Citrus Sinensis ID: 024646

---

Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-----
Protein Sequence
MADTICRTLRDGGLEGEHAPALTIKDSKASPFGFDVFNYVLTQLSNYILAGKSQSRGLVVVAYSRSPSFYVDLLKRRGIDIASSHDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNLDKLYSLIIEQGKGLIGQGKDRFSIAIDSVSEMVRHASISSVAGILSNLRSHDQVSSIFWLLHSDLHEIKFTSVLEYLSSMVASVEPFNQAAFGQRVDLENLSMLEQNFRKGKFHVRFKRRNGRVRVMASNLHQFCLKMK
Secondary Structure (PSIPRED)
cHHHHHHHHHcccccccccccEEEEccccccccHHHHHHHHHHHHHHHHHccccccEEEEEEEcccHHHHHHHHHHHcccccccccEEEEEEcccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHcccccccccccEEEEEEcHHHHHHHccHHHHHHHHHHHHccccEEEEEEEEEcccccHHHHHHHHHHccEEEEEEcccccccccccccHHHHHHHHHHccccEEEEEEcccccEEEEEHHHHHHHHccc
Secondary Structure Prediction (SSPRO)
cHHHHHHHHHccccccccccEEEEHccccccHHHHHHHHHHHHHHHHHHHHHHHcccEEEEEEcccHHHHHHHHHHccccccccccEEEEEEccccccccHHHHcccccccccccHHHHHHcHHHHHHHHHHHHHHcccHccccccEEEEEEccHHHHHHHccHHHHHHHHHHHcccHHHHHHHHHHcccccHHHHHHHHHHHHHHHEEEccccccccccccccHHHHHHHHHccccEEEEEEEcccccEEEEHHHHHHHHHccc
Coil and Loop (DISEMBL)
MADTICRTlrdgglegehapaltikdskaspfgfDVFNYVLTQLSNYILAGKSQSRGLVVVAYSRSPSFYVDLLKRRgidiasshdwIHILDcytdplgwknwlidKDISQEASSLSSFCQDVRNLDKLYSLIIEQGkgligqgkdrfsIAIDSVSEMVRHASISSVAGILSNLRSHDQVSSIFWLLHSDLHEIKFTSVLEYLSSMVasvepfnqaafgqrvdlENLSMLEQNFRKGKFHVRFKRRNGRVRVMASNLHQFCLKMK
Flexible Loop (DISEMBL)
madticrtlrdgglegehapaltikdskaspFGFDVFNYVLTQLSNYILAGKSQSRGLVVVAYSRSPSFYVDLLKRRGIDIASSHDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNLDKLYSLIIEQgkgligqgkdRFSIAIDSVSEMVRHASISSVAGILSNLRSHDQVSSIFWLLHSDLHEIKFTSVLEYLSSMVASVEPFNQAAFGQRVDLENLSMLEQNfrkgkfhvrfkrrngrvrvmASNLHQFCLKMK
Low Complexity Region (SEG)
MADTICRTLRDGGLEGEHAPALTIKDSKASPFGFDVFNYVLTQLSNYILAGKSQSRGLVVVAYSRSPSFYVDLLKRRGIDIASSHDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNLDKLYSLIIEQGKGLIGQGKDRFSIAIDSVSEMVRHASISSVAGILSNLRSHDQVSSIFWLLHSDLHEIKFTSVLEYLSSMVASVEPFNQAAFGQRVDLENLSMLEQNFRKGKFHVRFKRRNGRVRVMASNLHQFCLKMK
Disordered region (IsUnstruct)
**********************TI***KASPFGFDVFNYVLTQLSNYILAGKSQSRGLVVVAYSRSPSFYVDLLKRRGIDIASSHDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNLDKLYSLIIEQGKGLIGQGKDRFSIAIDSVSEMVRHASISSVAGILSNLRSHDQVSSIFWLLHSDLHEIKFTSVLEYLSSMVASVEPFNQAAFGQRVDLENLSMLEQNFRKGKFHVRFKRRNGRVRVMASNLHQFCL***
Disordered Region (DISOPRED)
***TICRTLRDGGLEGEHAPALTIKDSKASPFGFDVFNYVLTQLSNYIL**KSQSRGLVVVAYSRSPSFYVDLLKRRGIDIASSHDWIHILDCYTDPLGWK*****************FCQDVRNLDKLYSL**********QGKDRFSIAIDSVSEMVRHASISSVAGILSNLRSHDQVSSIFWLLHSDLHEIKFTSVLEYLSSMVASV****************LSMLEQNFRKGKFHVRFKRRNGRVRVMASNLHQFCLKM*
Disordered Region (DISEMBL)
MADTICRTLRDGGLEGEHAPALTIKDSKASPFGFDVFNYVLTQLSNYILAGKSQSRGLVVVAYSRSPSFYVDLLKRRGIDIASSHDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNLDKLYSLIIEQGKGLIGQGKDRFSIAIDSVSEMVRHASISSVAGILSNLRSHDQVSSIFWLLHSDLHEIKFTSVLEYLSSMVASVEPFNQAAFGQRVDLENLSMLEQNFRKGKFHVRFKRRNGRVRVMASNLHQFCLKMK
Disordered Region (DISPRO)
*****CRTLRDGGLEGEHAPALTIKDSKASPFGFDVFNYVLTQLSNYILAGKSQSRGLVVVAYSRSPSFYVDLLKRRGIDIASSHDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNLDKLYSLIIEQGKGLIGQGKDRFSIAIDSVSEMVRHASISSVAGILSNLRSHDQVSSIFWLLHSDLHEIKFTSVLEYLSSMVASVEPFNQAAFGQRVDLENLSMLEQNFRKGKFHVRFKRRNGRVRVMASNLHQFCLKMK
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MADTICRTLRDGGLEGEHAPALTIKDSKASPFGFDVFNYVLTQLSNYILAGKSQSRGLVVVAYSRSPSFYVDLLKRRGIDIASSHDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNLDKLYSLIIEQGKGLIGQGKDRFSIAIDSVSEMVRHASISSVAGILSNLRSHDQVSSIFWLLHSDLHEIKFTSVLEYLSSMVASVEPFNQAAFGQRVDLENLSMLEQNFRKGKFHVRFKRRNGRVRVMASNLHQFCLKMK
Positional Conservation
no confident homologs detected

---

Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	265	2.2.26 [Sep-21-2011]
F4IQJ2	374	Elongator complex protein	no	no	0.958	0.679	0.553	2e-77
A1A5V9	296	Elongator complex protein	yes	no	0.396	0.354	0.276	0.0007

>sp|F4IQJ2|ELP5_ARATH Elongator complex protein 5 OS=Arabidopsis thaliana GN=ELP5 PE=1 SV=1

 Score =  289 bits (739), Expect = 2e-77,   Method: Compositional matrix adjust.
 Identities = 144/260 (55%), Positives = 195/260 (75%), Gaps = 6/260 (2%)

Query: 1   MADTICRTLRDGGLEGEHAPALTIKDSKASPFGFDVFNYVLTQLSNYILAGKSQSRGLVV 60
           MA++I R LRDGG EGE APALTI+++ ASPFG DV  Y+LT LS+ ILAGKS S+GLV+
Sbjct: 1   MAESIFRKLRDGGEEGELAPALTIEETVASPFGLDVSGYLLTNLSSSILAGKSSSQGLVL 60

Query: 61  VAYSRSPSFYVDLLKRRGIDIASSHDWIHILDCYTDPLGWKNWLIDKDISQEASS--LSS 118
           + +SRSPSFY+ LLK++GI ++SS  WI ILDCYTDPLGW    ID+  +  +    L  
Sbjct: 61  ITFSRSPSFYLQLLKQKGIVVSSSSKWIRILDCYTDPLGW----IDQSSTSFSEGSSLIK 116

Query: 119 FCQDVRNLDKLYSLIIEQGKGLIGQGKDRFSIAIDSVSEMVRHASISSVAGILSNLRSHD 178
             + V +L KL+S IIE G+ L+G GK RF +AIDSV+E++RH+++  V+G+L++LRSH 
Sbjct: 117 LHKCVSDLKKLFSSIIEAGRELVGTGKTRFCVAIDSVNELLRHSAMPLVSGLLTDLRSHA 176

Query: 179 QVSSIFWLLHSDLHEIKFTSVLEYLSSMVASVEPFNQAAFGQRVDLENLSMLEQNFRKGK 238
           Q+SS+FW L++DLH+ K T+ LEY+S+M A++EP   ++ GQR  LENL  + Q+F KG+
Sbjct: 177 QISSVFWSLNTDLHQEKVTNALEYISTMKANLEPLCPSSDGQRNALENLFSVHQDFGKGR 236

Query: 239 FHVRFKRRNGRVRVMASNLH 258
           FHVRFK R GRVRVM+   H
Sbjct: 237 FHVRFKLRKGRVRVMSEEYH 256

Acts as subunit of the RNA polymerase II elongator complex, which is a histone acetyltransferase component of the RNA polymerase II (Pol II) holoenzyme and is involved in transcriptional elongation. Elongator may play a role in chromatin remodeling and is involved in acetylation of histones H3 and probably H4.
Arabidopsis thaliana (taxid: 3702)

>sp|A1A5V9|ELP5_DANRE Elongator complex protein 5 OS=Danio rerio GN=elp5 PE=2 SV=1

 Score = 44.7 bits (104), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 36/130 (27%), Positives = 56/130 (43%), Gaps = 25/130 (19%)

Query: 88  IHILDCYTDPLGWK---NWLIDKDISQEASSLSSFCQDVRNLDKLYSLIIEQGKGLIGQG 144
           +H    + DPLGW+   ++ + +  SQ  + L      +R+                 Q 
Sbjct: 67  LHFHKGFPDPLGWRGKSSFTVQQFTSQHITQL------IRD----------------SQP 104

Query: 145 KDRFSIAIDSVSEMVRHASISSVAGILSNLRSHDQVSSIFWLLHSDLHEIKFTSVLEYLS 204
                + +DS+S ++RH     V   L  LR    V +I  LLHSDLH      ++ +L+
Sbjct: 105 AKASVLVVDSLSLVLRHHDPVIVCQSLQELRKGGVVKTIIGLLHSDLHLQGIVGIVCHLA 164

Query: 205 SMVASVEPFN 214
           S V SV P N
Sbjct: 165 STVISVAPTN 174

May be involved in tp53-mediated transcriptional regulation.

Danio rerio (taxid: 7955)

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	265
255559196	376	conserved hypothetical protein [Ricinus	0.973	0.686	0.702	1e-107
118485334	379	unknown [Populus trichocarpa]	0.973	0.680	0.711	1e-106
224077180	386	predicted protein [Populus trichocarpa]	0.973	0.668	0.692	1e-104
225452057	376	PREDICTED: uncharacterized protein LOC10	0.969	0.683	0.669	6e-95
356500866	373	PREDICTED: dermal papilla-derived protei	0.947	0.672	0.634	7e-87
363814366	372	uncharacterized protein LOC100792556 [Gl	0.947	0.674	0.628	3e-86
449455826	375	PREDICTED: elongator complex protein 5-l	0.988	0.698	0.561	8e-83
297832500	378	hypothetical protein ARALYDRAFT_319792 [	0.958	0.671	0.561	3e-77
79322467	306	uncharacterized protein [Arabidopsis tha	0.958	0.830	0.553	8e-76
42569125	374	uncharacterized protein [Arabidopsis tha	0.958	0.679	0.553	9e-76

>gi|255559196|ref|XP_002520619.1| conserved hypothetical protein [Ricinus communis] gi|223540180|gb|EEF41755.1| conserved hypothetical protein [Ricinus communis]

 Score =  392 bits (1008), Expect = e-107,   Method: Compositional matrix adjust.
 Identities = 184/262 (70%), Positives = 227/262 (86%), Gaps = 4/262 (1%)

Query: 1   MADTICRTLRDGGLEGEHAPALTIKDSKASPFGFDVFNYVLTQLSNYILAGKSQSRGLVV 60
           MA++ICRTLRDG LEGEHAPALTIKD+ ASPFGFD+F +VL++LS++ILA KSQ +G+VV
Sbjct: 1   MAESICRTLRDGALEGEHAPALTIKDTSASPFGFDMFAHVLSRLSSFILAQKSQFQGIVV 60

Query: 61  VAYSRSPSFYVDLLKRRGIDIASSHDWIHILDCYTDPLGWKNWLIDK----DISQEASSL 116
           +AY+RSPSFYVDLLKRR ID+ASSH WI+ILDCYTDPLGWK+ L++     DIS EASS+
Sbjct: 61  LAYTRSPSFYVDLLKRRKIDVASSHKWIYILDCYTDPLGWKDKLVEPGSRMDISHEASSV 120

Query: 117 SSFCQDVRNLDKLYSLIIEQGKGLIGQGKDRFSIAIDSVSEMVRHASISSVAGILSNLRS 176
           +  C+DV++LD LY+LI+E GKGL+GQGK RFS+AIDSV+EM+R AS+S VAG+LSNLRS
Sbjct: 121 AHLCKDVKDLDSLYTLILELGKGLVGQGKARFSVAIDSVNEMLRDASMSKVAGLLSNLRS 180

Query: 177 HDQVSSIFWLLHSDLHEIKFTSVLEYLSSMVASVEPFNQAAFGQRVDLENLSMLEQNFRK 236
           HDQ+SSI+WLLHSDLHE++ TS+LEY+SSMVAS+EP N++  GQR +LENLS L+QNF K
Sbjct: 181 HDQISSIYWLLHSDLHEVRVTSMLEYMSSMVASIEPLNRSGNGQRWNLENLSQLQQNFGK 240

