 56899999999999999999


Q ss_pred             EEEEeCCceEEecCcc
Q 031066          149 WLYADTDGILISRAEL  164 (166)
Q Consensus       149 ~i~aD~dGVvviP~~l  164 (166)
                      +|+||.|||||||+++
T Consensus       432 iIvaD~dGVvvIP~~~  447 (500)
T PRK12764        432 VIVGDDDGVVVIPPAL  447 (500)
T ss_pred             EEEEcCCcEEEEcHHH
Confidence            9999999999999875

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	166
3c8o_A	162	The Crystal Structure Of Rraa From Pao1 Length = 16		4e-41
1j3l_A	164	Structure Of The Rna-Processing Inhibitor Rraa From		5e-34
2pcn_A	161	Crystal Structure Of S-Adenosylmethionine: 2-Dimeth		3e-31
1q5x_A	161	Structure Of Of Rraa (Meng), A Protein Inhibitor Of		7e-31
1nxj_A	183	Structure Of Rv3853 From Mycobacterium Tuberculosis		5e-28
1vi4_A	174	Crystal Structure Of Regulator Of Ribonuclease Aciv		2e-25
3k4i_A	244	Crystal Structure Of Uncharacterized Protein Pspto_		2e-04

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

Iteration: 1
 Score =  163 bits (412), Expect = 4e-41,   Method: Compositional matrix adjust.
 Identities = 81/161 (50%), Positives = 113/161 (70%), Gaps = 5/161 (3%)
Query: 6   TAEVCDANPQLIVSGELRALQPIFQIYGRRQVFSGPIVTLKVFEDNVLIREFLEEKGNGR 65
           T ++CDA P+L+     + ++P+F  +G R  F G IVT+K FEDN L++E +++ G G+
Sbjct: 5   TPDLCDAYPELV-----QVVEPMFSNFGGRDSFGGEIVTIKCFEDNSLVKEQVDKDGKGK 59
Query: 66  VLVVDGGGSLRCAILGGNPVVQAQNNGWAGIVVNGCIRDVDEINGCDIGVRALASHPMKA 125
           VLVVDGGGSLR A+LG     +A  NGW GIVV GCIRDVD I   D+GV+ALASHP+K 
Sbjct: 60  VLVVDGGGSLRRALLGDMLAEKAAKNGWEGIVVYGCIRDVDVIAQTDLGVQALASHPLKT 119
Query: 126 NKKGIGEKHVPITIGGTRISDGEWLYADTDGILISRAELSV 166
           +K+GIG+ +V +T GG     GE++YAD +GI++S   L +
Sbjct: 120 DKRGIGDLNVAVTFGGVTFRPGEFVYADNNGIIVSPQALKM 160

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

Iteration: 1
 Score =  139 bits (351), Expect = 5e-34,   Method: Compositional matrix adjust.
 Identities = 73/154 (47%), Positives = 103/154 (66%), Gaps = 6/154 (3%)
Query: 6   TAEVCDANPQLIVSGELRALQPIFQIYGRRQVFSGPIVTLKVFEDNVLIREFLEEKGNGR 65
           T ++ D  P+    GE  AL  +F+ +G R  F+G + TL+VFEDN L+R+ LEE+G G+
Sbjct: 5   TTDLSDLYPE----GE--ALPXVFKSFGGRARFAGRVRTLRVFEDNALVRKVLEEEGAGQ 58
Query: 66  VLVVDGGGSLRCAILGGNPVVQAQNNGWAGIVVNGCIRDVDEINGCDIGVRALASHPMKA 125
           VL VDGGGSLR A+LGGN   +A   GWAG+VV+G +RD +E+    IG+ ALA+ P K+
Sbjct: 59  VLFVDGGGSLRTALLGGNLARRAWEKGWAGVVVHGAVRDTEELREVPIGLLALAATPKKS 118
Query: 126 NKKGIGEKHVPITIGGTRISDGEWLYADTDGILI 159
            K+G GE  VP+ + G  +  G +L AD DG+L+
Sbjct: 119 AKEGKGEVDVPLKVLGVEVLPGSFLLADEDGLLL 152

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

Iteration: 1
 Score =  130 bits (328), Expect = 3e-31,   Method: Compositional matrix adjust.
 Identities = 72/161 (44%), Positives = 102/161 (63%), Gaps = 5/161 (3%)
Query: 4   VTTAEVCDANPQLIVSGELRALQPIFQIYGRRQVFSGPIVTLKVFEDNVLIREFLEEKGN 63
           + TA++CD   Q +   EL+  +  FQ YG +++FSGPI T+ VFEDNVL+RE LE    
Sbjct: 1   MKTADLCD---QFL--DELQVCELPFQSYGGKRMFSGPIATVDVFEDNVLVREALETVPP 55
Query: 64  GRVLVVDGGGSLRCAILGGNPVVQAQNNGWAGIVVNGCIRDVDEINGCDIGVRALASHPM 123
           G VLVVDG GS R A+LG      A   G AG++++GCIRD  EI    IGV A+ + P+
Sbjct: 56  GTVLVVDGKGSRRVALLGDRLAQIACERGLAGVIIHGCIRDSAEIGAMPIGVMAIGTCPV 115
Query: 124 KANKKGIGEKHVPITIGGTRISDGEWLYADTDGILISRAEL 164
           K+ K+G G + V +  GG R   G ++YAD DG++++  +L
Sbjct: 116 KSKKEGKGARDVVLEFGGVRWEPGAYVYADADGVVVANKDL 156

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

Iteration: 1
 Score =  129 bits (324), Expect = 7e-31,   Method: Compositional matrix adjust.
 Identities = 67/161 (41%), Positives = 99/161 (61%), Gaps = 5/161 (3%)
Query: 6   TAEVCDANPQLIVSGELRALQPIFQIYGRRQVFSGPIVTLKVFEDNVLIREFLEEKGNGR 65
           T+E+CD     I   ++  ++P+F  +G R  F G I+T+K FEDN L+ + LE+ G GR
Sbjct: 5   TSELCD-----IYQEDVNVVEPLFSNFGGRASFGGQIITVKCFEDNGLLYDLLEQNGRGR 59
Query: 66  VLVVDGGGSLRCAILGGNPVVQAQNNGWAGIVVNGCIRDVDEINGCDIGVRALASHPMKA 125
           VLVVDGGGS+R A++       A  N W G+V+ G +R VD++   DIG++A+A+ P+ A
Sbjct: 60  VLVVDGGGSVRRALVDAELARLAVQNEWEGLVIYGAVRQVDDLEELDIGIQAMAAIPVGA 119
Query: 126 NKKGIGEKHVPITIGGTRISDGEWLYADTDGILISRAELSV 166
             +GIGE  V +  GG     G+ LYAD  GI++S   L +
Sbjct: 120 AGEGIGESDVRVNFGGVTFFSGDHLYADNTGIILSEDPLDI 160

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

Iteration: 1
 Score =  120 bits (300), Expect = 5e-28,   Method: Compositional matrix adjust.
 Identities = 56/139 (40%), Positives = 89/139 (64%)
Query: 21  ELRALQPIFQIYGRRQVFSGPIVTLKVFEDNVLIREFLEEKGNGRVLVVDGGGSLRCAIL 80
           ++R+    F+ +G R  F+GPI T++ F+DN L++  L +   G VLV+DG GSL  A++
Sbjct: 44  DVRSCDLQFRQFGGRSQFAGPISTVRCFQDNALLKSVLSQPSAGGVLVIDGAGSLHTALV 103
Query: 81  GGNPVVQAQNNGWAGIVVNGCIRDVDEINGCDIGVRALASHPMKANKKGIGEKHVPITIG 140
           G      A++ GW G++V+G +RD   + G DIG++AL ++P K+ K G GE+ V IT+G
Sbjct: 104 GDVIAELARSTGWTGLIVHGAVRDAAALRGIDIGIKALGTNPRKSTKTGAGERDVEITLG 163
Query: 141 GTRISDGEWLYADTDGILI 159
           G     G+  Y+D DGI++
Sbjct: 164 GVTFVPGDIAYSDDDGIIV 182

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

Iteration: 1
 Score =  111 bits (277), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 58/161 (36%), Positives = 90/161 (55%), Gaps = 5/161 (3%)
Query: 6   TAEVCDANPQLIVSGELRALQPIFQIYGRRQVFSGPIVTLKVFEDNVLIREFLEEKGNGR 65
           T ++CD         ++  L    Q +G+R  F G IVT++ + DN  +R+ L + G G+
Sbjct: 8   TPDLCDK-----YESQVTLLNLPLQNFGQRSAFWGEIVTVRCYHDNSKVRDVLSQNGKGK 62
Query: 66  VLVVDGGGSLRCAILGGNPVVQAQNNGWAGIVVNGCIRDVDEINGCDIGVRALASHPMKA 125
           VLVVDG GS   A+ G    + A  N W G+++ G +RDV   +  D+G++AL + P K 
Sbjct: 63  VLVVDGHGSCHKALXGDQLAILAIKNDWEGVIIYGAVRDVVAXSEXDLGIKALGTSPFKT 122
Query: 126 NKKGIGEKHVPITIGGTRISDGEWLYADTDGILISRAELSV 166
            K+G G+ +V +T     +  G++LYAD +GIL S   L V
Sbjct: 123 EKRGAGQVNVTLTXQNQIVEPGDYLYADWNGILXSETALDV 163