Query: 237 GKFHVRFKRRNGRVRVMASNLH 258
           GK +VRFKRRNGRV VM     
Sbjct: 241 GKLNVRFKRRNGRVSVMCEEFE 262

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|118485334|gb|ABK94526.1| unknown [Populus trichocarpa]

 Score =  392 bits (1006), Expect = e-106,   Method: Compositional matrix adjust.
 Identities = 187/263 (71%), Positives = 224/263 (85%), Gaps = 5/263 (1%)

Query: 1   MADTICRTLRDGGLEGEHAPALTIKDSKASPFGFDVFNYVLTQLSNYILAGKSQSRGLVV 60
           MA+++CRTLRDG LEGE APALTIKD+ ASPFGF VF++VL+QLS++ILA KSQSRG+V+
Sbjct: 1   MAESMCRTLRDGSLEGEQAPALTIKDTAASPFGFHVFSHVLSQLSSFILASKSQSRGIVI 60

Query: 61  VAYSRSPSFYVDLLKRRGIDIASSHDWIHILDCYTDPLGWKNWLIDK----DISQE-ASS 115
           VA+SRSPSFYVDLLK RGID+ SSH W+ ILDCYTDPL WK+ L+      D S E +SS
Sbjct: 61  VAFSRSPSFYVDLLKSRGIDVNSSHKWVQILDCYTDPLCWKDQLMGSGNFMDASHETSSS 120

Query: 116 LSSFCQDVRNLDKLYSLIIEQGKGLIGQGKDRFSIAIDSVSEMVRHASISSVAGILSNLR 175
           LS  C+DV++LDKLYS+I+E GKGL+GQGKDRFS+AID+++EM+RH S  +VAG+LSNLR
Sbjct: 121 LSRVCKDVKDLDKLYSMILELGKGLVGQGKDRFSVAIDTINEMLRHTSTPTVAGLLSNLR 180

Query: 176 SHDQVSSIFWLLHSDLHEIKFTSVLEYLSSMVASVEPFNQAAFGQRVDLENLSMLEQNFR 235
           SH+Q+SSIFWLLHSDLHEIK TS LEYLSS+VASVEP +Q A G+R DLENLS+LEQNF 
Sbjct: 181 SHEQISSIFWLLHSDLHEIKVTSALEYLSSVVASVEPLHQTAGGKRGDLENLSLLEQNFG 240

Query: 236 KGKFHVRFKRRNGRVRVMASNLH 258
           KGK  VRFKRRNGRVRV+    H
Sbjct: 241 KGKLQVRFKRRNGRVRVVNEGFH 263

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224077180|ref|XP_002305167.1| predicted protein [Populus trichocarpa] gi|222848131|gb|EEE85678.1| predicted protein [Populus trichocarpa]

 Score =  384 bits (985), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 187/270 (69%), Positives = 224/270 (82%), Gaps = 12/270 (4%)

Query: 1   MADTICRTLRDGGLEGEHAPALTIKDSKASPFGFDVFNYVLTQLSNYILAGKSQSRGLVV 60
           MA+++CRTLRDG LEGE APALTIKD+ ASPFGF VF++VL+QLS++ILA KSQSRG+V+
Sbjct: 1   MAESMCRTLRDGSLEGEQAPALTIKDTAASPFGFHVFSHVLSQLSSFILASKSQSRGIVI 60

Query: 61  VAYSRSPSFYVDLLKRRGIDIASSHDWIHILDCYTDPLGWKNWLIDK----DISQE-ASS 115
           VA+SRSPSFYVDLLK RGID+ SSH W+ ILDCYTDPL WK+ L+      D S E +SS
Sbjct: 61  VAFSRSPSFYVDLLKSRGIDVNSSHKWVQILDCYTDPLCWKDQLMGSGNFMDASHETSSS 120

Query: 116 LSSFCQDVRNLDKLYSLIIEQGKG-------LIGQGKDRFSIAIDSVSEMVRHASISSVA 168
           LS  C+DV++LDKLYS+I+E GKG       L+GQGKDRFS+AID+++EM+RH S  +VA
Sbjct: 121 LSRVCKDVKDLDKLYSMILELGKGKFCVNFWLVGQGKDRFSVAIDTINEMLRHTSTPTVA 180

Query: 169 GILSNLRSHDQVSSIFWLLHSDLHEIKFTSVLEYLSSMVASVEPFNQAAFGQRVDLENLS 228
           G+LSNLRSH+Q+SSIFWLLHSDLHEIK TS LEYLSS+VASVEP +Q A G+R DLENLS
Sbjct: 181 GLLSNLRSHEQISSIFWLLHSDLHEIKVTSALEYLSSVVASVEPLHQTAGGKRGDLENLS 240

Query: 229 MLEQNFRKGKFHVRFKRRNGRVRVMASNLH 258
           +LEQNF KGK  VRFKRRNGRVRV+    H
Sbjct: 241 LLEQNFGKGKLQVRFKRRNGRVRVVNEGFH 270

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225452057|ref|XP_002283938.1| PREDICTED: uncharacterized protein LOC100258368 [Vitis vinifera] gi|296087267|emb|CBI33641.3| unnamed protein product [Vitis vinifera]

 Score =  352 bits (904), Expect = 6e-95,   Method: Compositional matrix adjust.
 Identities = 176/263 (66%), Positives = 208/263 (79%), Gaps = 6/263 (2%)

Query: 1   MADTICRTLRDGGLEGEHAPALTIKDSKASPFGFDVFNYVLTQLSNYILAGKSQSRGLVV 60
           MA++ICR LRDG LEGEHAPAL+IKDS A+PFG DVFNYVLT+LS+ ILAGKSQS+G+V+
Sbjct: 1   MAESICRNLRDGALEGEHAPALSIKDSIATPFGSDVFNYVLTKLSSNILAGKSQSKGIVL 60

Query: 61  VAYSRSPSFYVDLLKRRGIDIASSHDWIHILDCYTDPLGWKNWLIDKDISQEASSL---- 116
           VA+SRSPSFYVD LK  GID+ S+  WI ILDCYTDPLGWK+ L    +  E  SL    
Sbjct: 61  VAFSRSPSFYVDFLKTNGIDLVSAKKWISILDCYTDPLGWKDSL-KGPLDTENFSLKDPI 119

Query: 117 -SSFCQDVRNLDKLYSLIIEQGKGLIGQGKDRFSIAIDSVSEMVRHASISSVAGILSNLR 175
            +   + VRNLD L S IIE G+ L  QGK RFS++IDSV+EM+RHAS+SSVA +LS +R
Sbjct: 120 EAVLFRHVRNLDLLLSAIIEMGEALARQGKGRFSVSIDSVTEMLRHASLSSVANLLSKVR 179

Query: 176 SHDQVSSIFWLLHSDLHEIKFTSVLEYLSSMVASVEPFNQAAFGQRVDLENLSMLEQNFR 235
           SHD++SS FWLLHSDLHEI+  + LEYLSSMV S+EP N +  GQR DLE LS+LEQN R
Sbjct: 180 SHDRISSTFWLLHSDLHEIRAIAALEYLSSMVGSLEPMNLSLNGQRGDLEKLSLLEQNSR 239

Query: 236 KGKFHVRFKRRNGRVRVMASNLH 258
           KGKFHVRFKRRNGRVRVM  + H
Sbjct: 240 KGKFHVRFKRRNGRVRVMCEDFH 262

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356500866|ref|XP_003519251.1| PREDICTED: dermal papilla-derived protein 6 homolog [Glycine max]

 Score =  326 bits (835), Expect = 7e-87,   Method: Compositional matrix adjust.
 Identities = 163/257 (63%), Positives = 207/257 (80%), Gaps = 6/257 (2%)

Query: 1   MADTICRTLRDGGLEGEHAPALTIKDSKASPFGFDVFNYVLTQLSNYILAGKSQSRGLVV 60
           MAD+ICRTLRDG LEGE  P LTIKDS ASPF F VF+++L QLS++++A KSQS+G+V+
Sbjct: 1   MADSICRTLRDGALEGELVPTLTIKDSLASPFAFHVFSHILLQLSSHVIAQKSQSQGIVI 60

Query: 61  VAYSRSPSFYVDLLKRRGIDIASSHD-WIHILDCYTDPLGWKN----WLIDKDISQEASS 115
           VA SRSPS Y  LLK  G+D ASS++ WIHILDCYTDPLGWK+     +   + SQ+ S 
Sbjct: 61  VALSRSPSSYTSLLKMNGVDFASSNNKWIHILDCYTDPLGWKDKTRKTVNATNPSQQISL 120

Query: 116 LSSFCQDVRNLDKLYSLIIEQGKGLIGQGKDRFSIAIDSVSEMVRHASISSVAGILSNLR 175
            +S  + V+++DKL+S+I E G+GL+G+ K RF +AIDS+SE++RHAS+ SVAG+LSNLR
Sbjct: 121 ATSSYKSVKDVDKLFSVITELGRGLVGENKARFCVAIDSLSELLRHASLQSVAGLLSNLR 180

Query: 176 SHDQVSSIFWLLHSDLHEIKFTSVLEYLSSMVASVEPFNQAAFGQRVDLENLSMLEQNFR 235
           SHDQ+SSIF LLHSDLHE K  +VLEY+SSMVASV+P++ +A GQ+  LEN S+ EQNF 
Sbjct: 181 SHDQISSIFGLLHSDLHEEKAVAVLEYMSSMVASVDPYHHSADGQKECLEN-SVSEQNFT 239

Query: 236 KGKFHVRFKRRNGRVRV 252
           KGKF+ RFKRRNGRVRV
Sbjct: 240 KGKFNARFKRRNGRVRV 256

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|363814366|ref|NP_001242822.1| uncharacterized protein LOC100792556 [Glycine max] gi|255635746|gb|ACU18222.1| unknown [Glycine max]

 Score =  324 bits (830), Expect = 3e-86,   Method: Compositional matrix adjust.
 Identities = 161/256 (62%), Positives = 207/256 (80%), Gaps = 5/256 (1%)

Query: 1   MADTICRTLRDGGLEGEHAPALTIKDSKASPFGFDVFNYVLTQLSNYILAGKSQSRGLVV 60
           MAD+ICRTLRDG LEGE AP LTIKDS ASPF F VF+++L QLS++++A KSQS+G+V+
Sbjct: 1   MADSICRTLRDGALEGELAPTLTIKDSLASPFAFHVFSHILLQLSSHVIAQKSQSQGIVI 60

Query: 61  VAYSRSPSFYVDLLKRRGIDIASSHDWIHILDCYTDPLGWKNWLID----KDISQEASSL 116
           VA SRSPS Y  LLK  G+D+ASS+ WIHILDCYTDPLGWK+         D SQ+ S  
Sbjct: 61  VALSRSPSSYTSLLKMNGMDVASSNKWIHILDCYTDPLGWKDKARKSANVTDPSQQISLA 120

Query: 117 SSFCQDVRNLDKLYSLIIEQGKGLIGQGKDRFSIAIDSVSEMVRHASISSVAGILSNLRS 176
           +S  + V+++DKL+ +I E G+GLIG+ K RF +AIDS+SE++RHAS+ SVAG+LSNLRS
Sbjct: 121 TSSYKTVKDVDKLFLVIAELGRGLIGENKARFCVAIDSLSELLRHASMQSVAGLLSNLRS 180

Query: 177 HDQVSSIFWLLHSDLHEIKFTSVLEYLSSMVASVEPFNQAAFGQRVDLENLSMLEQNFRK 236
           HDQ+SS+F LLHSDLHE +  +VLEY+SSMVASV+P++ +A GQ+  LE+ S+ +Q+F K
Sbjct: 181 HDQISSMFGLLHSDLHEERAVAVLEYMSSMVASVDPYHHSADGQKRCLES-SLYDQSFTK 239

Query: 237 GKFHVRFKRRNGRVRV 252
           GKF+VRFKRRNGRVRV
Sbjct: 240 GKFNVRFKRRNGRVRV 255

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449455826|ref|XP_004145651.1| PREDICTED: elongator complex protein 5-like [Cucumis sativus]

 Score =  312 bits (800), Expect = 8e-83,   Method: Compositional matrix adjust.
 Identities = 151/269 (56%), Positives = 204/269 (75%), Gaps = 7/269 (2%)

Query: 1   MADTICRTLRDGGLEGEHAPALTIKDSKASPFGFDVFNYVLTQLSNYILAGKSQSRGLVV 60
           MA++ICR LRDG L+GE APALTIKD+  SPFGF  F++VLTQLS+ ILAGKSQSRGLV+
Sbjct: 1   MAESICRALRDGALQGELAPALTIKDNINSPFGFHAFSHVLTQLSSNILAGKSQSRGLVL 60

Query: 61  VAYSRSPSFYVDLLKRRGIDIASSHDWIHILDCYTDPLGWKNWLID----KDISQEASSL 116
           +++SRSP++YV LLK+RG+D+ SS  WI ILDCYTDPLGWK   ++     ++ QE S+L
Sbjct: 61  LSFSRSPAYYVQLLKKRGLDVGSSAKWIQILDCYTDPLGWKQRFMEGENVSNVDQEVSNL 120

Query: 117 SSFCQDVRNLDKLYSLIIEQGKGLIGQGKDRFSIAIDSVSEMVRHASISSVAGILSNLRS 176
           S  C +V ++DKL+S II  GKG +G+G  RF +A+DSV+ M+RH+SIS++AG+LS+LRS
Sbjct: 121 SHLCTNVGDMDKLFSSIIALGKGFVGEGTVRFCVAVDSVTNMLRHSSISALAGLLSSLRS 180

Query: 177 HDQVSSIFWLLHSDLHEIKFTSVLEYLSSMVASVEPFNQAAFGQRVDLENLSMLEQNFRK 236
           +D VSS  WL+H DLHE K  +  EY+SS+VA++E    + +  R +++N S LE    K
Sbjct: 181 NDSVSSTLWLVHEDLHEEKVIAAFEYMSSIVATLEALTPSPYVSRSNMDN-SYLEHRSTK 239

Query: 237 GKFHVRFKRRNGRVRVMAS--NLHQFCLK 263
           G+FHVR KRRNGRVRV++   N+ Q  +K
Sbjct: 240 GRFHVRMKRRNGRVRVISEDFNVEQSGIK 268

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297832500|ref|XP_002884132.1| hypothetical protein ARALYDRAFT_319792 [Arabidopsis lyrata subsp. lyrata] gi|297329972|gb|EFH60391.1| hypothetical protein ARALYDRAFT_319792 [Arabidopsis lyrata subsp. lyrata]

 Score =  294 bits (752), Expect = 3e-77,   Method: Compositional matrix adjust.
 Identities = 146/260 (56%), Positives = 197/260 (75%), Gaps = 6/260 (2%)

Query: 1   MADTICRTLRDGGLEGEHAPALTIKDSKASPFGFDVFNYVLTQLSNYILAGKSQSRGLVV 60
           MA++I R LRDGG EGE APALTI+++ ASPFG DV  Y+LT LS+ ILAGKS+S+GLV+
Sbjct: 1   MAESIFRKLRDGGEEGELAPALTIEETVASPFGIDVSGYLLTNLSSSILAGKSKSQGLVL 60

Query: 61  VAYSRSPSFYVDLLKRRGIDIASSHDWIHILDCYTDPLGWKNWLIDKDIS--QEASSLSS 118
           + +SRSPSFY+ LLK+RGI ++SS  WI ILDCYTDPLGW    I +  S   E SSL  
Sbjct: 61  ITFSRSPSFYLQLLKQRGIVVSSSSKWIRILDCYTDPLGW----IHEPSSGFSEGSSLIK 116

Query: 119 FCQDVRNLDKLYSLIIEQGKGLIGQGKDRFSIAIDSVSEMVRHASISSVAGILSNLRSHD 178
             + V +L KL+S +IE G+ L+G GK  F +AIDSV+E++RH+S+  V+G+L++LRSH 
Sbjct: 117 LHKCVSDLRKLFSTVIEAGRELVGAGKTHFCVAIDSVNELLRHSSMPLVSGLLTDLRSHA 176

Query: 179 QVSSIFWLLHSDLHEIKFTSVLEYLSSMVASVEPFNQAAFGQRVDLENLSMLEQNFRKGK 238
           Q++S+FW L++DLH+ K T+ LEY+S+M A++EP   ++ GQR  LENL ++ Q+F KG+
Sbjct: 177 QITSVFWSLNTDLHQEKVTNALEYISTMKANLEPLCPSSDGQRNALENLFLVHQDFGKGR 236

Query: 239 FHVRFKRRNGRVRVMASNLH 258
           FHVRFK R GRVRVM+   H
Sbjct: 237 FHVRFKLRKGRVRVMSEEYH 256

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|79322467|ref|NP_001031371.1| uncharacterized protein [Arabidopsis thaliana] gi|330251673|gb|AEC06767.1| uncharacterized protein [Arabidopsis thaliana]

 Score =  289 bits (739), Expect = 8e-76,   Method: Compositional matrix adjust.
 Identities = 144/260 (55%), Positives = 195/260 (75%), Gaps = 6/260 (2%)

Query: 1   MADTICRTLRDGGLEGEHAPALTIKDSKASPFGFDVFNYVLTQLSNYILAGKSQSRGLVV 60
           MA++I R LRDGG EGE APALTI+++ ASPFG DV  Y+LT LS+ ILAGKS S+GLV+
Sbjct: 1   MAESIFRKLRDGGEEGELAPALTIEETVASPFGLDVSGYLLTNLSSSILAGKSSSQGLVL 60

Query: 61  VAYSRSPSFYVDLLKRRGIDIASSHDWIHILDCYTDPLGWKNWLIDKDISQEASS--LSS 118
           + +SRSPSFY+ LLK++GI ++SS  WI ILDCYTDPLGW    ID+  +  +    L  
Sbjct: 61  ITFSRSPSFYLQLLKQKGIVVSSSSKWIRILDCYTDPLGW----IDQSSTSFSEGSSLIK 116

Query: 119 FCQDVRNLDKLYSLIIEQGKGLIGQGKDRFSIAIDSVSEMVRHASISSVAGILSNLRSHD 178
             + V +L KL+S IIE G+ L+G GK RF +AIDSV+E++RH+++  V+G+L++LRSH 
Sbjct: 117 LHKCVSDLKKLFSSIIEAGRELVGTGKTRFCVAIDSVNELLRHSAMPLVSGLLTDLRSHA 176

Query: 179 QVSSIFWLLHSDLHEIKFTSVLEYLSSMVASVEPFNQAAFGQRVDLENLSMLEQNFRKGK 238
           Q+SS+FW L++DLH+ K T+ LEY+S+M A++EP   ++ GQR  LENL  + Q+F KG+
Sbjct: 177 QISSVFWSLNTDLHQEKVTNALEYISTMKANLEPLCPSSDGQRNALENLFSVHQDFGKGR 236

Query: 239 FHVRFKRRNGRVRVMASNLH 258
           FHVRFK R GRVRVM+   H
Sbjct: 237 FHVRFKLRKGRVRVMSEEYH 256

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|42569125|ref|NP_179432.3| uncharacterized protein [Arabidopsis thaliana] gi|385178681|sp|F4IQJ2.1|ELP5_ARATH RecName: Full=Elongator complex protein 5; Short=AtELP5; AltName: Full=Elongator component 5 gi|330251672|gb|AEC06766.1| uncharacterized protein [Arabidopsis thaliana]

 Score =  289 bits (739), Expect = 9e-76,   Method: Compositional matrix adjust.
 Identities = 144/260 (55%), Positives = 195/260 (75%), Gaps = 6/260 (2%)

Query: 1   MADTICRTLRDGGLEGEHAPALTIKDSKASPFGFDVFNYVLTQLSNYILAGKSQSRGLVV 60
           MA++I R LRDGG EGE APALTI+++ ASPFG DV  Y+LT LS+ ILAGKS S+GLV+
Sbjct: 1   MAESIFRKLRDGGEEGELAPALTIEETVASPFGLDVSGYLLTNLSSSILAGKSSSQGLVL 60

Query: 61  VAYSRSPSFYVDLLKRRGIDIASSHDWIHILDCYTDPLGWKNWLIDKDISQEASS--LSS 118
           + +SRSPSFY+ LLK++GI ++SS  WI ILDCYTDPLGW    ID+  +  +    L  
Sbjct: 61  ITFSRSPSFYLQLLKQKGIVVSSSSKWIRILDCYTDPLGW----IDQSSTSFSEGSSLIK 116

Query: 119 FCQDVRNLDKLYSLIIEQGKGLIGQGKDRFSIAIDSVSEMVRHASISSVAGILSNLRSHD 178
             + V +L KL+S IIE G+ L+G GK RF +AIDSV+E++RH+++  V+G+L++LRSH 
Sbjct: 117 LHKCVSDLKKLFSSIIEAGRELVGTGKTRFCVAIDSVNELLRHSAMPLVSGLLTDLRSHA 176

Query: 179 QVSSIFWLLHSDLHEIKFTSVLEYLSSMVASVEPFNQAAFGQRVDLENLSMLEQNFRKGK 238
           Q+SS+FW L++DLH+ K T+ LEY+S+M A++EP   ++ GQR  LENL  + Q+F KG+
Sbjct: 177 QISSVFWSLNTDLHQEKVTNALEYISTMKANLEPLCPSSDGQRNALENLFSVHQDFGKGR 236

Query: 239 FHVRFKRRNGRVRVMASNLH 258
           FHVRFK R GRVRVM+   H
Sbjct: 237 FHVRFKLRKGRVRVMSEEYH 256

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

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	265
TAIR|locus:2062190	374	AT2G18410 "AT2G18410" [Arabido	0.958	0.679	0.565	1.6e-72

TAIR|locus:2062190 AT2G18410 "AT2G18410" [Arabidopsis thaliana (taxid:3702)]

 Score = 733 (263.1 bits), Expect = 1.6e-72, P = 1.6e-72
 Identities = 147/260 (56%), Positives = 197/260 (75%)

Query:     1 MADTICRTLRDGGLEGEHAPALTIKDSKASPFGFDVFNYVLTQLSNYILAGKSQSRGLVV 60
             MA++I R LRDGG EGE APALTI+++ ASPFG DV  Y+LT LS+ ILAGKS S+GLV+
Sbjct:     1 MAESIFRKLRDGGEEGELAPALTIEETVASPFGLDVSGYLLTNLSSSILAGKSSSQGLVL 60

Query:    61 VAYSRSPSFYVDLLKRRGIDIASSHDWIHILDCYTDPLGWKNWLIDKDISQ--EASSLSS 118
             + +SRSPSFY+ LLK++GI ++SS  WI ILDCYTDPLGW    ID+  +   E SSL  
Sbjct:    61 ITFSRSPSFYLQLLKQKGIVVSSSSKWIRILDCYTDPLGW----IDQSSTSFSEGSSLIK 116

Query:   119 FCQDVRNLDKLYSLIIEQGKGLIGQGKDRFSIAIDSVSEMVRHASISSVAGILSNLRSHD 178
               + V +L KL+S IIE G+ L+G GK RF +AIDSV+E++RH+++  V+G+L++LRSH 
Sbjct:   117 LHKCVSDLKKLFSSIIEAGRELVGTGKTRFCVAIDSVNELLRHSAMPLVSGLLTDLRSHA 176

Query:   179 QVSSIFWLLHSDLHEIKFTSVLEYLSSMVASVEPFNQAAFGQRVDLENLSMLEQNFRKGK 238
             Q+SS+FW L++DLH+ K T+ LEY+S+M A++EP   ++ GQR  LENL  + Q+F KG+
Sbjct:   177 QISSVFWSLNTDLHQEKVTNALEYISTMKANLEPLCPSSDGQRNALENLFSVHQDFGKGR 236

Query:   239 FHVRFKRRNGRVRVMASNLH 258
             FHVRFK R GRVRVM+   H
Sbjct:   237 FHVRFKLRKGRVRVMSEEYH 256


Parameters:
  V=100
  filter=SEG
  E=0.001

  ctxfactor=1.00

  Query                        -----  As Used  -----    -----  Computed  ----
  Frame  MatID Matrix name     Lambda    K       H      Lambda    K       H
   +0      0   BLOSUM62        0.322   0.136   0.400    same    same    same
               Q=9,R=2         0.244   0.0300  0.180     n/a     n/a     n/a

  Query
  Frame  MatID  Length  Eff.Length     E     S W   T  X   E2     S2
   +0      0      265       265   0.00093  114 3  11 22  0.43    33
                                                     32  0.50    36


Statistics:

  Database:  /share/blast/go-seqdb.fasta
   Title:  go_20130330-seqdb.fasta
   Posted:  5:47:42 AM PDT Apr 1, 2013
   Created:  5:47:42 AM PDT Apr 1, 2013
   Format:  XDF-1
   # of letters in database:  169,044,731
   # of sequences in database:  368,745
   # of database sequences satisfying E:  1
  No. of states in DFA:  601 (64 KB)
  Total size of DFA:  197 KB (2112 KB)
  Time to generate neighborhood:  0.00u 0.00s 0.00t   Elapsed:  00:00:00
  No. of threads or processors used:  24
  Search cpu time:  22.51u 0.08s 22.59t   Elapsed:  00:00:04
  Total cpu time:  22.51u 0.08s 22.59t   Elapsed:  00:00:04
  Start:  Fri May 10 17:26:36 2013   End:  Fri May 10 17:26:40 2013

GO:0003674 "molecular_function" evidence=ND

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

GO:0006626 "protein targeting to mitochondrion" evidence=RCA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: estExt_Genewise1_v1.C_LG_IV3252 SubName- Full=Putative uncharacterized protein; (386 aa) (Populus trichocarpa)

Predicted Functional Partners:

Sorry, there are no predicted associations at the current settings.