>pdb|3K4I|A Chain A, Crystal Structure Of Uncharacterized Protein Pspto_3204 From Pseudomonas Syringae Pv. Tomato Str. Dc3000 Length = 244

Iteration: 1
 Score = 41.6 bits (96), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 27/110 (24%), Positives = 49/110 (44%), Gaps = 1/110 (0%)
Query: 57  FLEEKGNGRVLVVDGGGSLRCAILGGNPVVQAQNNGWAGIVVNGCIRDVDEINGCDIGVR 116
           ++++  +G V+V    G   C + G      A  NG  G V++G  RD+D +  C+  + 
Sbjct: 77  YIDQVPSGSVIVSSNSGRHDCTVWGDIXTHFALANGIKGTVIDGVARDIDTVINCNYPLF 136
Query: 117 ALASHPMKA-NKKGIGEKHVPITIGGTRISDGEWLYADTDGILISRAELS 165
           +       A N+  +    VP+ I G  I  G+    D  G ++   +L+
Sbjct: 137 SRGRFXQSAKNRTQLKAVQVPLVIDGITIQPGDLXVCDGSGCVVVPQQLA 186

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	166
1vi4_A	174	Regulator of ribonuclease acivity A protein 1; str	1e-75
3c8o_A	162	Regulator of ribonuclease activity A; RRAA, PAO1,	3e-74
1j3l_A	164	Demethylmenaquinone methyltransferase; vitamine K2	7e-74
2pcn_A	161	S-adenosylmethionine:2-demethylmenaquinone methylt	1e-73
1nxj_A	183	Probable S-adenosylmethionine:2- demethylmenaquino	2e-72
1q5x_A	161	Regulator of RNAse E activity A; 3-layer sandwich,	2e-70
3noj_A	238	4-carboxy-4-hydroxy-2-oxoadipate aldolase/oxaloac	9e-39
3k4i_A	244	Uncharacterized protein; structural genomics, prot	5e-29
2c5q_A	240	RRAA-like protein YER010C; structural genomics,unk	4e-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 =  222 bits (569), Expect = 1e-75
 Identities = 58/166 (34%), Positives = 95/166 (57%), Gaps = 5/166 (3%)

Query: 1   MALVTTAEVCDANPQLIVSGELRALQPIFQIYGRRQVFSGPIVTLKVFEDNVLIREFLEE 60
           +    T ++CD         ++  L    Q +G+R  F G IVT++ + DN  +R+ L +
Sbjct: 3   LMRDITPDLCDKYES-----QVTLLNLPLQNFGQRSAFWGEIVTVRCYHDNSKVRDVLSQ 57

Query: 61  KGNGRVLVVDGGGSLRCAILGGNPVVQAQNNGWAGIVVNGCIRDVDEINGCDIGVRALAS 120
            G G+VLVVDG GS   A++G    + A  N W G+++ G +RDV  ++  D+G++AL +
Sbjct: 58  NGKGKVLVVDGHGSCHKALMGDQLAILAIKNDWEGVIIYGAVRDVVAMSEMDLGIKALGT 117

Query: 121 HPMKANKKGIGEKHVPITIGGTRISDGEWLYADTDGILISRAELSV 166
            P K  K+G G+ +V +T+    +  G++LYAD +GIL+S   L V
Sbjct: 118 SPFKTEKRGAGQVNVTLTMQNQIVEPGDYLYADWNGILMSETALDV 163

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

 Score =  218 bits (558), Expect = 3e-74
 Identities = 81/163 (49%), Positives = 113/163 (69%), Gaps = 5/163 (3%)

Query: 4   VTTAEVCDANPQLIVSGELRALQPIFQIYGRRQVFSGPIVTLKVFEDNVLIREFLEEKGN 63
             T ++CDA P+L+     + ++P+F  +G R  F G IVT+K FEDN L++E +++ G 
Sbjct: 3   YVTPDLCDAYPELV-----QVVEPMFSNFGGRDSFGGEIVTIKCFEDNSLVKEQVDKDGK 57

Query: 64  GRVLVVDGGGSLRCAILGGNPVVQAQNNGWAGIVVNGCIRDVDEINGCDIGVRALASHPM 123
           G+VLVVDGGGSLR A+LG     +A  NGW GIVV GCIRDVD I   D+GV+ALASHP+
Sbjct: 58  GKVLVVDGGGSLRRALLGDMLAEKAAKNGWEGIVVYGCIRDVDVIAQTDLGVQALASHPL 117

Query: 124 KANKKGIGEKHVPITIGGTRISDGEWLYADTDGILISRAELSV 166
           K +K+GIG+ +V +T GG     GE++YAD +GI++S   L +
Sbjct: 118 KTDKRGIGDLNVAVTFGGVTFRPGEFVYADNNGIIVSPQALKM 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 =  217 bits (556), Expect = 7e-74
 Identities = 73/162 (45%), Positives = 102/162 (62%), Gaps = 6/162 (3%)

Query: 4   VTTAEVCDANPQLIVSGELRALQPIFQIYGRRQVFSGPIVTLKVFEDNVLIREFLEEKGN 63
             T ++ D  P      E  AL  +F+ +G R  F+G + TL+VFEDN L+R+ LEE+G 
Sbjct: 3   ARTTDLSDLYP------EGEALPMVFKSFGGRARFAGRVRTLRVFEDNALVRKVLEEEGA 56

Query: 64  GRVLVVDGGGSLRCAILGGNPVVQAQNNGWAGIVVNGCIRDVDEINGCDIGVRALASHPM 123
           G+VL VDGGGSLR A+LGGN   +A   GWAG+VV+G +RD +E+    IG+ ALA+ P 
Sbjct: 57  GQVLFVDGGGSLRTALLGGNLARRAWEKGWAGVVVHGAVRDTEELREVPIGLLALAATPK 116

Query: 124 KANKKGIGEKHVPITIGGTRISDGEWLYADTDGILISRAELS 165
           K+ K+G GE  VP+ + G  +  G +L AD DG+L+     S
Sbjct: 117 KSAKEGKGEVDVPLKVLGVEVLPGSFLLADEDGLLLLPEPPS 158

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

 Score =  217 bits (554), Expect = 1e-73
 Identities = 71/161 (44%), Positives = 100/161 (62%), Gaps = 5/161 (3%)

Query: 4   VTTAEVCDANPQLIVSGELRALQPIFQIYGRRQVFSGPIVTLKVFEDNVLIREFLEEKGN 63
           + TA++CD         EL+  +  FQ YG +++FSGPI T+ VFEDNVL+RE LE    
Sbjct: 1   MKTADLCDQFLD-----ELQVCELPFQSYGGKRMFSGPIATVDVFEDNVLVREALETVPP 55

Query: 64  GRVLVVDGGGSLRCAILGGNPVVQAQNNGWAGIVVNGCIRDVDEINGCDIGVRALASHPM 123
           G VLVVDG GS R A+LG      A   G AG++++GCIRD  EI    IGV A+ + P+
Sbjct: 56  GTVLVVDGKGSRRVALLGDRLAQIACERGLAGVIIHGCIRDSAEIGAMPIGVMAIGTCPV 115

Query: 124 KANKKGIGEKHVPITIGGTRISDGEWLYADTDGILISRAEL 164
           K+ K+G G + V +  GG R   G ++YAD DG++++  +L
Sbjct: 116 KSKKEGKGARDVVLEFGGVRWEPGAYVYADADGVVVANKDL 156

>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 =  214 bits (548), Expect = 2e-72
 Identities = 59/159 (37%), Positives = 97/159 (61%), Gaps = 5/159 (3%)

Query: 1   MALVTTAEVCDANPQLIVSGELRALQPIFQIYGRRQVFSGPIVTLKVFEDNVLIREFLEE 60
           ++   TA++ D      +  ++R+    F+ +G R  F+GPI T++ F+DN L++  L +
Sbjct: 29  ISFRPTADLVDD-----IGPDVRSCDLQFRQFGGRSQFAGPISTVRCFQDNALLKSVLSQ 83

Query: 61  KGNGRVLVVDGGGSLRCAILGGNPVVQAQNNGWAGIVVNGCIRDVDEINGCDIGVRALAS 120
              G VLV+DG GSL  A++G      A++ GW G++V+G +RD   + G DIG++AL +
Sbjct: 84  PSAGGVLVIDGAGSLHTALVGDVIAELARSTGWTGLIVHGAVRDAAALRGIDIGIKALGT 143

Query: 121 HPMKANKKGIGEKHVPITIGGTRISDGEWLYADTDGILI 159
           +P K+ K G GE+ V IT+GG     G+  Y+D DGI++
Sbjct: 144 NPRKSTKTGAGERDVEITLGGVTFVPGDIAYSDDDGIIV 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 =  209 bits (533), Expect = 2e-70
 Identities = 66/163 (40%), Positives = 98/163 (60%), Gaps = 5/163 (3%)

Query: 4   VTTAEVCDANPQLIVSGELRALQPIFQIYGRRQVFSGPIVTLKVFEDNVLIREFLEEKGN 63
             T+E+CD         ++  ++P+F  +G R  F G I+T+K FEDN L+ + LE+ G 
Sbjct: 3   YDTSELCDIYQ-----EDVNVVEPLFSNFGGRASFGGQIITVKCFEDNGLLYDLLEQNGR 57