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	265
PF10483	280	Elong_Iki1: Elongator subunit Iki1; InterPro: IPR0	99.92
PF09807	249	DUF2348: Uncharacterized conserved protein (DUF234	99.18
PF06745	226	KaiC: KaiC; InterPro: IPR014774 This entry represe	98.24
TIGR03877	237	thermo_KaiC_1 KaiC domain protein, Ph0284 family.	97.89
PRK06067	234	flagellar accessory protein FlaH; Validated	97.79
PRK04328	249	hypothetical protein; Provisional	97.67
COG2874	235	FlaH Predicted ATPases involved in biogenesis of a	97.39
PRK09302	509	circadian clock protein KaiC; Reviewed	97.26
PRK09302	509	circadian clock protein KaiC; Reviewed	96.77
TIGR02655	484	circ_KaiC circadian clock protein KaiC. Members of	96.22
TIGR03881	229	KaiC_arch_4 KaiC domain protein, PAE1156 family. M	96.12
cd01124	187	KaiC KaiC is a circadian clock protein primarily f	96.01
TIGR02655	484	circ_KaiC circadian clock protein KaiC. Members of	95.77
COG0467	260	RAD55 RecA-superfamily ATPases implicated in signa	95.4
TIGR03878	259	thermo_KaiC_2 KaiC domain protein, AF_0795 family.	95.35
PRK08533	230	flagellar accessory protein FlaH; Reviewed	94.77
TIGR03880	224	KaiC_arch_3 KaiC domain protein, AF_0351 family. T	94.33
KOG4723	248	consensus Uncharacterized conserved protein [Funct	94.26
PRK05973	237	replicative DNA helicase; Provisional	93.33
TIGR02237	209	recomb_radB DNA repair and recombination protein R	93.02
PF05625	363	PAXNEB: PAXNEB protein; InterPro: IPR008728 The RN	91.66
PRK04301	317	radA DNA repair and recombination protein RadA; Va	90.71
cd01121	372	Sms Sms (bacterial radA) DNA repair protein. This	90.22
PRK11823	446	DNA repair protein RadA; Provisional	90.12
cd01393	226	recA_like RecA is a bacterial enzyme which has rol	89.31
TIGR02236	310	recomb_radA DNA repair and recombination protein R	88.8
PRK09361	225	radB DNA repair and recombination protein RadB; Pr	88.23
cd01123	235	Rad51_DMC1_radA Rad51_DMC1_radA,B. This group of r	87.26
cd01122	271	GP4d_helicase GP4d_helicase is a homohexameric 5'-	85.63
PTZ00035	337	Rad51 protein; Provisional	83.76
cd00984	242	DnaB_C DnaB helicase C terminal domain. The hexame	83.26
PF03192	210	DUF257: Pyrococcus protein of unknown function, DU	81.67
TIGR02238	313	recomb_DMC1 meiotic recombinase Dmc1. This model d	81.14
TIGR02239	316	recomb_RAD51 DNA repair protein RAD51. This eukary	80.31
cd01394	218	radB RadB. The archaeal protein radB shares simila	80.04

>PF10483 Elong_Iki1: Elongator subunit Iki1; InterPro: IPR019519 Histone acetylation protein (Hap) 2 (also known as Elongator complex protein 5) is one of three histone acetyltransferases proteins that, in yeasts, are found associated with elongating forms of RNA polymerase II (Elongator)

Probab=99.92  E-value=1.4e-25  Score=206.50  Aligned_cols=184  Identities=22%  Similarity=0.230  Sum_probs=110.5

Q ss_pred             CCCCceeeccCCCCCchhhHHHHHHHHHHHHHHhhccccceeEEEEeeCChHHHHHHHhhcCCCccCCCCeEEEEeccCC
Q 024646           17 EHAPALTIKDSKASPFGFDVFNYVLTQLSNYILAGKSQSRGLVVVAYSRSPSFYVDLLKRRGIDIASSHDWIHILDCYTD   96 (265)
Q Consensus        17 e~ap~l~i~Dsl~~~~g~~~~~h~~~~l~s~i~a~~~q~~~Vhvl~fe~spe~y~~~lk~~G~d~~~~~~~v~i~D~ysD   96 (265)
                      |..|+++|.||++.|+ ..+++++       |+..+.++..||+|+||.+++  .+     |+|...        +|-  
T Consensus        10 d~spl~Li~DSl~q~a-~~Ll~e~-------i~~a~~~~~~V~~lsfEt~~~--~~-----~~d~~~--------~~~--   64 (280)
T PF10483_consen   10 DASPLTLILDSLEQSA-RPLLKEF-------IRRAKSRNEKVHFLSFETLNK--PE-----YADSFI--------NAR--   64 (280)
T ss_dssp             S--SEEEEEEBTTB-S-HHHHHHH-------HHHHTS----EEEEESS--S----T-----T-SEEE--------ETT--
T ss_pred             CCCCeEEEEEcccccC-HHHHHHH-------HHHHHcCCCeEEEEEeEeCCC--cc-----cCCeec--------ccc--
Confidence            3789999999999985 6666664       445688899999999999876  44     665333        222  


Q ss_pred             CCCCcccccCccccccccccccccccchhhhHHHHHHHHhccCccCCCCCcEEEEEechhHHHHhcChHHHHHHHHhhhc
Q 024646           97 PLGWKNWLIDKDISQEASSLSSFCQDVRNLDKLYSLIIEQGKGLIGQGKDRFSIAIDSVSEMVRHASISSVAGILSNLRS  176 (265)
Q Consensus        97 PlgW~~~~~~~~~~~~~s~~~~~~~~v~~L~sl~~~~~e~~~~~~~~~k~r~~VaIDSLS~LL~h~s~~~vc~lL~~Lr~  176 (265)
                        +|+-                        .+++..+.........+++.+++|+|||||||+.|+++ +++++|++|++
T Consensus        65 --~~~~------------------------~~i~~~i~s~~~~~~~~~~~~~lVvIDSLn~ll~~~~~-~l~~fLssl~~  117 (280)
T PF10483_consen   65 --GKSL------------------------QDIVKEIKSHLPSSSSSPTKKFLVVIDSLNYLLNHHPC-QLSQFLSSLLS  117 (280)
T ss_dssp             --SS-H------------------------HHHHHHHHHTS--SS-SS---EEEEES-GGGS-GG----GHHHHHHHH--
T ss_pred             --CCCH------------------------HHHHHHHHhhcccccccCCCCeEEEEEcchHHHHHHHH-HHHHHHHhccc
Confidence              3321                        11112222221111222344599999999999999999 99999999998


Q ss_pred             CCceeEEEEeecccc-------cchhHHHHHHhhheeEEEeeeCCcccccccchhhhhhhhh------hccccceEEEEe
Q 024646          177 HDQVSSIFWLLHSDL-------HEIKFTSVLEYLSSMVASVEPFNQAAFGQRVDLENLSMLE------QNFRKGKFHVRF  243 (265)
Q Consensus       177 ~~~vssVl~LLHsDL-------He~~vv~ALe~LAs~vv~v~P~~~~~~~~~~~~~~~~~l~------~n~~kg~~~vr~  243 (265)
                      +++ ++|||++|+|+       |+|+++.+|+|||||+++|+|........+++.+++.-++      .|..+.++++++
T Consensus       118 ~p~-~svv~~~H~Dl~~~~~~~~~P~~l~lL~~LATtii~v~~~~~~~~~~~~~~~~l~~~~~g~~~~~~~~~~~~~l~~  196 (280)
T PF10483_consen  118 SPQ-SSVVGLYHTDLLPPSQNPYYPSPLSLLSYLATTIITVEPLSHISADKEALDRSLSKPEFGLGEGLNGVGFVLELEN  196 (280)
T ss_dssp             -TT-EEEEEEEETTS---TTB-TS--HHHHHHHH-SEEEEEEE---SS--HHHHHHHHHTT---SS---S-SEEEEEEEE
T ss_pred             CCC-cEEEEEEccCcCcccccccCcCHHHHHHHhceEEEEEcccCccchhHHHHHhhhhhcccChhhhccCceEEEEEEE
Confidence            888 78999999999       9999999999999999999999998888877777766554      445577899999


Q ss_pred             ecCCCchhhh
Q 024646          244 KRRNGRVRVM  253 (265)
Q Consensus       244 KrrnGRV~~~  253 (265)
                      |||+||+...
T Consensus       197 RrksGR~~~e  206 (280)
T PF10483_consen  197 RRKSGRVVSE  206 (280)
T ss_dssp             E-TTS-EEEE
T ss_pred             EcCCCCcEeE
Confidence            9999998654

The Haps can be isolated in two forms, as a six-subunit complex with Elongator, and as a complex of the three proteins on their own. The role of the Hap complex in transcription is still speculative, being possibly to keep the histone acetylation activity of free Elongator in check, allowing histone acetylation only in the presence of a transcribing polymerase, or the interaction with Haps might render Elongator susceptible to modifications thereby altering its activity []. This protein family also contains Dermal papilla-derived protein 6, which also belong to the ELP5 family. ; PDB: 4A8J_B 4EJS_B.

>PF09807 DUF2348: Uncharacterized conserved protein (DUF2348); InterPro: IPR018627 Members of this family of putative uncharacterised proteins have no known function

Probab=99.18  E-value=2e-09  Score=98.31  Aligned_cols=185  Identities=18%  Similarity=0.244  Sum_probs=128.9

Q ss_pred             CCCceeeccCCCCCchhhHHHHHHHHHHHHHHhhccccceeEEEEeeCChHHHHHHHhhcCCCccCC--CCeEEEEeccC
Q 024646           18 HAPALTIKDSKASPFGFDVFNYVLTQLSNYILAGKSQSRGLVVVAYSRSPSFYVDLLKRRGIDIASS--HDWIHILDCYT   95 (265)
Q Consensus        18 ~ap~l~i~Dsl~~~~g~~~~~h~~~~l~s~i~a~~~q~~~Vhvl~fe~spe~y~~~lk~~G~d~~~~--~~~v~i~D~ys   95 (265)
                      ..-+++|+|+ .+++ .=+..|++.   .+++    .+..|.+|+|..+.+.|...++|-|++-...  +.+++++|..+
T Consensus        18 ~g~~ili~d~-~~dg-sFLlh~~L~---~~Lk----~~~~V~fv~~~q~~~HY~~v~~KLG~NL~~~~~~gql~fiD~l~   88 (249)
T PF09807_consen   18 PGKLILIEDC-ETDG-SFLLHHFLS---QYLK----AGCKVCFVAFSQSFSHYNNVAQKLGVNLSAAKEKGQLVFIDGLK   88 (249)
T ss_pred             CCeEEEEEcC-CCCc-hhHHHHHHH---HHhc----CCCcEEEEEccCCHHHHHHHHHhhEecchHhccCCcEEEeehhh
Confidence            3447999999 8875 556666553   3333    4558999999999999999999999987652  34799999999


Q ss_pred             CCCCCcccccCccccccccccccccccchhhhHHHHHHHHhccCccCCCCCcEEEEEechhHHHH-hcChHHHHHHHHhh
Q 024646           96 DPLGWKNWLIDKDISQEASSLSSFCQDVRNLDKLYSLIIEQGKGLIGQGKDRFSIAIDSVSEMVR-HASISSVAGILSNL  174 (265)
Q Consensus        96 DPlgW~~~~~~~~~~~~~s~~~~~~~~v~~L~sl~~~~~e~~~~~~~~~k~r~~VaIDSLS~LL~-h~s~~~vc~lL~~L  174 (265)
                      ++++|--....++...  +..+.--.+...|.+++..+.+..+...+ .++ ++|+||-||.|+- ..+..+|..+++.+
T Consensus        89 ~~~~~l~~~~~~~~~~--~~~~l~~~~~~~L~~L~~~I~~~l~~~~~-~~~-~~liIDdls~Ll~lG~s~~~vldF~~yc  164 (249)
T PF09807_consen   89 SSLDLLFDEDSSDEPN--PLKFLREDNASSLRSLYEFIQEALSPADS-NGS-VVLIIDDLSVLLSLGVSSNDVLDFIHYC  164 (249)
T ss_pred             hhhhhhhccccccCCc--cccccccCCcchHHHHHHHHHHHHhhccC-CCC-eEEEEeCHHHHHHcCCCHHHHHHHHHHH
Confidence            8887743211000000  11111111234578887777665552222 233 8999999999997 34556889999999


Q ss_pred             hc---CCceeEEEEeecccccc----hh-HHHHHHhhheeEEEeeeCCc
Q 024646          175 RS---HDQVSSIFWLLHSDLHE----IK-FTSVLEYLSSMVASVEPFNQ  215 (265)
Q Consensus       175 r~---~~~vssVl~LLHsDLHe----~~-vv~ALe~LAs~vv~v~P~~~  215 (265)
                      |.   ...-.+++.+.|.|-..    .. ....|+|+|..+|+++|...
T Consensus       165 ra~l~~~~~~~lVvl~h~d~~~~~e~~~~l~~~L~h~a~l~i~v~~L~T  213 (249)
T PF09807_consen  165 RATLCSESNGSLVVLVHCDIDDEDEENDLLLNSLAHMADLVITVEPLPT  213 (249)
T ss_pred             HHHhccccCCCEEEEEecCCCCccchHHHHHHHHHHHhcEEEEecCCCC
Confidence            84   23346899999998652    22 78999999999999999654

>PF06745 KaiC: KaiC; InterPro: IPR014774 This entry represents a domain within bacterial and archaeal proteins, most of which are hypothetical

Probab=98.24  E-value=4.7e-06  Score=72.99  Aligned_cols=137  Identities=20%  Similarity=0.243  Sum_probs=90.5

Q ss_pred             hhccc-cceeEEEEeeCChHHHHHHHhhcCCCccCC--CCeEEEEeccCCCCCCcccccCccccccccccccccccchhh
Q 024646           50 AGKSQ-SRGLVVVAYSRSPSFYVDLLKRRGIDIASS--HDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNL  126 (265)
Q Consensus        50 a~~~q-~~~Vhvl~fe~spe~y~~~lk~~G~d~~~~--~~~v~i~D~ysDPlgW~~~~~~~~~~~~~s~~~~~~~~v~~L  126 (265)
                      ++..+ ++.+..+.+|.+|+++.+-++..|+|.+..  +.++.++|+++...+|..  .                ++..+
T Consensus        42 ~~~~~~ge~vlyvs~ee~~~~l~~~~~s~g~d~~~~~~~g~l~~~d~~~~~~~~~~--~----------------~~~~l  103 (226)
T PF06745_consen   42 NGLKNFGEKVLYVSFEEPPEELIENMKSFGWDLEEYEDSGKLKIIDAFPERIGWSP--N----------------DLEEL  103 (226)
T ss_dssp             HHHHHHT--EEEEESSS-HHHHHHHHHTTTS-HHHHHHTTSEEEEESSGGGST-TS--C----------------CHHHH
T ss_pred             HhhhhcCCcEEEEEecCCHHHHHHHHHHcCCcHHHHhhcCCEEEEecccccccccc--c----------------CHHHH
Confidence            45666 899999999999999999999999875541  336999999999988872  1                12232


Q ss_pred             hHHHHHHHHhccCccCCCCCcEEEEEechhHHHHhcChHHHHHHHHhhhcC---CceeEEEEeecccccchhHHHHHHh-
Q 024646          127 DKLYSLIIEQGKGLIGQGKDRFSIAIDSVSEMVRHASISSVAGILSNLRSH---DQVSSIFWLLHSDLHEIKFTSVLEY-  202 (265)
Q Consensus       127 ~sl~~~~~e~~~~~~~~~k~r~~VaIDSLS~LL~h~s~~~vc~lL~~Lr~~---~~vssVl~LLHsDLHe~~vv~ALe~-  202 (265)
                      ...+...++..       ++ -.|+||||+.|....+...+-.+|+.|.+.   ..+..++..-..+-+++.....+++ 
T Consensus       104 ~~~i~~~i~~~-------~~-~~vVIDsls~l~~~~~~~~~r~~l~~l~~~l~~~~~t~llt~~~~~~~~~~~~~~i~~~  175 (226)
T PF06745_consen  104 LSKIREAIEEL-------KP-DRVVIDSLSALLLYDDPEELRRFLRALIKFLKSRGVTTLLTSEMPSGSEDDGTFGIEHY  175 (226)
T ss_dssp             HHHHHHHHHHH-------TS-SEEEEETHHHHTTSSSGGGHHHHHHHHHHHHHHTTEEEEEEEEESSSSSSSSSTSHHHH
T ss_pred             HHHHHHHHHhc-------CC-CEEEEECHHHHhhcCCHHHHHHHHHHHHHHHHHCCCEEEEEEccccCcccccccchhhh
Confidence            22223333322       22 589999999997777777666666666652   4455555544344555666666766 


Q ss_pred             hheeEEEeee
Q 024646          203 LSSMVASVEP  212 (265)
Q Consensus       203 LAs~vv~v~P  212 (265)
                      ++.++|.+.-
T Consensus       176 l~D~vI~L~~  185 (226)
T PF06745_consen  176 LADGVIELRY  185 (226)
T ss_dssp             HSSEEEEEEE
T ss_pred             cccEEEEEEE
Confidence            9999999965

More than one copy is sometimes found in each protein in this entry. These include KaiC, which is one of the Kai proteins among which direct protein-protein association may be a critical process in the generation of circadian rhythms in cyanobacteria []. The circadian clock protein KaiC, is encoded in the kaiABC operon that controls circadian rhythms and may be universal in Cyanobacteria. Each member contains two copies of this domain, which is also found in other proteins. KaiC performs autophosphorylation and acts as its own transcriptional repressor. RadA/Sms is a highly conserved eubacterial protein that shares sequence similarity with both RecA strand transferase and lon protease. The RadA/Sms family are probable ATP-dependent proteases involved in both DNA repair and degradation of proteins, peptides, glycopeptides. They are classified in as non-peptidase homologues and unassigned peptidases in MEROPS peptidase family S16 (lon protease family, clan SJ). RadA/Sms is involved in recombination and recombinational repair, most likely involving the stabilisation or processing of branched DNA molecules or blocked replication forks because of its genetic redundancy with RecG and RuvABC [].; PDB: 2W0M_A 2ZTS_C 4DUG_B 3K0E_B 3K09_B 3S1A_E 3JZM_E 2GBL_B 3DVL_A 1TF7_C ....

>TIGR03877 thermo_KaiC_1 KaiC domain protein, Ph0284 family

Probab=97.89  E-value=0.00013  Score=65.18  Aligned_cols=143  Identities=17%  Similarity=0.181  Sum_probs=83.9

Q ss_pred             hccccceeEEEEeeCChHHHHHHHhhcCCCccC--CCCeEEEEeccCCCCCCcccccCccccccccccccccccchhhhH
Q 024646           51 GKSQSRGLVVVAYSRSPSFYVDLLKRRGIDIAS--SHDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNLDK  128 (265)
Q Consensus        51 ~~~q~~~Vhvl~fe~spe~y~~~lk~~G~d~~~--~~~~v~i~D~ysDPlgW~~~~~~~~~~~~~s~~~~~~~~v~~L~s  128 (265)
                      +..+++.+..+.+|-+|+++.+-++..|+|...  -..++.++|||++-.++......          + +..+..++..
T Consensus        45 ~~~~ge~~lyvs~ee~~~~i~~~~~~~g~~~~~~~~~g~l~~~d~~~~~~~~~~~~~~----------~-~~~~~~~~~~  113 (237)
T TIGR03877        45 GLQMGEPGIYVALEEHPVQVRRNMAQFGWDVRKYEEEGKFAIVDAFTGGIGEAAEREK----------Y-VVKDPTDVRE  113 (237)
T ss_pred             HHHcCCcEEEEEeeCCHHHHHHHHHHhCCCHHHHhhcCCEEEEecccccccccccccc----------c-cccCcccHHH
Confidence            445689999999999999999999999987532  13479999999986554431110          0 1112224444


Q ss_pred             HHHHHHHhccCccCCCCCcEEEEEechhHHHHhcCh---HHHHHHHHhhhcCCceeEEEEeecccccchhH-HHHHHhhh
Q 024646          129 LYSLIIEQGKGLIGQGKDRFSIAIDSVSEMVRHASI---SSVAGILSNLRSHDQVSSIFWLLHSDLHEIKF-TSVLEYLS  204 (265)
Q Consensus       129 l~~~~~e~~~~~~~~~k~r~~VaIDSLS~LL~h~s~---~~vc~lL~~Lr~~~~vssVl~LLHsDLHe~~v-v~ALe~LA  204 (265)
                      ++..+.+..+    +.++ -.|+||||+.++...+.   ..+.++.+.+++.. +..++ .-|.+..+... ...++|++
T Consensus       114 ~~~~i~~~i~----~~~~-~~vVIDSls~l~~~~~~~~r~~l~~l~~~lk~~~-~t~ll-t~~~~~~~~~~~~~~~~~~~  186 (237)
T TIGR03877       114 LIDVLRQAIR----DINA-KRVVIDSVTTLYITKPAMARSIVMQLKRVLSGLG-CTSIF-VSQVSVGERGFGGPGVEHAV  186 (237)
T ss_pred             HHHHHHHHHH----HhCC-CEEEEcChhHhhcCChHHHHHHHHHHHHHHHhCC-CEEEE-EECcccccccccccceEEEE
Confidence            4344333221    1123 37999999998764432   22344444555433 33333 23332222111 12478999


Q ss_pred             eeEEEee
Q 024646          205 SMVASVE  211 (265)
Q Consensus       205 s~vv~v~  211 (265)
                      -++|.+.
T Consensus       187 D~vI~L~  193 (237)
T TIGR03877       187 DGIIRLD  193 (237)
T ss_pred             eEEEEEE
Confidence            9999986

Members of this family contain a single copy of the KaiC domain (pfam06745) that occurs in two copies of the circadian clock protein kinase KaiC itself. Members occur primarily in thermophilic archaea and in Thermotoga.

>PRK06067 flagellar accessory protein FlaH; Validated

Probab=97.79  E-value=0.00059  Score=60.30  Aligned_cols=136  Identities=17%  Similarity=0.236  Sum_probs=93.9

Q ss_pred             ccccceeEEEEeeCChHHHHHHHhhcCCCccCC--CCeEEEEeccCCCCCCcccccCccccccccccccccccchhhhHH
Q 024646           52 KSQSRGLVVVAYSRSPSFYVDLLKRRGIDIASS--HDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNLDKL  129 (265)
Q Consensus        52 ~~q~~~Vhvl~fe~spe~y~~~lk~~G~d~~~~--~~~v~i~D~ysDPlgW~~~~~~~~~~~~~s~~~~~~~~v~~L~sl  129 (265)
                      ..+++.+..+.+|.+|+++.+-+.+.|+|....  ...+.++|.+..+..|...                  +.+++-..
T Consensus        50 ~~~g~~~~y~~~e~~~~~~~~~~~~~g~~~~~~~~~g~l~i~~~~~~~~~~~~~------------------~~~~ll~~  111 (234)
T PRK06067         50 LKQGKKVYVITTENTSKSYLKQMESVKIDISDFFLWGYLRIFPLNTEGFEWNST------------------LANKLLEL  111 (234)
T ss_pred             HhCCCEEEEEEcCCCHHHHHHHHHHCCCChhHHHhCCCceEEeccccccccCcc------------------hHHHHHHH
Confidence            346899999999999999999999999876541  3357778877766665541                  11222222


Q ss_pred             HHHHHHhccCccCCCCCcEEEEEechhHHHHhcChHHHHHHHHhhhcC-CceeEEEEeecccccchhHHHHHHhhheeEE
Q 024646          130 YSLIIEQGKGLIGQGKDRFSIAIDSVSEMVRHASISSVAGILSNLRSH-DQVSSIFWLLHSDLHEIKFTSVLEYLSSMVA  208 (265)
Q Consensus       130 ~~~~~e~~~~~~~~~k~r~~VaIDSLS~LL~h~s~~~vc~lL~~Lr~~-~~vssVl~LLHsDLHe~~vv~ALe~LAs~vv  208 (265)
                      +...++.       .++ -.|+|||++.++...+...+..++..|+.. ..=..++...|.+.+.......+++++-.++
T Consensus       112 l~~~i~~-------~~~-~~iviDs~t~~~~~~~~~~~~~~l~~l~~l~~~g~tvllt~~~~~~~~~~~~~~~~l~DgvI  183 (234)
T PRK06067        112 IIEFIKS-------KRE-DVIIIDSLTIFATYAEEDDILNFLTEAKNLVDLGKTILITLHPYAFSEELLSRIRSICDVYL  183 (234)
T ss_pred             HHHHHHh-------cCC-CEEEEecHHHHHhcCCHHHHHHHHHHHHHHHhCCCEEEEEecCCcCCHHHHHHHHhheEEEE
Confidence            2222321       233 379999999998888888888876655432 1124567777877776777788999999999


Q ss_pred             EeeeC
Q 024646          209 SVEPF  213 (265)
Q Consensus       209 ~v~P~  213 (265)
                      .+...
T Consensus       184 ~L~~~  188 (234)
T PRK06067        184 KLRAE  188 (234)
T ss_pred             EEEee
Confidence            99764

>PRK04328 hypothetical protein; Provisional

Probab=97.67  E-value=0.00048  Score=62.33  Aligned_cols=144  Identities=19%  Similarity=0.171  Sum_probs=84.6

Q ss_pred             hhccccceeEEEEeeCChHHHHHHHhhcCCCccC--CCCeEEEEeccCCCCCCcccccCccccccccccccccccchhhh
Q 024646           50 AGKSQSRGLVVVAYSRSPSFYVDLLKRRGIDIAS--SHDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNLD  127 (265)
Q Consensus        50 a~~~q~~~Vhvl~fe~spe~y~~~lk~~G~d~~~--~~~~v~i~D~ysDPlgW~~~~~~~~~~~~~s~~~~~~~~v~~L~  127 (265)
                      .+..+++.+..+.+|-+|+.+.+-+++.|+|...  -+.++.++|+|+.-.+......          .+ +..+..++.
T Consensus        46 ~~~~~ge~~lyis~ee~~~~i~~~~~~~g~d~~~~~~~~~l~iid~~~~~~~~~~~~~----------~~-~~~~~~~~~  114 (249)
T PRK04328         46 NGLQMGEPGVYVALEEHPVQVRRNMRQFGWDVRKYEEEGKFAIVDAFTGGIGSAAKRE----------KY-VVKDPDDVR  114 (249)
T ss_pred             HHHhcCCcEEEEEeeCCHHHHHHHHHHcCCCHHHHhhcCCEEEEeccccccccccccc----------cc-cccCcccHH
Confidence            3456789999999999999999999999987533  1347999999998776543111          01 111223344


Q ss_pred             HHHHHHHHhccCccCCCCCcEEEEEechhHHHHhcCh---HHHHHHHHhhhcCCceeEEEEeecccccchhH-HHHHHhh
Q 024646          128 KLYSLIIEQGKGLIGQGKDRFSIAIDSVSEMVRHASI---SSVAGILSNLRSHDQVSSIFWLLHSDLHEIKF-TSVLEYL  203 (265)
Q Consensus       128 sl~~~~~e~~~~~~~~~k~r~~VaIDSLS~LL~h~s~---~~vc~lL~~Lr~~~~vssVl~LLHsDLHe~~v-v~ALe~L  203 (265)
                      .++..+.+..+    +.++ -.||||||+.|....+-   ..+.++.+.|++.. +..++. .|.+..+... -..++|+
T Consensus       115 ~~~~~i~~~i~----~~~~-~~vVIDSlt~l~~~~~~~~r~~~~~l~~~lk~~g-~t~llt-~e~~~~~~~~~~~~~~~~  187 (249)
T PRK04328        115 ELIDVLRQAIK----DIGA-KRVVIDSVSTLYLTKPAMARSIVMQLKRVLSGLG-CTAIFV-SQVSVGERGFGGPGVEHA  187 (249)
T ss_pred             HHHHHHHHHHH----hhCC-CEEEEeChhHhhcCChHHHHHHHHHHHHHHHhCC-CEEEEE-ECccccccccCCCCcEEE
Confidence            44333333221    1123 37999999998764321   22344555566543 333322 2333222111 1246899