Query: 64  GRVLVVDGGGSLRCAILGGNPVVQAQNNGWAGIVVNGCIRDVDEINGCDIGVRALASHPM 123
           GRVLVVDGGGS+R A++       A  N W G+V+ G +R VD++   DIG++A+A+ P+
Sbjct: 58  GRVLVVDGGGSVRRALVDAELARLAVQNEWEGLVIYGAVRQVDDLEELDIGIQAMAAIPV 117

Query: 124 KANKKGIGEKHVPITIGGTRISDGEWLYADTDGILISRAELSV 166
            A  +GIGE  V +  GG     G+ LYAD  GI++S   L +
Sbjct: 118 GAAGEGIGESDVRVNFGGVTFFSGDHLYADNTGIILSEDPLDI 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 =  130 bits (330), Expect = 9e-39
 Identities = 37/162 (22%), Positives = 64/162 (39%), Gaps = 7/162 (4%)

Query: 4   VTTAEVCDANPQLIVSGELRALQPIFQIYGRRQVFSGPIVTLKVFE-DNVLIREFLEEKG 62
           +  A V +A            L    +   +    +G  VT+ V   DN +    +E+  
Sbjct: 29  LGVATVHEAQ------NRKGLLSSKMRPIQQGTSLAGSAVTVLVAPGDNWMFHVAVEQCR 82

Query: 63  NGRVLVVDGGGSLRCAILGGNPVVQAQNNGWAGIVVNGCIRDVDEINGCDIGVRALASHP 122
            G VLVV           G       Q  G   ++V+  +RD   +      V A A + 
Sbjct: 83  PGDVLVVSPSSPCTDGYFGDLLATSLQARGVRALIVDAGVRDTQTLRDMGFAVWARAINA 142

Query: 123 MKANKKGIGEKHVPITIGGTRISDGEWLYADTDGILISRAEL 164
               K+ +G  ++P+  GG  I+ G+ + AD DG+++ R + 
Sbjct: 143 QGTVKETLGSVNLPVICGGQLINPGDIVVADDDGVVVVRRDE 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 =  105 bits (265), Expect = 5e-29
 Identities = 36/167 (21%), Positives = 64/167 (38%), Gaps = 10/167 (5%)

Query: 4   VTTAEVCDANPQLIVSGELRALQPIFQIYGRRQVFSGPIVTLKVF-----EDNVLIREFL 58
           + TA + DA   L + G L  +              G   T++       E       ++
Sbjct: 23  LDTASLSDALDSLGIDGGLPGIASQV----PGTRCVGIAFTVQYQPVDASEGFRGAANYI 78

Query: 59  EEKGNGRVLVVDGGGSLRCAILGGNPVVQAQNNGWAGIVVNGCIRDVDEINGCDIGVRAL 118
           ++  +G V+V    G   C + G      A  NG  G V++G  RD+D +  C+  + + 
Sbjct: 79  DQVPSGSVIVSSNSGRHDCTVWGDIMTHFALANGIKGTVIDGVARDIDTVINCNYPLFSR 138

Query: 119 ASHPMKANKK-GIGEKHVPITIGGTRISDGEWLYADTDGILISRAEL 164
                 A  +  +    VP+ I G  I  G+ +  D  G ++   +L
Sbjct: 139 GRFMQSAKNRTQLKAVQVPLVIDGITIQPGDLMVCDGSGCVVVPQQL 185

>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 = 85.3 bits (211), Expect = 4e-21
 Identities = 35/177 (19%), Positives = 56/177 (31%), Gaps = 23/177 (12%)

Query: 4   VTTAEVCDA---NPQLIVSGELRALQPIFQIYGRRQVFSGPIVTLKVF--EDNVLIREFL 58
            +T ++ D       +   G    L  I           G   T+     +D      ++
Sbjct: 10  FSTCDISDGLLNVYNIPTGGYFPNLTAISPPQNSS--IVGTAYTVLFAPIDDPRPAVNYI 67

Query: 59  EEKGNGRVLVVDGGGSLR----------CAILGGNPVVQAQNNGWAGIVVNGCIRDVDEI 108
           +      +LV+     L+           A+ GG    +AQ     G VV G IRDVDE 
Sbjct: 68  DSVPPNSILVLALEPHLQSQFHPFIKITQAMYGGLMSTRAQYLKSNGTVVFGRIRDVDEH 127

Query: 109 NGCDIGVRALASHPMKAN---KKGIGEKHVPITIGG---TRISDGEWLYADTDGILI 159
              +  V A            K       + I         I  G+++  D +GI+ 
Sbjct: 128 RTLNHPVFAYGVGSCAPKAVVKAVGTNVQLKILTSDGVTQTICPGDYIAGDNNGIVR 184

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	166
1j3l_A	164	Demethylmenaquinone methyltransferase; vitamine K2	100.0
3c8o_A	162	Regulator of ribonuclease activity A; RRAA, PAO1,	100.0
1q5x_A	161	Regulator of RNAse E activity A; 3-layer sandwich,	100.0
2pcn_A	161	S-adenosylmethionine:2-demethylmenaquinone methylt	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

>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=2.8e-53  Score=329.30  Aligned_cols=158  Identities=46%  Similarity=0.776  Sum_probs=149.6

Q ss_pred             CCchhhHhhhccCCccCCeeeeccccccccCCCeeEEEEEEEEEeecCcHHHHHHHhhcCCCcEEEEeCCCCCccceech
Q 031066            3 LVTTAEVCDANPQLIVSGELRALQPIFQIYGRRQVFSGPIVTLKVFEDNVLIREFLEEKGNGRVLVVDGGGSLRCAILGG   82 (166)
Q Consensus         3 ~~~t~~v~Da~~~~~~~g~~~~l~p~~~~~~~~~~~~G~A~Tv~~~~d~~~~~~~i~~~~~G~VlVvd~~g~~~~a~~G~   82 (166)
                      +++|++|||+|+++      +.+.|.++++++.++++|+|+|+++.+||+.+++++++.+||+|||||+.++.++|+|||
T Consensus         2 ~~~t~~v~Da~~~~------~~~~~~~~~~~~~~~~~G~A~Tv~~~~dn~~~~~al~~~~~G~VlVvd~~g~~~~a~~G~   75 (164)
T 1j3l_A            2 EARTTDLSDLYPEG------EALPMVFKSFGGRARFAGRVRTLRVFEDNALVRKVLEEEGAGQVLFVDGGGSLRTALLGG   75 (164)
T ss_dssp             CCCHHHHHHHCTTS------EEECSCSEECSSBSSEEEEEEEEECSSBCHHHHHHHTSCCBTEEEEEECTTCCSSBSCCH
T ss_pred             cCCcccHhhccccc------CCCCcceeeCCCCCEEEEEEEEEEeeCCchHHHHHHhccCCCcEEEEECCCCCCceeehH
Confidence            58999999999973      456677888887889999999999999999999999999999999999998899999999


Q ss_pred             HHHHHHHHcCCcEEEeeCccCCHHHHhcCCccEEEeeeecCCCCCccceeeeeeEEECCEEEccCCEEEEeCCceEEecC
Q 031066           83 NPVVQAQNNGWAGIVVNGCIRDVDEINGCDIGVRALASHPMKANKKGIGEKHVPITIGGTRISDGEWLYADTDGILISRA  162 (166)
Q Consensus        83 ~~a~~a~~~G~~G~VidG~vRD~~~i~~~~~pv~a~g~~p~~~~~~~~~~~~~pV~igGv~V~pGD~i~aD~dGVvviP~  162 (166)
                      +|+++|++|||+|+|+||++||++||++++|||||++++|.++.+...+++|+||+|+|++|+|||||+||.|||+|||+
T Consensus        76 ~la~~a~~~G~~GiVidG~vRD~~~i~~~~~pV~a~g~~p~~~~~~~~g~~nvpV~~gGv~V~PGD~i~aD~dGVvviP~  155 (164)
T 1j3l_A           76 NLARRAWEKGWAGVVVHGAVRDTEELREVPIGLLALAATPKKSAKEGKGEVDVPLKVLGVEVLPGSFLLADEDGLLLLPE  155 (164)
T ss_dssp             HHHHHHHHTTBCEEEEESEECCHHHHTTSSSEEEESEECSSBCBCSCCCEESCCEEETTEEECTTCEEEEETTEEEEESS
T ss_pred             HHHHHHHHCCCeEEEecCcccCHHHHhcCCCcEEEeecCCCCCccceeeeeCCCEEECCEEECCCCEEEECCCeEEEECh
Confidence            99999999999999999999999999999999999999999998888999999999999999999999999999999999


Q ss_pred             ccCC
Q 031066          163 ELSV  166 (166)
Q Consensus       163 ~l~~  166 (166)
                      +|++
T Consensus       156 ~l~~  159 (164)
T 1j3l_A          156 PPSG  159 (164)
T ss_dssp             SCCC
T ss_pred             hhcC
Confidence            9874

>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=4e-53  Score=327.89  Aligned_cols=157  Identities=51%  Similarity=0.940  Sum_probs=149.0

Q ss_pred             CCchhhHhhhcc-CCccCCeeeeccccccccCCCeeEEEEEEEEEeecCcHHHHHHHhhcCCCcEEEEeCCCCCccceec
Q 031066            3 LVTTAEVCDANP-QLIVSGELRALQPIFQIYGRRQVFSGPIVTLKVFEDNVLIREFLEEKGNGRVLVVDGGGSLRCAILG   81 (166)
Q Consensus         3 ~~~t~~v~Da~~-~~~~~g~~~~l~p~~~~~~~~~~~~G~A~Tv~~~~d~~~~~~~i~~~~~G~VlVvd~~g~~~~a~~G   81 (166)
                      +++|++|||+|. ++      +.+.|.++++++.++++|+|+|+++.+||..+++++++.+||+|||||+.++.++|+||
T Consensus         2 ~~~t~~l~Da~~~~~------~~~~~~~~~~~~~~~~~G~A~Tv~~~~dn~~~~~al~~~~~G~VlVvd~~g~~~~a~~G   75 (162)
T 3c8o_A            2 HYVTPDLCDAYPELV------QVVEPMFSNFGGRDSFGGEIVTIKCFEDNSLVKEQVDKDGKGKVLVVDGGGSLRRALLG   75 (162)
T ss_dssp             CCCHHHHHHHCTTTC------EECCSCCEECSSCSCEEEEEEEEECSSCCHHHHHHHTSCCBTEEEEEECTTCSSSBSCC
T ss_pred             cCChhhHHHhhhccc------CccCcccccCCCCCEEEEEEEEEEEeCCchHHHHHHhccCCCCEEEEECCCCCCccchH
Confidence            489999999997 43      45677888888889999999999999999999999999999999999999989999999


Q ss_pred             hHHHHHHHHcCCcEEEeeCccCCHHHHhcCCccEEEeeeecCCCCCccceeeeeeEEECCEEEccCCEEEEeCCceEEec
Q 031066           82 GNPVVQAQNNGWAGIVVNGCIRDVDEINGCDIGVRALASHPMKANKKGIGEKHVPITIGGTRISDGEWLYADTDGILISR  161 (166)
Q Consensus        82 ~~~a~~a~~~G~~G~VidG~vRD~~~i~~~~~pv~a~g~~p~~~~~~~~~~~~~pV~igGv~V~pGD~i~aD~dGVvviP  161 (166)
                      |+|+++|++|||+|+|+||++||++||++++|||||++++|.++.+...+++|+||+|+|++|+|||+|+||.|||+|||
T Consensus        76 ~~la~~a~~~G~~GiVidG~vRD~~~l~~~~~pv~a~g~~p~~~~~~~~g~~nvpV~~gGv~V~PGD~i~aD~dGVvviP  155 (162)
T 3c8o_A           76 DMLAEKAAKNGWEGIVVYGCIRDVDVIAQTDLGVQALASHPLKTDKRGIGDLNVAVTFGGVTFRPGEFVYADNNGIIVSP  155 (162)
T ss_dssp             HHHHHHHHHTTBCEEEEEEEECCHHHHTTSSSEEEEEEECCCBCCCCSCCEESCCEEETTEEECTTSEEEECSSCEEEES
T ss_pred             HHHHHHHHHCCCeEEEecCCCCCHHHHhcCCCcEEEeecCCCCCcceeeeeeCCCEEECCEEECCCCEEEEcCCeEEEEC
Confidence            99999999999999999999999999999999999999999999888899999999999999999999999999999999


Q ss_pred             CccC
Q 031066          162 AELS  165 (166)
Q Consensus       162 ~~l~  165 (166)
                      ++|+
T Consensus       156 ~~l~  159 (162)
T 3c8o_A          156 QALK  159 (162)
T ss_dssp             SCCC
T ss_pred             cccc
Confidence            9986

>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=9.1e-53  Score=325.63  Aligned_cols=157  Identities=42%  Similarity=0.794  Sum_probs=147.2

Q ss_pred             CCchhhHhhhcc-CCccCCeeeeccccccccCCCeeEEEEEEEEEeecCcHHHHHHHhhcCCCcEEEEeCCCCCccceec
Q 031066            3 LVTTAEVCDANP-QLIVSGELRALQPIFQIYGRRQVFSGPIVTLKVFEDNVLIREFLEEKGNGRVLVVDGGGSLRCAILG   81 (166)
Q Consensus         3 ~~~t~~v~Da~~-~~~~~g~~~~l~p~~~~~~~~~~~~G~A~Tv~~~~d~~~~~~~i~~~~~G~VlVvd~~g~~~~a~~G   81 (166)
                      +++|++|||+|+ ++      +.+.|.++++++.++++|+|+|+++.+||..++++|++++||+|||||+.++.++|+||
T Consensus         2 ~~~ta~l~Dal~~~~------~~~~~~i~~~~~~~~~~G~A~Tv~~~~dn~~~~~al~~~~~G~VlVvd~~g~~~~a~~G   75 (161)
T 1q5x_A            2 KYDTSELCDIYQEDV------NVVEPLFSNFGGRASFGGQIITVKCFEDNGLLYDLLEQNGRGRVLVVDGGGSVRRALVD   75 (161)
T ss_dssp             CCCHHHHHHHHGGGS------EECCSCCEECSSCSSEEEEEEEEECSSBCHHHHHHHTSCCTTEEEEEECTTCSSSEEEC
T ss_pred             ccccccHhhhhhhcc------CCccCcceECCCCCEEEEEEEEEEEeCCcHHHHHHHhhcCCCCEEEEECCCCCCceeeh
Confidence            589999999998 43      23556667777778999999999999999999999999999999999999889999999


Q ss_pred             hHHHHHHHHcCCcEEEeeCccCCHHHHhcCCccEEEeeeecCCCCCccceeeeeeEEECCEEEccCCEEEEeCCceEEec
Q 031066           82 GNPVVQAQNNGWAGIVVNGCIRDVDEINGCDIGVRALASHPMKANKKGIGEKHVPITIGGTRISDGEWLYADTDGILISR  161 (166)
Q Consensus        82 ~~~a~~a~~~G~~G~VidG~vRD~~~i~~~~~pv~a~g~~p~~~~~~~~~~~~~pV~igGv~V~pGD~i~aD~dGVvviP  161 (166)
                      |+++++|++|||+|+|+||++||++||++++|||||++++|.++.+...+++|+||+|+|++|+|||+|+||.|||+|||
T Consensus        76 ~~la~~a~~~G~~G~VidG~vRD~~~i~~~~~pv~a~g~~p~~~~~~~~g~~nvpV~~gGv~V~PGD~i~aD~dGVvviP  155 (161)
T 1q5x_A           76 AELARLAVQNEWEGLVIYGAVRQVDDLEELDIGIQAMAAIPVGAAGEGIGESDVRVNFGGVTFFSGDHLYADNTGIILSE  155 (161)
T ss_dssp             HHHHHHHHHTTCCEEEEEEEECCHHHHTTSSSEEEEEEECSSBCBCSCCSEESCCEEETTEEECTTCEEEECSSCEEEES
T ss_pred             HHHHHHHHHCCCeEEEecCccCCHHHHhcCCCcEEEeEeccCCCCcCceeeeCCCEEECCEEECCCCEEEEcCCeEEEEc
Confidence            99999999999999999999999999999999999999999999888899999999999999999999999999999999


Q ss_pred             CccC
Q 031066          162 AELS  165 (166)
Q Consensus       162 ~~l~  165 (166)
                      ++|.
T Consensus       156 ~~l~  159 (161)
T 1q5x_A          156 DPLD  159 (161)
T ss_dssp             SCSS
T ss_pred             hHHc
Confidence            9985

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

Probab=100.00  E-value=1.1e-52  Score=325.07  Aligned_cols=157  Identities=45%  Similarity=0.786  Sum_probs=148.3

Q ss_pred             CchhhHhhhccCCccCCeeeeccccccccCCCeeEEEEEEEEEeecCcHHHHHHHhhcCCCcEEEEeCCCCCccceechH
Q 031066            4 VTTAEVCDANPQLIVSGELRALQPIFQIYGRRQVFSGPIVTLKVFEDNVLIREFLEEKGNGRVLVVDGGGSLRCAILGGN   83 (166)
Q Consensus         4 ~~t~~v~Da~~~~~~~g~~~~l~p~~~~~~~~~~~~G~A~Tv~~~~d~~~~~~~i~~~~~G~VlVvd~~g~~~~a~~G~~   83 (166)
                      ++|++|||+|..     ..+.+.|.++++++.++++|+|+|+++.+||..++++|++++||+|||||+.++.++|+|||+
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     245677888888888999999999999999999999999999999999999988899999999


Q ss_pred             HHHHHHHcCCcEEEeeCccCCHHHHhcCCccEEEeeeecCCCCCccceeeeeeEEECCEEEccCCEEEEeCCceEEecCc
Q 031066           84 PVVQAQNNGWAGIVVNGCIRDVDEINGCDIGVRALASHPMKANKKGIGEKHVPITIGGTRISDGEWLYADTDGILISRAE  163 (166)
Q Consensus        84 ~a~~a~~~G~~G~VidG~vRD~~~i~~~~~pv~a~g~~p~~~~~~~~~~~~~pV~igGv~V~pGD~i~aD~dGVvviP~~  163 (166)
                      |+++|+++||+|+|+||++||++||++++|||||++++|.++.++..+++|+||+|+|++|+|||+|+||.|||||||++
T Consensus        76 la~~a~~~G~~GiVidG~vRD~~~i~~~~~pv~a~g~~p~~~~~~~~g~~nvpV~~gGv~V~PGD~i~aD~dGVvviP~~  155 (161)
T 2pcn_A           76 LAQIACERGLAGVIIHGCIRDSAEIGAMPIGVMAIGTCPVKSKKEGKGARDVVLEFGGVRWEPGAYVYADADGVVVANKD  155 (161)
T ss_dssp             HHHHHHHTTCCEEEEEEEESCHHHHTTSSSEEEEEEECCSCCBCSCCSEESCCEEETTEEECTTCEEEEETTEEEEESSC
T ss_pred             HHHHHHHcCCcEEEecccccCHHHHhcCCCcEEEeecCCCCCccceeeeeCCCEEECCEEECCCCEEEECCCeEEEEChH
Confidence            99999999999999999999999999999999999999999988889999999999999999999999999999999999