Q ss_pred             heeEEEee
Q 024646          204 SSMVASVE  211 (265)
Q Consensus       204 As~vv~v~  211 (265)
                      +-++|.++
T Consensus       188 ~D~vI~L~  195 (249)
T PRK04328        188 VDGIIRLD  195 (249)
T ss_pred             EEEEEEEE
Confidence            99999886

>COG2874 FlaH Predicted ATPases involved in biogenesis of archaeal flagella [Cell motility and secretion / Intracellular trafficking and secretion]

Probab=97.39  E-value=0.0083  Score=55.08  Aligned_cols=137  Identities=16%  Similarity=0.163  Sum_probs=106.3

Q ss_pred             hccccceeEEEEeeCChHHHHHHHhhcCCCccC--CCCeEEEEeccCCCCCCcccccCccccccccccccccccchhhhH
Q 024646           51 GKSQSRGLVVVAYSRSPSFYVDLLKRRGIDIAS--SHDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNLDK  128 (265)
Q Consensus        51 ~~~q~~~Vhvl~fe~spe~y~~~lk~~G~d~~~--~~~~v~i~D~ysDPlgW~~~~~~~~~~~~~s~~~~~~~~v~~L~s  128 (265)
                      .-.++..|..+.-|.+--+|..-|..-+.|..-  ++.++.|.-.-.+|.+|+....                     ++
T Consensus        52 ~L~~g~~v~yvsTe~T~refi~qm~sl~ydv~~~~l~G~l~~~~~~~~~~~~~~~~~---------------------~~  110 (235)
T COG2874          52 FLMNGYRVTYVSTELTVREFIKQMESLSYDVSDFLLSGRLLFFPVNLEPVNWGRRSA---------------------RK  110 (235)
T ss_pred             HHhCCceEEEEEechhHHHHHHHHHhcCCCchHHHhcceeEEEEecccccccChHHH---------------------HH
Confidence            456788999999999999999999988777543  4567777777779999998443                     11


Q ss_pred             HHHHHHHhccCccCCCCCcEEEEEechhHHHHhcChHHHHHHHHhhhc-CCceeEEEEeecccccchhHHHHHHhhheeE
Q 024646          129 LYSLIIEQGKGLIGQGKDRFSIAIDSVSEMVRHASISSVAGILSNLRS-HDQVSSIFWLLHSDLHEIKFTSVLEYLSSMV  207 (265)
Q Consensus       129 l~~~~~e~~~~~~~~~k~r~~VaIDSLS~LL~h~s~~~vc~lL~~Lr~-~~~vssVl~LLHsDLHe~~vv~ALe~LAs~v  207 (265)
                      ++..+++..|   ..-+  =+|.|||||..+.+.+..+|-+++..+|+ ++.=.-|+--+|.+.-.+.++.-++..+++-
T Consensus       111 ~L~~l~~~~k---~~~~--dViIIDSls~~~~~~~~~~vl~fm~~~r~l~d~gKvIilTvhp~~l~e~~~~rirs~~d~~  185 (235)
T COG2874         111 LLDLLLEFIK---RWEK--DVIIIDSLSAFATYDSEDAVLNFMTFLRKLSDLGKVIILTVHPSALDEDVLTRIRSACDVY  185 (235)
T ss_pred             HHHHHHhhHH---hhcC--CEEEEecccHHhhcccHHHHHHHHHHHHHHHhCCCEEEEEeChhhcCHHHHHHHHHhhhee
Confidence            2223333222   1113  48999999999999999999999999998 4566678888999999999999999999999


Q ss_pred             EEeeeC
Q 024646          208 ASVEPF  213 (265)
Q Consensus       208 v~v~P~  213 (265)
                      +.++-.
T Consensus       186 l~L~~~  191 (235)
T COG2874         186 LRLRLE  191 (235)
T ss_pred             EEEEhh
Confidence            988643

>PRK09302 circadian clock protein KaiC; Reviewed

Probab=97.26  E-value=0.0021  Score=63.64  Aligned_cols=131  Identities=18%  Similarity=0.252  Sum_probs=84.3

Q ss_pred             hccccceeEEEEeeCChHHHHHHHhhcCCCccC--CCCeEEEEeccCCCCCCcccccCccccccccccccccccchhhhH
Q 024646           51 GKSQSRGLVVVAYSRSPSFYVDLLKRRGIDIAS--SHDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNLDK  128 (265)
Q Consensus        51 ~~~q~~~Vhvl~fe~spe~y~~~lk~~G~d~~~--~~~~v~i~D~ysDPlgW~~~~~~~~~~~~~s~~~~~~~~v~~L~s  128 (265)
                      +..+++.+..+.||-+|+.+.+-++..|+|.+.  -...+.++|.+.++.+|+.                      .+..
T Consensus       297 ~~~~g~~~~yis~e~~~~~i~~~~~~~g~~~~~~~~~g~l~i~~~~~~~~~~~~----------------------~~~~  354 (509)
T PRK09302        297 ACRRGERCLLFAFEESRAQLIRNARSWGIDLEKMEEKGLLKIICARPESYGLED----------------------HLII  354 (509)
T ss_pred             HHhCCCcEEEEEecCCHHHHHHHHHHcCCChHHHhhcCCceeecCCcccCCHHH----------------------HHHH
Confidence            456789999999999999999999988887543  1235778887776665543                      1122


Q ss_pred             HHHHHHHhccCccCCCCCcEEEEEechhHHHHhcChHHHHHHHHhhhcC---CceeEEEEeecccc--cchhHHHHHHhh
Q 024646          129 LYSLIIEQGKGLIGQGKDRFSIAIDSVSEMVRHASISSVAGILSNLRSH---DQVSSIFWLLHSDL--HEIKFTSVLEYL  203 (265)
Q Consensus       129 l~~~~~e~~~~~~~~~k~r~~VaIDSLS~LL~h~s~~~vc~lL~~Lr~~---~~vssVl~LLHsDL--He~~vv~ALe~L  203 (265)
                      + ...++.       .++ -.|+||||+.+....+...+-+.|..|.+.   -.+..++...-.+.  +.+.....++|+
T Consensus       355 i-~~~i~~-------~~~-~~vVIDslt~l~~~~~~~~~~~~l~~l~~~~k~~~~t~l~t~~~~~~~g~~~~~~~~~~~l  425 (509)
T PRK09302        355 I-KREIEE-------FKP-SRVAIDPLSALARGGSLNEFRQFVIRLTDYLKSEEITGLFTNLTPDFMGSHSITESHISSL  425 (509)
T ss_pred             H-HHHHHH-------cCC-CEEEEcCHHHHHHhCCHHHHHHHHHHHHHHHHhCCCeEEEEeccccccCCCCCCcCceEEe
Confidence            2 222331       234 379999999999877776655555544331   34555555332222  233333458999


Q ss_pred             heeEEEeee
Q 024646          204 SSMVASVEP  212 (265)
Q Consensus       204 As~vv~v~P  212 (265)
                      +-++|.+.=
T Consensus       426 ~D~vI~L~~  434 (509)
T PRK09302        426 TDTWILLQY  434 (509)
T ss_pred             eeEEEEEEE
Confidence            999999963

>PRK09302 circadian clock protein KaiC; Reviewed

Probab=96.77  E-value=0.011  Score=58.44  Aligned_cols=136  Identities=18%  Similarity=0.160  Sum_probs=84.8

Q ss_pred             hccc-cceeEEEEeeCChHHHHHHHhhcCCCccCC--CCeEEEEeccCCCCCCcccccCccccccccccccccccchhhh
Q 024646           51 GKSQ-SRGLVVVAYSRSPSFYVDLLKRRGIDIASS--HDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNLD  127 (265)
Q Consensus        51 ~~~q-~~~Vhvl~fe~spe~y~~~lk~~G~d~~~~--~~~v~i~D~ysDPlgW~~~~~~~~~~~~~s~~~~~~~~v~~L~  127 (265)
                      +..+ ++.+..+.+|-+++++.+-++.-|+|.+..  +.++.++|.+.+|..|.. ..                 -.++.
T Consensus        55 ~~~~~ge~~lyis~ee~~~~i~~~~~~~g~d~~~~~~~g~l~~~~~~~~~~~~~~-~~-----------------~~~~~  116 (509)
T PRK09302         55 GIKRFDEPGVFVTFEESPEDIIRNVASFGWDLQKLIDEGKLFILDASPDPSEQEE-AG-----------------EYDLE  116 (509)
T ss_pred             HHHhcCCCEEEEEccCCHHHHHHHHHHcCCCHHHHhhCCeEEEEecCcccccccc-cc-----------------cccHH
Confidence            4445 889999999999999999999999886542  346999999999988864 11                 01233


Q ss_pred             HHHHHHHHhccCccCCCCCcEEEEEechhHHHHhcChH-----HHHHHHHhhhcCCceeEEEEeecccccch--hHHHHH
Q 024646          128 KLYSLIIEQGKGLIGQGKDRFSIAIDSVSEMVRHASIS-----SVAGILSNLRSHDQVSSIFWLLHSDLHEI--KFTSVL  200 (265)
Q Consensus       128 sl~~~~~e~~~~~~~~~k~r~~VaIDSLS~LL~h~s~~-----~vc~lL~~Lr~~~~vssVl~LLHsDLHe~--~vv~AL  200 (265)
                      .++..+.+..+    +.++ -.|+|||++.+.......     .+.+++..|++. .+..++. -|..-...  ...+..
T Consensus       117 ~l~~~l~~~i~----~~~~-~~vVIDSls~l~~~~d~~~~~r~~l~~L~~~Lk~~-g~TvLlt-~~~~~~~~~~~~~~~~  189 (509)
T PRK09302        117 ALFIRIEYAID----KIGA-KRVVLDSIEALFSGFSNEAVVRRELRRLFAWLKQK-GVTAVIT-GERGDEYGPLTRYGVE  189 (509)
T ss_pred             HHHHHHHHHHH----hhCC-CEEEECCHHHHHhhccCHHHHHHHHHHHHHHHHhC-CCEEEEE-ECCccCcCCccccCce
Confidence            33333333221    1233 479999999987654332     345555556543 3333333 34332111  112245


Q ss_pred             HhhheeEEEee
Q 024646          201 EYLSSMVASVE  211 (265)
Q Consensus       201 e~LAs~vv~v~  211 (265)
                      ++++..++.++
T Consensus       190 ~~laDgVI~L~  200 (509)
T PRK09302        190 EFVSDCVIILR  200 (509)
T ss_pred             EEEeeEEEEEe
Confidence            88999999886

>TIGR02655 circ_KaiC circadian clock protein KaiC

Probab=96.22  E-value=0.081  Score=52.53  Aligned_cols=131  Identities=18%  Similarity=0.260  Sum_probs=77.8

Q ss_pred             hhccccceeEEEEeeCChHHHHHHHhhcCCCccC--CCCeEEEEeccCCCCCCcccccCccccccccccccccccchhhh
Q 024646           50 AGKSQSRGLVVVAYSRSPSFYVDLLKRRGIDIAS--SHDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNLD  127 (265)
Q Consensus        50 a~~~q~~~Vhvl~fe~spe~y~~~lk~~G~d~~~--~~~~v~i~D~ysDPlgW~~~~~~~~~~~~~s~~~~~~~~v~~L~  127 (265)
                      +++.+++.+..++||-|++++..-+++-|+|.+.  ...++.+++.+....+...                      .+.
T Consensus       286 ~~~~~ge~~~y~s~eEs~~~i~~~~~~lg~~~~~~~~~g~l~~~~~~p~~~~~~~----------------------~~~  343 (484)
T TIGR02655       286 NACANKERAILFAYEESRAQLLRNAYSWGIDFEEMEQQGLLKIICAYPESAGLED----------------------HLQ  343 (484)
T ss_pred             HHHHCCCeEEEEEeeCCHHHHHHHHHHcCCChHHHhhCCcEEEEEcccccCChHH----------------------HHH
Confidence            3456789999999999999999999999987433  1235888887643332111                      122


Q ss_pred             HHHHHHHHhccCccCCCCCcEEEEEechhHHHHhcChHHHHHHHHhhhc---CCceeEEEEeecccccc--hhHHHHHHh
Q 024646          128 KLYSLIIEQGKGLIGQGKDRFSIAIDSVSEMVRHASISSVAGILSNLRS---HDQVSSIFWLLHSDLHE--IKFTSVLEY  202 (265)
Q Consensus       128 sl~~~~~e~~~~~~~~~k~r~~VaIDSLS~LL~h~s~~~vc~lL~~Lr~---~~~vssVl~LLHsDLHe--~~vv~ALe~  202 (265)
                      .+...+.+        .++ -.|+||||+.+....+..++-..++.|.+   ...|..++...=.++=+  +-.-.-++|
T Consensus       344 ~i~~~i~~--------~~~-~~vvIDsi~~~~~~~~~~~~r~~~~~l~~~lk~~~it~~~t~~~~~~~~~~~~~~~~~s~  414 (484)
T TIGR02655       344 IIKSEIAD--------FKP-ARIAIDSLSALARGVSNNAFRQFVIGVTGYAKQEEITGFFTNTSDQFMGSHSITDSHIST  414 (484)
T ss_pred             HHHHHHHH--------cCC-CEEEEcCHHHHHHhcCHHHHHHHHHHHHHHHhhCCCeEEEeecccccccCCccCCCCeeE
Confidence            33222222        123 38999999999876666655444443333   24455554433222111  111134688


Q ss_pred             hheeEEEee
Q 024646          203 LSSMVASVE  211 (265)
Q Consensus       203 LAs~vv~v~  211 (265)
                      |+-.+|.+.
T Consensus       415 l~D~ii~l~  423 (484)
T TIGR02655       415 ITDTILMLQ  423 (484)
T ss_pred             eeeEEEEEE
Confidence            888888774

Members of this family are the circadian clock protein KaiC, part of the kaiABC operon that controls circadian rhythm. It may be universal in Cyanobacteria. Each member has two copies of the KaiC domain (Pfam model pfam06745), which is also found in other proteins. KaiC performs autophosphorylation and acts as its own transcriptional repressor.