Q ss_pred             cC
Q 031066          164 LS  165 (166)
Q Consensus       164 l~  165 (166)
                      |.
T Consensus       156 l~  157 (161)
T 2pcn_A          156 LL  157 (161)
T ss_dssp             TT
T ss_pred             Hh
Confidence            85

>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=1.5e-52  Score=327.82  Aligned_cols=158  Identities=36%  Similarity=0.698  Sum_probs=149.7

Q ss_pred             CCchhhHhhhccCCccCCeeeeccccccccCCCeeEEEEEEEEEeecCcHHHHHHHhhcCCCcEEEEeCCCCCccceech
Q 031066            3 LVTTAEVCDANPQLIVSGELRALQPIFQIYGRRQVFSGPIVTLKVFEDNVLIREFLEEKGNGRVLVVDGGGSLRCAILGG   82 (166)
Q Consensus         3 ~~~t~~v~Da~~~~~~~g~~~~l~p~~~~~~~~~~~~G~A~Tv~~~~d~~~~~~~i~~~~~G~VlVvd~~g~~~~a~~G~   82 (166)
                      +++|++|||+|.+ .    ++.+.|.++++++.++|+|+|+|+++.+||..++++|++.+||+|||||+.++.++|+|||
T Consensus         5 ~~~tadl~D~l~~-~----~~v~~~~~~~~~~~~~~~G~A~Tv~~~~dn~~~~~al~~~~~G~VlVvd~~g~~~~A~~G~   79 (174)
T 1vi4_A            5 RDITPDLCDKYES-Q----VTLLNLPLQNFGQRSAFWGEIVTVRCYHDNSKVRDVLSQNGKGKVLVVDGHGSCHKALMGD   79 (174)
T ss_dssp             CCCHHHHHHHSGG-G----CEECCCCCEECSSCSCEEEEEEEEECSSCCHHHHHHHTSCCTTEEEEEECTTCCSSEEECH
T ss_pred             cccHHHHHHHhhc-c----cccccccceECCCCCEEEEEEEEEEEeCccHHHHHHHhccCCCEEEEEECCCCCCceehHH
Confidence            5899999999987 1    3557788888888889999999999999999999999999999999999998899999999


Q ss_pred             HHHHHHHHcCCcEEEeeCccCCHHHHhcCCccEEEeeeecCCCCCccceeeeeeEEECCEEEccCCEEEEeCCceEEecC
Q 031066           83 NPVVQAQNNGWAGIVVNGCIRDVDEINGCDIGVRALASHPMKANKKGIGEKHVPITIGGTRISDGEWLYADTDGILISRA  162 (166)
Q Consensus        83 ~~a~~a~~~G~~G~VidG~vRD~~~i~~~~~pv~a~g~~p~~~~~~~~~~~~~pV~igGv~V~pGD~i~aD~dGVvviP~  162 (166)
                      +++++|++|||+|+|+||++||++||++++|||||++++|.++.+...+++|+||+|+|++|+|||||+||.|||||||+
T Consensus        80 ~la~~a~~~G~aGiVidG~vRD~~~l~~~~~pV~a~g~~p~~~~~~~~g~~nvpV~igGv~V~PGD~I~aD~dGVvviP~  159 (174)
T 1vi4_A           80 QLAILAIKNDWEGVIIYGAVRDVVAMSEMDLGIKALGTSPFKTEKRGAGQVNVTLTMQNQIVEPGDYLYADWNGILMSET  159 (174)
T ss_dssp             HHHHHHHHTTCCEEEEEEEECCHHHHTTSSSEEEEEEECSCCCCCCSCCEESCCEEETTEEECTTSEEEEETTEEEEESS
T ss_pred             HHHHHHHHCCCeEEEeccccCCHHHHHhCCCCeEEeecCCCCCCCCCcceeCCCEEECCEEECCCCEEEEcCCeEEEECh
Confidence            99999999999999999999999999999999999999999988888999999999999999999999999999999999


Q ss_pred             ccC
Q 031066          163 ELS  165 (166)
Q Consensus       163 ~l~  165 (166)
                      +|.
T Consensus       160 ~l~  162 (174)
T 1vi4_A          160 ALD  162 (174)
T ss_dssp             CCC
T ss_pred             HHc
Confidence            875

>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=1.1e-50  Score=319.51  Aligned_cols=155  Identities=38%  Similarity=0.761  Sum_probs=144.3

Q ss_pred             CCCCchhhHhhhccCCccCCeeeeccccccccCCCeeEEEEEEEEEeecCcHHHHHHHhhcCCCcEEEEeCCCCCcccee
Q 031066            1 MALVTTAEVCDANPQLIVSGELRALQPIFQIYGRRQVFSGPIVTLKVFEDNVLIREFLEEKGNGRVLVVDGGGSLRCAIL   80 (166)
Q Consensus         1 ~~~~~t~~v~Da~~~~~~~g~~~~l~p~~~~~~~~~~~~G~A~Tv~~~~d~~~~~~~i~~~~~G~VlVvd~~g~~~~a~~   80 (166)
                      |.+++|++|||+|..     .++.+.|.++++++.++++|+|+|+++.+||..+++++++++||+|||||+.++.++|+|
T Consensus        29 L~~~~t~dv~Dal~~-----~~~~~~~~i~~~~~~~~~~G~A~TV~~~~dn~~~~~al~~~~~G~VlVvd~~g~~~~A~~  103 (183)
T 1nxj_A           29 ISFRPTADLVDDIGP-----DVRSCDLQFRQFGGRSQFAGPISTVRCFQDNALLKSVLSQPSAGGVLVIDGAGSLHTALV  103 (183)
T ss_dssp             CCCCCHHHHHHHHCT-----TCEECCCCCEECSSBSCEEEEEEEEECSSBCHHHHHHHHSCCSSCEEEEECTTCCSSEEE
T ss_pred             hcCCCHHHHHhhhhc-----ccCccCcceeECCCCCEEEEEEEEEEEeCCchHHHHHHHhcCCCCEEEEECCCCCCceee
Confidence            456899999999972     134466777778778899999999999999999999999999999999999998999999


Q ss_pred             chHHHHHHHHcCCcEEEeeCccCCHHHHhcCCccEEEeeeecCCCCCccceeeeeeEEECCEEEccCCEEEEeCCceEEe
Q 031066           81 GGNPVVQAQNNGWAGIVVNGCIRDVDEINGCDIGVRALASHPMKANKKGIGEKHVPITIGGTRISDGEWLYADTDGILIS  160 (166)
Q Consensus        81 G~~~a~~a~~~G~~G~VidG~vRD~~~i~~~~~pv~a~g~~p~~~~~~~~~~~~~pV~igGv~V~pGD~i~aD~dGVvvi  160 (166)
                      ||+++++|++|||+|+|+||++||++||++++|||||++++|.++.+..++++|+||+|+|++|+|||+|+||+||||||
T Consensus       104 G~~la~~a~~~G~aGiVidG~vRD~~ei~~l~fPV~a~g~~p~~~~~~~~g~~nvPV~igGv~V~PGD~I~aD~dGVVvI  183 (183)
T 1nxj_A          104 GDVIAELARSTGWTGLIVHGAVRDAAALRGIDIGIKALGTNPRKSTKTGAGERDVEITLGGVTFVPGDIAYSDDDGIIVV  183 (183)
T ss_dssp             CHHHHHHHHHHTCCEEEEEEEESCHHHHTTSSSEEEEEEECCSBCBCSCCSEESCCEEETTEEECTTSEEEECSSCEEEC
T ss_pred             HHHHHHHHHHCCCcEEEeccccCCHHHHhcCCCcEEEeeeCCCCCCCCccceeCCCEEECCEEECCCCEEEECCCeEEEC
Confidence            99999999999999999999999999999999999999999999888889999999999999999999999999999986

>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=8.9e-50  Score=325.74  Aligned_cols=157  Identities=24%  Similarity=0.331  Sum_probs=145.1

Q ss_pred             CCCchhhHhhhccCCccCCeeeeccccccccCCCeeEEEEEEEEEeec-CcHHHHHHHhhcCCCcEEEEeCCCCCcccee
Q 031066            2 ALVTTAEVCDANPQLIVSGELRALQPIFQIYGRRQVFSGPIVTLKVFE-DNVLIREFLEEKGNGRVLVVDGGGSLRCAIL   80 (166)
Q Consensus         2 ~~~~t~~v~Da~~~~~~~g~~~~l~p~~~~~~~~~~~~G~A~Tv~~~~-d~~~~~~~i~~~~~G~VlVvd~~g~~~~a~~   80 (166)
                      ++++|++|||+|.+++      .+.|.++++.+.++++|+|+|+++.+ ||..+++++++++||||||||++++.++|+|
T Consensus        27 ~~~~tatv~dal~r~g------~~~~~i~p~~~~~~~~G~A~TV~~~p~dn~~~~~ai~~~~~G~VlVvd~~g~~~~A~~  100 (238)
T 3noj_A           27 GRLGVATVHEAQNRKG------LLSSKMRPIQQGTSLAGSAVTVLVAPGDNWMFHVAVEQCRPGDVLVVSPSSPCTDGYF  100 (238)
T ss_dssp             HHHCHHHHHHHTTSCC------BCCTTCEESSSSCCEEEEEEEEEECTTBCHHHHHHHTTCCTTEEEEEEESSCCCSBCC
T ss_pred             hCCChhHHHHHhhccC------CCchhceECCCCCeEEEEEEEEEEECCCcHHHHHHHHhcCCCCEEEEECCCCCCeEeh
Confidence            4679999999998754      23455666666789999999999985 8999999999999999999999999999999


Q ss_pred             chHHHHHHHHcCCcEEEeeCccCCHHHHhcCCccEEEeeeecCCCCCccceeeeeeEEECCEEEccCCEEEEeCCceEEe
Q 031066           81 GGNPVVQAQNNGWAGIVVNGCIRDVDEINGCDIGVRALASHPMKANKKGIGEKHVPITIGGTRISDGEWLYADTDGILIS  160 (166)
Q Consensus        81 G~~~a~~a~~~G~~G~VidG~vRD~~~i~~~~~pv~a~g~~p~~~~~~~~~~~~~pV~igGv~V~pGD~i~aD~dGVvvi  160 (166)
                      ||+++++|+++||+|+|+||+|||+++|++++|||||+|++|.++.+...+++|+||+|+|++|+|||+|+||.||||||
T Consensus       101 G~~la~~a~~~G~aGiVidG~vRD~~~l~~~~fPV~a~g~~p~~~~k~~~g~invPV~igGv~V~PGD~V~aD~dGVvvi  180 (238)
T 3noj_A          101 GDLLATSLQARGVRALIVDAGVRDTQTLRDMGFAVWARAINAQGTVKETLGSVNLPVICGGQLINPGDIVVADDDGVVVV  180 (238)
T ss_dssp             CHHHHHHHHHTTCCEEEEEEEECCHHHHHHHTCEEEEEEECCCCCBCCSCCEESSCEEETTEEECTTCEEEEETTEEEEE
T ss_pred             HHHHHHHHHHCCCcEEEeecccCCHHHHHhCCCCEEEeecCCCCCCCCCeeeeCCCEEECCEEECCCCEEEEcCCeEEEE
Confidence            99999999999999999999999999999999999999999998888789999999999999999999999999999999


Q ss_pred             cCcc
Q 031066          161 RAEL  164 (166)
Q Consensus       161 P~~l  164 (166)
                      |+++
T Consensus       181 P~~~  184 (238)
T 3noj_A          181 RRDE  184 (238)
T ss_dssp             CGGG
T ss_pred             cHHH
Confidence            9875

>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=1.1e-48  Score=320.30  Aligned_cols=159  Identities=23%  Similarity=0.337  Sum_probs=138.4

Q ss_pred             CCCchhhHhhhccCCccCCeeeeccccccccCCCeeEEEEEEEEEeec-CcHHHH----HHHhhcCCCcEEEEeCCCCCc
Q 031066            2 ALVTTAEVCDANPQLIVSGELRALQPIFQIYGRRQVFSGPIVTLKVFE-DNVLIR----EFLEEKGNGRVLVVDGGGSLR   76 (166)
Q Consensus         2 ~~~~t~~v~Da~~~~~~~g~~~~l~p~~~~~~~~~~~~G~A~Tv~~~~-d~~~~~----~~i~~~~~G~VlVvd~~g~~~   76 (166)
                      ++++|++|||+|+++++.+...    .++++.+.++++|+|+||++.+ |+...+    ++|++++||||||||+.++.+
T Consensus        21 ~~~~ta~v~Dal~~~g~~~~~~----~i~p~~~~~~~~G~A~TV~~~p~d~~~~~~~~~~~id~~~~GdVlVvd~~g~~~   96 (244)
T 3k4i_A           21 EHLDTASLSDALDSLGIDGGLP----GIASQVPGTRCVGIAFTVQYQPVDASEGFRGAANYIDQVPSGSVIVSSNSGRHD   96 (244)
T ss_dssp             TTCCHHHHHHHHHHTTCCCBCT----TCEECSTTCCEEEEEEEEEEEEC----------CGGGGCCTTEEEEEECTTCSS
T ss_pred             cCCChHHHHHHHHhcCCcccCc----cceECCCCCeEEEEEEEEEEecCCCchhhhhhHHHHHcCCCCeEEEEECCCCCC
Confidence            5799999999999977655443    4444555789999999999996 444444    359999999999999999999


Q ss_pred             cceechHHHHHHHHcCCcEEEeeCccCCHHHHhcCCccEEEeeeecCCCCC-ccceeeeeeEEECCEEEccCCEEEEeCC
Q 031066           77 CAILGGNPVVQAQNNGWAGIVVNGCIRDVDEINGCDIGVRALASHPMKANK-KGIGEKHVPITIGGTRISDGEWLYADTD  155 (166)
Q Consensus        77 ~a~~G~~~a~~a~~~G~~G~VidG~vRD~~~i~~~~~pv~a~g~~p~~~~~-~~~~~~~~pV~igGv~V~pGD~i~aD~d  155 (166)
                      +|+|||+|+++|+++||+|+|+||+|||+++|++++|||||+|++|..+.. ..++++|+||+|+|++|+|||||+||.|
T Consensus        97 ~A~~G~lla~~a~~~G~aGvVidG~vRD~~ei~~~~fPV~a~g~~p~~~~~~~~~g~~nvPV~igGv~V~PGD~V~aD~d  176 (244)
T 3k4i_A           97 CTVWGDIMTHFALANGIKGTVIDGVARDIDTVINCNYPLFSRGRFMQSAKNRTQLKAVQVPLVIDGITIQPGDLMVCDGS  176 (244)
T ss_dssp             SBSCCHHHHHHHHHHTCCEEEEESBBSCHHHHHHTTCCEEESCBCCCCSTTTEEEEEESSCEEETTEEECTTCEEEEETT
T ss_pred             eEehHHHHHHHHHHCCCeEEEeCCccCCHHHHHhCCCCEEEeecCCCCCCCccccceecccEEECCEEECCCCEEEEcCC
Confidence            999999999999999999999999999999999999999999999986543 4789999999999999999999999999


Q ss_pred             ceEEecCcc
Q 031066          156 GILISRAEL  164 (166)
Q Consensus       156 GVvviP~~l  164 (166)
                      ||||||+++
T Consensus       177 GVVviP~~~  185 (244)
T 3k4i_A          177 GCVVVPQQL  185 (244)
T ss_dssp             EEEEECGGG
T ss_pred             eEEEEcHHH
Confidence            999999876

>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=6.4e-48  Score=315.17  Aligned_cols=161  Identities=21%  Similarity=0.208  Sum_probs=141.8

Q ss_pred             CCCchhhHhhhccC-CccC--CeeeeccccccccCCCeeEEEEEEEEEeecCc-H-HHHHHHhhcCCCcEEEEeCCCCCc
Q 031066            2 ALVTTAEVCDANPQ-LIVS--GELRALQPIFQIYGRRQVFSGPIVTLKVFEDN-V-LIREFLEEKGNGRVLVVDGGGSLR   76 (166)
Q Consensus         2 ~~~~t~~v~Da~~~-~~~~--g~~~~l~p~~~~~~~~~~~~G~A~Tv~~~~d~-~-~~~~~i~~~~~G~VlVvd~~g~~~   76 (166)
                      ++++|++|||+|.+ ++..  ++...++|+.+  ++..+|+|+|+||++.+++ + ..+++|++++||+|||||+.++.+
T Consensus         8 ~~~~t~~v~Dal~~~~g~~~~~~~~~~~~~~~--g~~~~~~G~A~TV~~~~~~~~~~~~~aid~~~~G~VlVvd~~g~~~   85 (240)
T 2c5q_A            8 QRFSTCDISDGLLNVYNIPTGGYFPNLTAISP--PQNSSIVGTAYTVLFAPIDDPRPAVNYIDSVPPNSILVLALEPHLQ   85 (240)
T ss_dssp             TTSCHHHHHHHHHHHHCCTTTTEECSCEEEEC--CSSSCEEEEEEEEEEEETTSSSCCCCCGGGCCTTEEEEEEECGGGB
T ss_pred             cCCCHHHHHHHHHHhhCcCccccCcceeECcc--CCCCEEEEEEEEEEEECCCCcHHHHHHHhcCCCCEEEEEECCCCcc
Confidence            57899999999998 6543  44455666432  2357899999999999755 3 245799999999999999988888


Q ss_pred             ----------cceechHHHHHHHHcCCcEEEeeCccCCHHHHhcCCccEEEeeeecCCCCCc-cceeeeeeEEECC----
Q 031066           77 ----------CAILGGNPVVQAQNNGWAGIVVNGCIRDVDEINGCDIGVRALASHPMKANKK-GIGEKHVPITIGG----  141 (166)
Q Consensus        77 ----------~a~~G~~~a~~a~~~G~~G~VidG~vRD~~~i~~~~~pv~a~g~~p~~~~~~-~~~~~~~pV~igG----  141 (166)
                                +|+|||+|+++|+++||+|+|+||+|||++||++++|||||+|++|..+.+. .++++|+||+|+|    
T Consensus        86 ~~~~~~~~~~~A~~G~l~a~~a~~~G~aGiVidG~vRD~~el~~l~~PV~a~g~~p~~~~~~~~~g~~nvPV~igG~~~~  165 (240)
T 2c5q_A           86 SQFHPFIKITQAMYGGLMSTRAQYLKSNGTVVFGRIRDVDEHRTLNHPVFAYGVGSCAPKAVVKAVGTNVQLKILTSDGV  165 (240)
T ss_dssp             CSSTTCBSCCSCSCCHHHHHHHHHTTCCEEEEEEEECCHHHHHHHTCCEEEEEECSSCSTTTEEEEEESCCEEEECTTSC
T ss_pred             cccccccccceeeehHHHHHHHHHcCCeEEEecCCcCCHHHHhcCCCcEEEeecCCCCCCCcccccccCccEEECCcCcc
Confidence                      9999999999999999999999999999999999999999999999888765 6999999999999    