>TIGR03881 KaiC_arch_4 KaiC domain protein, PAE1156 family

Probab=96.12  E-value=0.17  Score=44.20  Aligned_cols=135  Identities=12%  Similarity=0.047  Sum_probs=76.0

Q ss_pred             cccceeEEEEeeCChHHHHHHHhhcCCCccCC--CCeEEEEeccCCCC--CCcccccCccccccccccccccccchhhhH
Q 024646           53 SQSRGLVVVAYSRSPSFYVDLLKRRGIDIASS--HDWIHILDCYTDPL--GWKNWLIDKDISQEASSLSSFCQDVRNLDK  128 (265)
Q Consensus        53 ~q~~~Vhvl~fe~spe~y~~~lk~~G~d~~~~--~~~v~i~D~ysDPl--gW~~~~~~~~~~~~~s~~~~~~~~v~~L~s  128 (265)
                      .+++.+..+.+|.+++.+.+-+++.|++....  +.++.+.|.+....  .|.- ..           +    ++.++..
T Consensus        46 ~~g~~~~~is~e~~~~~i~~~~~~~g~~~~~~~~~~~l~i~d~~~~~~~~~~~~-~~-----------~----~~~~~~~  109 (229)
T TIGR03881        46 RDGDPVIYVTTEESRESIIRQAAQFGMDFEKAIEEGKLVIIDALMKEKEDEWSL-RE-----------L----SIEELLN  109 (229)
T ss_pred             hcCCeEEEEEccCCHHHHHHHHHHhCCCHHHHhhcCCEEEEEcccccccccccc-cc-----------C----CHHHHHH
Confidence            45789999999999999988888889876542  34688888775431  1221 00           1    2223322


Q ss_pred             HHHHHHHhccCccCCCCCcEEEEEechhHHHHhcChHHHHHHHH----hhhcCCceeEEEEeecc-cccchhHHHHHHhh
Q 024646          129 LYSLIIEQGKGLIGQGKDRFSIAIDSVSEMVRHASISSVAGILS----NLRSHDQVSSIFWLLHS-DLHEIKFTSVLEYL  203 (265)
Q Consensus       129 l~~~~~e~~~~~~~~~k~r~~VaIDSLS~LL~h~s~~~vc~lL~----~Lr~~~~vssVl~LLHs-DLHe~~vv~ALe~L  203 (265)
                      -+....+..    + .++ -.|+|||++.++...+.. .-..+.    .++. ..+..++. -|- +.-++.....++|+
T Consensus       110 ~i~~~~~~~----~-~~~-~~vvIDsl~~l~~~~~~~-~r~~~~~l~~~l~~-~~~tvil~-~~~~~~~~~~~~~~~~~l  180 (229)
T TIGR03881       110 KVIEAKKYL----G-YGH-ARLVIDSMSAFWLDKPAM-ARKYSYYLKRVLNR-WNFTILLT-SQYAITTSQAFGFGIEHV  180 (229)
T ss_pred             HHHHHHHhh----c-cCc-eEEEecCchhhhccChHH-HHHHHHHHHHHHHh-CCCEEEEE-ecccccCCCCcccceEEE
Confidence            212222211    0 022 478999999998755432 122222    2333 23444443 342 22222222458999


Q ss_pred             heeEEEeee
Q 024646          204 SSMVASVEP  212 (265)
Q Consensus       204 As~vv~v~P  212 (265)
                      +-.+|.++-
T Consensus       181 ~D~vI~L~~  189 (229)
T TIGR03881       181 ADGIIRFRK  189 (229)
T ss_pred             EeEEEEEEE
Confidence            999999874

Members of this protein family are archaeal single-domain KaiC_related proteins, homologous to the Cyanobacterial circadian clock cycle protein KaiC, an autokinase/autophosphorylase that has two copies of the domain.

>cd01124 KaiC KaiC is a circadian clock protein primarily found in cyanobacteria KaiC is a RecA-like ATPase, having both Walker A and Walker B motifs

Probab=96.01  E-value=0.11  Score=43.46  Aligned_cols=136  Identities=19%  Similarity=0.121  Sum_probs=81.6

Q ss_pred             hccccceeEEEEeeCChHHHHHHHhhcCCCccCC--CCeEEEEeccCCCCCCcccccCccccccccccccccccchhhhH
Q 024646           51 GKSQSRGLVVVAYSRSPSFYVDLLKRRGIDIASS--HDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNLDK  128 (265)
Q Consensus        51 ~~~q~~~Vhvl~fe~spe~y~~~lk~~G~d~~~~--~~~v~i~D~ysDPlgW~~~~~~~~~~~~~s~~~~~~~~v~~L~s  128 (265)
                      +..+++.+.++.+|-+++.+.+-+++.|++.+.+  ...+.+.|.+...+..... .                ...++..
T Consensus        23 ~~~~g~~v~~~s~e~~~~~~~~~~~~~g~~~~~l~~~g~l~~~d~~~~~~s~~~~-~----------------~~~~~~~   85 (187)
T cd01124          23 GLARGEPGLYVTLEESPEELIENAESLGWDLERLEDEGLLAIVDADPDEIGPAES-S----------------LRLELIQ   85 (187)
T ss_pred             HHHCCCcEEEEECCCCHHHHHHHHHHcCCChHHHHhcCCeEEEecCccccchhhh-h----------------hhHHHHH
Confidence            3456889999999999999999999888875431  2346777755544421110 0                0001111


Q ss_pred             HHHHHHHhccCccCCCCCcEEEEEechhHHHH---hcChHHHHHHHHhhhcCCceeEEEEeeccccc-c-hhHHHHHHhh
Q 024646          129 LYSLIIEQGKGLIGQGKDRFSIAIDSVSEMVR---HASISSVAGILSNLRSHDQVSSIFWLLHSDLH-E-IKFTSVLEYL  203 (265)
Q Consensus       129 l~~~~~e~~~~~~~~~k~r~~VaIDSLS~LL~---h~s~~~vc~lL~~Lr~~~~vssVl~LLHsDLH-e-~~vv~ALe~L  203 (265)
                      .+...+..       .++ -.|+||+++.++.   ......+-.++..|++. .+. ++..-|..-. + ......++++
T Consensus        86 ~i~~~~~~-------~~~-~~lviD~~~~~~~~~~~~~~~~i~~l~~~l~~~-g~t-vi~v~~~~~~~~~~~~~~~~~~~  155 (187)
T cd01124          86 RLKDAIEE-------FKA-KRVVIDSVSGLLLMEQSTARLEIRRLLFALKRF-GVT-TLLTSEQSGLEGTGFGGGDVEYL  155 (187)
T ss_pred             HHHHHHHH-------hCC-CEEEEeCcHHHhhcChHHHHHHHHHHHHHHHHC-CCE-EEEEeccccCCCcccCcCceeEe
Confidence            11222221       123 5899999999987   44455566777787764 333 3333443222 1 2334678999


Q ss_pred             heeEEEeeeC
Q 024646          204 SSMVASVEPF  213 (265)
Q Consensus       204 As~vv~v~P~  213 (265)
                      +..++.++-.
T Consensus       156 aD~ii~l~~~  165 (187)
T cd01124         156 VDGVIRLRLD  165 (187)
T ss_pred             eeEEEEEEEE
Confidence            9999988754

A related protein is found in archaea.

>TIGR02655 circ_KaiC circadian clock protein KaiC

Probab=95.77  E-value=0.096  Score=52.02  Aligned_cols=138  Identities=19%  Similarity=0.174  Sum_probs=83.2

Q ss_pred             hhccc-cceeEEEEeeCChHHHHHHHhhcCCCccCC--CCeEEEEeccCCCCCCcccccCccccccccccccccccchhh
Q 024646           50 AGKSQ-SRGLVVVAYSRSPSFYVDLLKRRGIDIASS--HDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNL  126 (265)
Q Consensus        50 a~~~q-~~~Vhvl~fe~spe~y~~~lk~~G~d~~~~--~~~v~i~D~ysDPlgW~~~~~~~~~~~~~s~~~~~~~~v~~L  126 (265)
                      ++..+ ++.+..++||-+|+++.+-+++.|+|-+..  ..++.++|.+..+  |.....               + --++
T Consensus        44 ~g~~~~ge~~lyvs~eE~~~~l~~~~~~~G~~~~~~~~~g~l~~~~~~~~~--~~~~~~---------------~-~~~l  105 (484)
T TIGR02655        44 NGIIHFDEPGVFVTFEESPQDIIKNARSFGWDLQKLVDEGKLFILDASPDP--EGQDVV---------------G-GFDL  105 (484)
T ss_pred             HHHHhCCCCEEEEEEecCHHHHHHHHHHcCCCHHHHhhcCceEEEecCchh--cccccc---------------c-cCCH
Confidence            45556 899999999999999999999999986531  3468888875433  222110               0 0123


Q ss_pred             hHHHHHHHHhccCccCCCCCcEEEEEechhHHHHhcCh-----HHHHHHHHhhhcCCceeEEEEeecccccchh-HHHHH
Q 024646          127 DKLYSLIIEQGKGLIGQGKDRFSIAIDSVSEMVRHASI-----SSVAGILSNLRSHDQVSSIFWLLHSDLHEIK-FTSVL  200 (265)
Q Consensus       127 ~sl~~~~~e~~~~~~~~~k~r~~VaIDSLS~LL~h~s~-----~~vc~lL~~Lr~~~~vssVl~LLHsDLHe~~-vv~AL  200 (265)
                      ..++..+.+...   + +++ --|+|||++.+....+.     ..+..+++.|++. .+..++.--+.+...+. ..+..
T Consensus       106 ~~~l~~i~~~ls---~-g~~-qRVvIDSl~aL~~~~~~~~~~r~~l~~Li~~L~~~-g~TvLLtsh~~~~~~~~~~~~~~  179 (484)
T TIGR02655       106 SALIERINYAIR---K-YKA-KRVSIDSVTAVFQQYDAVSVVRREIFRLVARLKQI-GVTTVMTTERIEEYGPIARYGVE  179 (484)
T ss_pred             HHHHHHHHHHHH---H-hCC-cEEEEeehhHhhhhcCchHHHHHHHHHHHHHHHHC-CCEEEEEecCcccccccccCCce
Confidence            333333333211   1 233 47999999998766554     2456677777653 45545543333332221 12234


Q ss_pred             HhhheeEEEee
Q 024646          201 EYLSSMVASVE  211 (265)
Q Consensus       201 e~LAs~vv~v~  211 (265)
                      +|++-.+|.+.
T Consensus       180 e~laDgVI~L~  190 (484)
T TIGR02655       180 EFVSDNVVILR  190 (484)
T ss_pred             eEeeeeEEEEE
Confidence            99999999886

Members of this family are the circadian clock protein KaiC, part of the kaiABC operon that controls circadian rhythm. It may be universal in Cyanobacteria. Each member has two copies of the KaiC domain (Pfam model pfam06745), which is also found in other proteins. KaiC performs autophosphorylation and acts as its own transcriptional repressor.