Q ss_pred             -EEEccCCEEEEeCCceEEecC--cc
Q 031066          142 -TRISDGEWLYADTDGILISRA--EL  164 (166)
Q Consensus       142 -v~V~pGD~i~aD~dGVvviP~--~l  164 (166)
                       ++|+|||||+||.|||||||+  ++
T Consensus       166 ~v~V~PGD~I~aD~dGVVviP~~~~~  191 (240)
T 2c5q_A          166 TQTICPGDYIAGDNNGIVRIPVQETD  191 (240)
T ss_dssp             EEEECTTCEEEEETTEEEEECTTTSC
T ss_pred             eEEECCCCEEEEcCCcEEEeCCcHHH
Confidence             999999999999999999998  64

---

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	166
d1q5xa_	160	c.8.7.1 (A:) Regulator of RNase E activity RraA (M	5e-52
d1vi4a_	162	c.8.7.1 (A:) Hypothetical protein VC2366 {Vibrio c	9e-51
d1nxja_	156	c.8.7.1 (A:) Hypothetical protein Rv3853 {Mycobact	1e-49
d1j3la_	164	c.8.7.1 (A:) Demethylmenaquinone methyltransferase	7e-49

>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 =  161 bits (408), Expect = 5e-52
 Identities = 66/162 (40%), Positives = 99/162 (61%), Gaps = 5/162 (3%)

Query: 5   TTAEVCDANPQLIVSGELRALQPIFQIYGRRQVFSGPIVTLKVFEDNVLIREFLEEKGNG 64
            T+E+CD   +     ++  ++P+F  +G R  F G I+T+K FEDN L+ + LE+ G G
Sbjct: 3   DTSELCDIYQE-----DVNVVEPLFSNFGGRASFGGQIITVKCFEDNGLLYDLLEQNGRG 57

Query: 65  RVLVVDGGGSLRCAILGGNPVVQAQNNGWAGIVVNGCIRDVDEINGCDIGVRALASHPMK 124
           RVLVVDGGGS+R A++       A  N W G+V+ G +R VD++   DIG++A+A+ P+ 
Sbjct: 58  RVLVVDGGGSVRRALVDAELARLAVQNEWEGLVIYGAVRQVDDLEELDIGIQAMAAIPVG 117

Query: 125 ANKKGIGEKHVPITIGGTRISDGEWLYADTDGILISRAELSV 166
           A  +GIGE  V +  GG     G+ LYAD  GI++S   L +
Sbjct: 118 AAGEGIGESDVRVNFGGVTFFSGDHLYADNTGIILSEDPLDI 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 =  158 bits (400), Expect = 9e-51
 Identities = 58/163 (35%), Positives = 94/163 (57%), Gaps = 5/163 (3%)

Query: 4   VTTAEVCDANPQLIVSGELRALQPIFQIYGRRQVFSGPIVTLKVFEDNVLIREFLEEKGN 63
             T ++CD         ++  L    Q +G+R  F G IVT++ + DN  +R+ L + G 
Sbjct: 3   DITPDLCDKYES-----QVTLLNLPLQNFGQRSAFWGEIVTVRCYHDNSKVRDVLSQNGK 57

Query: 64  GRVLVVDGGGSLRCAILGGNPVVQAQNNGWAGIVVNGCIRDVDEINGCDIGVRALASHPM 123
           G+VLVVDG GS   A++G    + A  N W G+++ G +RDV  ++  D+G++AL + P 
Sbjct: 58  GKVLVVDGHGSCHKALMGDQLAILAIKNDWEGVIIYGAVRDVVAMSEMDLGIKALGTSPF 117

Query: 124 KANKKGIGEKHVPITIGGTRISDGEWLYADTDGILISRAELSV 166
           K  K+G G+ +V +T+    +  G++LYAD +GIL+S   L V
Sbjct: 118 KTEKRGAGQVNVTLTMQNQIVEPGDYLYADWNGILMSETALDV 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 =  154 bits (391), Expect = 1e-49
 Identities = 59/159 (37%), Positives = 96/159 (60%), Gaps = 5/159 (3%)

Query: 1   MALVTTAEVCDANPQLIVSGELRALQPIFQIYGRRQVFSGPIVTLKVFEDNVLIREFLEE 60
           ++   TA++ D         ++R+    F+ +G R  F+GPI T++ F+DN L++  L +
Sbjct: 2   ISFRPTADLVDDIG-----PDVRSCDLQFRQFGGRSQFAGPISTVRCFQDNALLKSVLSQ 56

Query: 61  KGNGRVLVVDGGGSLRCAILGGNPVVQAQNNGWAGIVVNGCIRDVDEINGCDIGVRALAS 120
              G VLV+DG GSL  A++G      A++ GW G++V+G +RD   + G DIG++AL +
Sbjct: 57  PSAGGVLVIDGAGSLHTALVGDVIAELARSTGWTGLIVHGAVRDAAALRGIDIGIKALGT 116

Query: 121 HPMKANKKGIGEKHVPITIGGTRISDGEWLYADTDGILI 159
           +P K+ K G GE+ V IT+GG     G+  Y+D DGI++
Sbjct: 117 NPRKSTKTGAGERDVEITLGGVTFVPGDIAYSDDDGIIV 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 =  153 bits (387), Expect = 7e-49
 Identities = 73/162 (45%), Positives = 102/162 (62%), Gaps = 6/162 (3%)

Query: 4   VTTAEVCDANPQLIVSGELRALQPIFQIYGRRQVFSGPIVTLKVFEDNVLIREFLEEKGN 63
             T ++ D  P      E  AL  +F+ +G R  F+G + TL+VFEDN L+R+ LEE+G 
Sbjct: 3   ARTTDLSDLYP------EGEALPMVFKSFGGRARFAGRVRTLRVFEDNALVRKVLEEEGA 56

Query: 64  GRVLVVDGGGSLRCAILGGNPVVQAQNNGWAGIVVNGCIRDVDEINGCDIGVRALASHPM 123
           G+VL VDGGGSLR A+LGGN   +A   GWAG+VV+G +RD +E+    IG+ ALA+ P 
Sbjct: 57  GQVLFVDGGGSLRTALLGGNLARRAWEKGWAGVVVHGAVRDTEELREVPIGLLALAATPK 116

Query: 124 KANKKGIGEKHVPITIGGTRISDGEWLYADTDGILISRAELS 165
           K+ K+G GE  VP+ + G  +  G +L AD DG+L+     S
Sbjct: 117 KSAKEGKGEVDVPLKVLGVEVLPGSFLLADEDGLLLLPEPPS 158

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	166
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=3.5e-53  Score=325.82  Aligned_cols=159  Identities=42%  Similarity=0.797  Sum_probs=151.9

Q ss_pred             CCchhhHhhhccCCccCCeeeeccccccccCCCeeEEEEEEEEEeecCcHHHHHHHhhcCCCcEEEEeCCCCCccceech
Q 031066            3 LVTTAEVCDANPQLIVSGELRALQPIFQIYGRRQVFSGPIVTLKVFEDNVLIREFLEEKGNGRVLVVDGGGSLRCAILGG   82 (166)
Q Consensus         3 ~~~t~~v~Da~~~~~~~g~~~~l~p~~~~~~~~~~~~G~A~Tv~~~~d~~~~~~~i~~~~~G~VlVvd~~g~~~~a~~G~   82 (166)
                      +++||+|||++..     .++.++|.|++|++..+|+|+|+|+++.+||..+++++++++||+|||+|+.+..++|+|||
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            6899999999875     35779999999999999999999999999999999999999999999999998889999999


Q ss_pred             HHHHHHHHcCCcEEEeeCccCCHHHHhcCCccEEEeeeecCCCCCccceeeeeeEEECCEEEccCCEEEEeCCceEEecC
Q 031066           83 NPVVQAQNNGWAGIVVNGCIRDVDEINGCDIGVRALASHPMKANKKGIGEKHVPITIGGTRISDGEWLYADTDGILISRA  162 (166)
Q Consensus        83 ~~a~~a~~~G~~G~VidG~vRD~~~i~~~~~pv~a~g~~p~~~~~~~~~~~~~pV~igGv~V~pGD~i~aD~dGVvviP~  162 (166)
                      ++++.|+++|++|+|+||++||+++|++++|||||+|++|.++.+...+++|+||+|+|++|+|||||+||.|||||||+
T Consensus        76 ~~a~~a~~~G~~G~VidG~vRD~~~i~~~~~pv~a~g~~p~~~~~~~~~~~nvpi~igGv~V~pGD~I~aD~dGvvVip~  155 (160)
T d1q5xa_          76 ELARLAVQNEWEGLVIYGAVRQVDDLEELDIGIQAMAAIPVGAAGEGIGESDVRVNFGGVTFFSGDHLYADNTGIILSED  155 (160)
T ss_dssp             HHHHHHHHTTCCEEEEEEEECCHHHHTTSSSEEEEEEECSSBCBCSCCSEESCCEEETTEEECTTCEEEECSSCEEEESS
T ss_pred             HHHHHHHHcCcCEEeCccccCCHHHHhhCCCCeeeeeeeecCCccccccEECCeEEECCEEECCCCEEEEeCCcEEEEch
Confidence            99999999999999999999999999999999999999999888778899999999999999999999999999999999


Q ss_pred             ccCC
Q 031066          163 ELSV  166 (166)
Q Consensus       163 ~l~~  166 (166)
                      ||++
T Consensus       156 ~l~~  159 (160)
T d1q5xa_         156 PLDI  159 (160)
T ss_dssp             CSSC
T ss_pred             hcCC
Confidence            9975

>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=2.4e-52  Score=321.68  Aligned_cols=159  Identities=36%  Similarity=0.709  Sum_probs=151.1

Q ss_pred             CCchhhHhhhccCCccCCeeeeccccccccCCCeeEEEEEEEEEeecCcHHHHHHHhhcCCCcEEEEeCCCCCccceech
Q 031066            3 LVTTAEVCDANPQLIVSGELRALQPIFQIYGRRQVFSGPIVTLKVFEDNVLIREFLEEKGNGRVLVVDGGGSLRCAILGG   82 (166)
Q Consensus         3 ~~~t~~v~Da~~~~~~~g~~~~l~p~~~~~~~~~~~~G~A~Tv~~~~d~~~~~~~i~~~~~G~VlVvd~~g~~~~a~~G~   82 (166)
                      ++.|++|||++..     .++.+.|.|++|++..+|+|+|+||++.+||..++++|++.+||+|||||+.++.++|+|||
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            4568999999865     46789999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHcCCcEEEeeCccCCHHHHhcCCccEEEeeeecCCCCCccceeeeeeEEECCEEEccCCEEEEeCCceEEecC
Q 031066           83 NPVVQAQNNGWAGIVVNGCIRDVDEINGCDIGVRALASHPMKANKKGIGEKHVPITIGGTRISDGEWLYADTDGILISRA  162 (166)
Q Consensus        83 ~~a~~a~~~G~~G~VidG~vRD~~~i~~~~~pv~a~g~~p~~~~~~~~~~~~~pV~igGv~V~pGD~i~aD~dGVvviP~  162 (166)
                      ++++.|+++||+|+|+||++||+++|++++|||||++++|.++.+...+++|+||+|+|++|+|||||+||.||||++|+
T Consensus        77 ~~a~~a~~~G~~G~VidG~vRD~~~i~~~~~pv~a~g~~p~~~~~~~~~~~n~pv~iggv~V~PGD~i~aD~dGvvvip~  156 (162)
T d1vi4a_          77 QLAILAIKNDWEGVIIYGAVRDVVAMSEMDLGIKALGTSPFKTEKRGAGQVNVTLTMQNQIVEPGDYLYADWNGILMSET  156 (162)
T ss_dssp             HHHHHHHHTTCCEEEEEEEECCHHHHTTSSSEEEEEEECSCCCCCCSCCEESCCEEETTEEECTTSEEEEETTEEEEESS
T ss_pred             HHHHHHHHhCCCEEecccccCCHHHHhhCCCCeeeecccccCCcccccceeCCeEEECCEEECCCCEEEEeCCcEEEECc
Confidence            99999999999999999999999999999999999999999988888899999999999999999999999999999999


Q ss_pred             ccCC
Q 031066          163 ELSV  166 (166)
Q Consensus       163 ~l~~  166 (166)
                      +|++
T Consensus       157 ~Le~  160 (162)
T d1vi4a_         157 ALDV  160 (162)
T ss_dssp             CCCC
T ss_pred             cccc
Confidence            9864

>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=4.1e-52  Score=320.86  Aligned_cols=157  Identities=46%  Similarity=0.788  Sum_probs=149.8

Q ss_pred             CCchhhHhhhccCCccCCeeeeccccccccCCCeeEEEEEEEEEeecCcHHHHHHHhhcCCCcEEEEeCCCCCccceech
Q 031066            3 LVTTAEVCDANPQLIVSGELRALQPIFQIYGRRQVFSGPIVTLKVFEDNVLIREFLEEKGNGRVLVVDGGGSLRCAILGG   82 (166)
Q Consensus         3 ~~~t~~v~Da~~~~~~~g~~~~l~p~~~~~~~~~~~~G~A~Tv~~~~d~~~~~~~i~~~~~G~VlVvd~~g~~~~a~~G~   82 (166)
                      +++|++|||++++      .+.|.|.|++|++..+|+|+|+|+++.+||..++++|++.+||||||||+.++.++|+|||
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            5789999999986      2568899999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHcCCcEEEeeCccCCHHHHhcCCccEEEeeeecCCCCCccceeeeeeEEECCEEEccCCEEEEeCCceEEecC
Q 031066           83 NPVVQAQNNGWAGIVVNGCIRDVDEINGCDIGVRALASHPMKANKKGIGEKHVPITIGGTRISDGEWLYADTDGILISRA  162 (166)
Q Consensus        83 ~~a~~a~~~G~~G~VidG~vRD~~~i~~~~~pv~a~g~~p~~~~~~~~~~~~~pV~igGv~V~pGD~i~aD~dGVvviP~  162 (166)
                      +++++|+++||+|+|+||++||+++|++++|||||++++|.++.+...+++|+||+|+|++|+|||||+||.||||+||+
T Consensus        76 ~~a~~a~~~G~~G~VidG~vRD~~~i~~~~~pv~a~g~~p~~~~~~~~~~~n~pi~iggv~I~PGD~i~aD~dGVvviP~  155 (164)
T d1j3la_          76 NLARRAWEKGWAGVVVHGAVRDTEELREVPIGLLALAATPKKSAKEGKGEVDVPLKVLGVEVLPGSFLLADEDGLLLLPE  155 (164)
T ss_dssp             HHHHHHHHTTBCEEEEESEECCHHHHTTSSSEEEESEECSSBCBCSCCCEESCCEEETTEEECTTCEEEEETTEEEEESS
T ss_pred             HHHHHHHHhCCCEEeCccccCCHHHHhhCCCCceeEeeeccCCcccccceECCcEEECCEEEcCCCEEEEcCCcEEEEcc
Confidence            99999999999999999999999999999999999999999888888899999999999999999999999999999999


Q ss_pred             ccC
Q 031066          163 ELS  165 (166)
Q Consensus       163 ~l~  165 (166)
                      ++.
T Consensus       156 ~~~  158 (164)
T d1j3la_         156 PPS  158 (164)
T ss_dssp             SCC
T ss_pred             ccc
Confidence            874

>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=3e-50  Score=308.19  Aligned_cols=155  Identities=38%  Similarity=0.761  Sum_probs=147.5

Q ss_pred             CCCCchhhHhhhccCCccCCeeeeccccccccCCCeeEEEEEEEEEeecCcHHHHHHHhhcCCCcEEEEeCCCCCcccee
Q 031066            1 MALVTTAEVCDANPQLIVSGELRALQPIFQIYGRRQVFSGPIVTLKVFEDNVLIREFLEEKGNGRVLVVDGGGSLRCAIL   80 (166)
Q Consensus         1 ~~~~~t~~v~Da~~~~~~~g~~~~l~p~~~~~~~~~~~~G~A~Tv~~~~d~~~~~~~i~~~~~G~VlVvd~~g~~~~a~~   80 (166)
                      |+-.+|++|||++..     .++.+.|.+++|++.++|+|+|+||++.+||..++++|++.+||||||||+.++.++|+|
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            566799999999875     356788999999999999999999999999999999999999999999999999999999


Q ss_pred             chHHHHHHHHcCCcEEEeeCccCCHHHHhcCCccEEEeeeecCCCCCccceeeeeeEEECCEEEccCCEEEEeCCceEEe
Q 031066           81 GGNPVVQAQNNGWAGIVVNGCIRDVDEINGCDIGVRALASHPMKANKKGIGEKHVPITIGGTRISDGEWLYADTDGILIS  160 (166)
Q Consensus        81 G~~~a~~a~~~G~~G~VidG~vRD~~~i~~~~~pv~a~g~~p~~~~~~~~~~~~~pV~igGv~V~pGD~i~aD~dGVvvi  160 (166)
                      ||++++.|++|||+|+|+||++||+++|++++||+||++++|.++.+...+++|+||+|+|++|+|||||+||.||||||
T Consensus        77 G~~~a~~a~~~G~~GiVidG~vRD~~~i~~~~~pv~a~g~~p~~~~~~~~~~~n~pv~iggv~V~pGD~I~aD~dGvvvI  156 (156)
T d1nxja_          77 GDVIAELARSTGWTGLIVHGAVRDAAALRGIDIGIKALGTNPRKSTKTGAGERDVEITLGGVTFVPGDIAYSDDDGIIVV  156 (156)
T ss_dssp             CHHHHHHHHHHTCCEEEEEEEESCHHHHTTSSSEEEEEEECCSBCBCSCCSEESCCEEETTEEECTTSEEEECSSCEEEC
T ss_pred             chHHHHHHHHcCCCEEECcccccCHHHHhcCCceEEEeecccCCCcccccceECCeEEECCEEECCCCEEEEcCCeEEEC
Confidence            99999999999999999999999999999999999999999999888888999999999999999999999999999986