>COG0467 RAD55 RecA-superfamily ATPases implicated in signal transduction [Signal transduction mechanisms]

Probab=95.40  E-value=0.069  Score=48.11  Aligned_cols=145  Identities=19%  Similarity=0.240  Sum_probs=88.0

Q ss_pred             hhccccceeEEEEeeCChHHHHHHHhhcCCCccC--CCCeEEEEeccCCCCCCcccccCccccccccccccccccchhhh
Q 024646           50 AGKSQSRGLVVVAYSRSPSFYVDLLKRRGIDIAS--SHDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNLD  127 (265)
Q Consensus        50 a~~~q~~~Vhvl~fe~spe~y~~~lk~~G~d~~~--~~~~v~i~D~ysDPlgW~~~~~~~~~~~~~s~~~~~~~~v~~L~  127 (265)
                      .++..++.+..+++|-+|+++.+-+++.|.|.+.  -+..+.++|.++.+.+=.....               .+..++.
T Consensus        46 ~~~~~ge~vlyvs~~e~~~~l~~~~~~~g~d~~~~~~~g~l~i~d~~~~~~~~~~~~~---------------~~~~~~~  110 (260)
T COG0467          46 EGAREGEPVLYVSTEESPEELLENARSFGWDLEVYIEKGKLAILDAFLSEKGLVSIVV---------------GDPLDLE  110 (260)
T ss_pred             HHHhcCCcEEEEEecCCHHHHHHHHHHcCCCHHHHhhcCCEEEEEccccccccccccc---------------cCCccHH
Confidence            4555599999999999999999999999988753  2346889998888774322000               0112333


Q ss_pred             HHHHHHHHhccCccCCCCCcEEEEEechhHHHHhcChHHHH-HHHHhhhcC-CceeEEEEeecccccchhHH--HHHHhh
Q 024646          128 KLYSLIIEQGKGLIGQGKDRFSIAIDSVSEMVRHASISSVA-GILSNLRSH-DQVSSIFWLLHSDLHEIKFT--SVLEYL  203 (265)
Q Consensus       128 sl~~~~~e~~~~~~~~~k~r~~VaIDSLS~LL~h~s~~~vc-~lL~~Lr~~-~~vssVl~LLHsDLHe~~vv--~ALe~L  203 (265)
                      ++...+.+..+    .-++ ..++|||++.+......+... ..+..|.+. ..-. +.+++.+|.......  +-.+++
T Consensus       111 ~l~~~I~~~~~----~~~~-~~~ViDsi~~~~~~~~~~~~~r~~~~~l~~~~~~~~-~t~~~~~~~~~~~~~~~~~~~~~  184 (260)
T COG0467         111 ELLDRIREIVE----KEGA-DRVVIDSITELTLYLNDPALVRRILLLLKRFLKKLG-VTSLLTTEAPVEERGESGVEEYI  184 (260)
T ss_pred             HHHHHHHHHHH----HhCC-CEEEEeCCchHhhhcCchHHHHHHHHHHHHHHHhCC-CEEEEEecccccCCCccceEEEE
Confidence            33333333222    1122 689999999766666655553 444444442 1222 455555554332221  455668


Q ss_pred             heeEEEeeeCCc
Q 024646          204 SSMVASVEPFNQ  215 (265)
Q Consensus       204 As~vv~v~P~~~  215 (265)
                      +..+|.+.....
T Consensus       185 vdgvI~l~~~~~  196 (260)
T COG0467         185 VDGVIRLDLKEI  196 (260)
T ss_pred             EEEEEEEeeecc
Confidence            888888877544

>TIGR03878 thermo_KaiC_2 KaiC domain protein, AF_0795 family

Probab=95.35  E-value=0.13  Score=46.89  Aligned_cols=133  Identities=14%  Similarity=0.107  Sum_probs=70.3

Q ss_pred             hccccceeEEEEeeCChHH----HHHHHhhcCCCccCCCCeEEEEeccCCCCCCcccccCccccccccccccccccchhh
Q 024646           51 GKSQSRGLVVVAYSRSPSF----YVDLLKRRGIDIASSHDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNL  126 (265)
Q Consensus        51 ~~~q~~~Vhvl~fe~spe~----y~~~lk~~G~d~~~~~~~v~i~D~ysDPlgW~~~~~~~~~~~~~s~~~~~~~~v~~L  126 (265)
                      +..+++.+..+.+|-++++    +..-.++.|+|.+...++++++|..+.+.-     .                  .++
T Consensus        60 ~a~~Ge~vlyis~Ee~~~~~~~~l~~~a~~~g~d~~~~~~~l~~id~~~~~~~-----~------------------~~~  116 (259)
T TIGR03878        60 QASRGNPVLFVTVESPANFVYTSLKERAKAMGVDFDKIEENIILIDAASSTEL-----R------------------ENV  116 (259)
T ss_pred             HHhCCCcEEEEEecCCchHHHHHHHHHHHHcCCCHHHHhCCEEEEECCCchhh-----h------------------hhH
Confidence            4457899999999976654    333345667775544567888887653210     0                  012


Q ss_pred             hHHHHHHHHhccCccCCCCCcEEEEEechhHHHHhcChH---HHHHHHHhhhcCCceeEEEEeeccccc---c-hhHHHH
Q 024646          127 DKLYSLIIEQGKGLIGQGKDRFSIAIDSVSEMVRHASIS---SVAGILSNLRSHDQVSSIFWLLHSDLH---E-IKFTSV  199 (265)
Q Consensus       127 ~sl~~~~~e~~~~~~~~~k~r~~VaIDSLS~LL~h~s~~---~vc~lL~~Lr~~~~vssVl~LLHsDLH---e-~~vv~A  199 (265)
                      ..++..+.+..+    +.++ =.||||||+.+.+.....   .+.++++.|++...-.=++.-.+.+..   . +..-..
T Consensus       117 ~~l~~~l~~~i~----~~~~-~~vVIDSls~l~~~~~~~~r~~~~~L~~~lk~~~~t~ll~~e~~~~~~~~~~~~~~~~~  191 (259)
T TIGR03878       117 PNLLATLAYAIK----EYKV-KNTVIDSITGLYEAKEMMAREIVRQLFNFMKKWYQTALFVSQKRSGHEELSAEAAGGYA  191 (259)
T ss_pred             HHHHHHHHHHHH----hhCC-CEEEEcCchHhcccchHHHHHHHHHHHHHHHHcCCeEEEEeccccCcccccccccCCcc
Confidence            222222222111    1223 379999999876543221   223344555543332223333333221   1 111125


Q ss_pred             HHhhheeEEEee
Q 024646          200 LEYLSSMVASVE  211 (265)
Q Consensus       200 Le~LAs~vv~v~  211 (265)
                      ++|++-.+|.+.
T Consensus       192 ~~~l~D~vI~L~  203 (259)
T TIGR03878       192 VSHIVDGTIVLA  203 (259)
T ss_pred             eeEeeccEEEEe
Confidence            899999999887

This KaiC domain-containing protein family occurs sporadically across a broad taxonomic range (Euryarchaeota, Aquificae, Dictyoglomi, Epsilonproteobacteria, and Firmicutes), but exclusively in thermophiles.

>PRK08533 flagellar accessory protein FlaH; Reviewed

Probab=94.77  E-value=0.29  Score=43.93  Aligned_cols=130  Identities=13%  Similarity=0.194  Sum_probs=74.7

Q ss_pred             cccceeEEEEeeCChHHHHHHHhhcCCCccC--CCCeEEEEeccCCCCCCcccccCccccccccccccccccchhhhHHH
Q 024646           53 SQSRGLVVVAYSRSPSFYVDLLKRRGIDIAS--SHDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNLDKLY  130 (265)
Q Consensus        53 ~q~~~Vhvl~fe~spe~y~~~lk~~G~d~~~--~~~~v~i~D~ysDPlgW~~~~~~~~~~~~~s~~~~~~~~v~~L~sl~  130 (265)
                      .+++.+..+.+|.+++++.+.+++.|+|.+.  ....+.++++|..-.++.                       +.+..+
T Consensus        50 ~~g~~~~yi~~e~~~~~~~~~~~~~g~~~~~~~~~~~l~~~~~~~~~~~~~-----------------------~~~~~l  106 (230)
T PRK08533         50 QNGYSVSYVSTQLTTTEFIKQMMSLGYDINKKLISGKLLYIPVYPLLSGNS-----------------------EKRKFL  106 (230)
T ss_pred             hCCCcEEEEeCCCCHHHHHHHHHHhCCchHHHhhcCcEEEEEecccccChH-----------------------HHHHHH
Confidence            3568889999999999999999988887543  234677777763211111                       111111


Q ss_pred             HHHHHhccCccCCCCCcEEEEEechhHHHHhcC----hHHHHHHHHhhhcCCceeEEEEeecccccchhHHHHHHhhhee
Q 024646          131 SLIIEQGKGLIGQGKDRFSIAIDSVSEMVRHAS----ISSVAGILSNLRSHDQVSSIFWLLHSDLHEIKFTSVLEYLSSM  206 (265)
Q Consensus       131 ~~~~e~~~~~~~~~k~r~~VaIDSLS~LL~h~s----~~~vc~lL~~Lr~~~~vssVl~LLHsDLHe~~vv~ALe~LAs~  206 (265)
                      ..+.+..+    ..++ -.++||+++.++....    ...+.++|+.|++...  .++-..|.+.-......-++|++-+
T Consensus       107 ~~il~~~~----~~~~-~~lVIDe~t~~l~~~~d~~~~~~l~~~l~~l~~~g~--tvi~t~~~~~~~~~~~~~~~~~~Dg  179 (230)
T PRK08533        107 KKLMNTRR----FYEK-DVIIIDSLSSLISNDASEVAVNDLMAFFKRISSLNK--VIILTANPKELDESVLTILRTAATM  179 (230)
T ss_pred             HHHHHHHH----hcCC-CEEEEECccHHhcCCcchHHHHHHHHHHHHHHhCCC--EEEEEecccccccccceeEEEeeeE
Confidence            22222111    1123 3799999999985432    2456677777755322  2222222221112222357999999


Q ss_pred             EEEeee
Q 024646          207 VASVEP  212 (265)
Q Consensus       207 vv~v~P  212 (265)
                      +|.+.-
T Consensus       180 vI~L~~  185 (230)
T PRK08533        180 LIRLEV  185 (230)
T ss_pred             EEEEEE
Confidence            998864

>TIGR03880 KaiC_arch_3 KaiC domain protein, AF_0351 family

Probab=94.33  E-value=0.56  Score=41.06  Aligned_cols=130  Identities=14%  Similarity=0.194  Sum_probs=75.4

Q ss_pred             hccccceeEEEEeeCChHHHHHHHhhcCCCccC-CCCeEEEEeccCCCCCCcccccCccccccccccccccccchhhhHH
Q 024646           51 GKSQSRGLVVVAYSRSPSFYVDLLKRRGIDIAS-SHDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNLDKL  129 (265)
Q Consensus        51 ~~~q~~~Vhvl~fe~spe~y~~~lk~~G~d~~~-~~~~v~i~D~ysDPlgW~~~~~~~~~~~~~s~~~~~~~~v~~L~sl  129 (265)
                      +..+++.+..+.+|-+++.+.+-++..|++.+. .++++.++|....-.                     ...+..+...
T Consensus        40 ~~~~g~~~~y~s~e~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~---------------------~~~~~~l~~~   98 (224)
T TIGR03880        40 GLKNGEKAMYISLEEREERILGYAKSKGWDLEDYIDKSLYIVRLDPSDF---------------------KTSLNRIKNE   98 (224)
T ss_pred             HHhCCCeEEEEECCCCHHHHHHHHHHcCCChHHHHhCCeEEEecCHHHH---------------------HhhHHHHHHH
Confidence            345689999999999999999999888876543 122466776321100                     0011222211


Q ss_pred             HHHHHHhccCccCCCCCcEEEEEechhHHHHhcCh-----HHHHHHHHhhhcCCceeEEEEeecccccch--hHHHHHHh
Q 024646          130 YSLIIEQGKGLIGQGKDRFSIAIDSVSEMVRHASI-----SSVAGILSNLRSHDQVSSIFWLLHSDLHEI--KFTSVLEY  202 (265)
Q Consensus       130 ~~~~~e~~~~~~~~~k~r~~VaIDSLS~LL~h~s~-----~~vc~lL~~Lr~~~~vssVl~LLHsDLHe~--~vv~ALe~  202 (265)
                      +...++.       .++ -.|+|||++.+-.-.+.     ..+..++..|++. .+ .++..-|.+-..+  .....+++
T Consensus        99 ~~~~i~~-------~~~-~~vVIDsls~l~~~~~~~~~~r~~l~~l~~~lk~~-~~-tvll~s~~~~~~~~~~~~~~~~~  168 (224)
T TIGR03880        99 LPILIKE-------LGA-SRVVIDPISLLETLFDDDAERRTELFRFYSSLRET-GV-TTILTSEADKTNVFASKYGLIEY  168 (224)
T ss_pred             HHHHHHH-------hCC-CEEEEcChHHHhhhcCCHHHHHHHHHHHHHHHHhC-CC-EEEEEEcccCCCCCccCCCceEE
Confidence            1222221       123 36789999987221222     3566788888764 33 3444455443322  22355899


Q ss_pred             hheeEEEee
Q 024646          203 LSSMVASVE  211 (265)
Q Consensus       203 LAs~vv~v~  211 (265)
                      ++..++.+.
T Consensus       169 l~D~vI~L~  177 (224)
T TIGR03880       169 LADGVIILK  177 (224)
T ss_pred             EEeEEEEEe
Confidence            999999994

This model represents a rather narrowly distributed archaeal protein family in which members have a single copy of the KaiC domain. This stands in contrast to the circadian clock protein KaiC itself, with two copies of the domain. Members are expected to have weak ATPase activity, by homology to the autokinase/autophosphorylase KaiC itself.

>KOG4723 consensus Uncharacterized conserved protein [Function unknown]

Probab=94.26  E-value=0.26  Score=45.28  Aligned_cols=72  Identities=19%  Similarity=0.343  Sum_probs=56.0

Q ss_pred             CCCCCceeeccCCCCCchhhHHHHHHHHHHHHHHhhccccceeEEEEeeCChHHHHHHHhhcCCCccC--CCCeEEEEec
Q 024646           16 GEHAPALTIKDSKASPFGFDVFNYVLTQLSNYILAGKSQSRGLVVVAYSRSPSFYVDLLKRRGIDIAS--SHDWIHILDC   93 (265)
Q Consensus        16 ge~ap~l~i~Dsl~~~~g~~~~~h~~~~l~s~i~a~~~q~~~Vhvl~fe~spe~y~~~lk~~G~d~~~--~~~~v~i~D~   93 (265)
                      .|+--..+++|+..+|+ .-+|-|++.   -..+++    +.+.+++|.++.+.|--.+++-|.|-..  .+.+++++|.
T Consensus        16 ~EqgkltLl~d~~eT~g-sFl~H~~l~---~~Lkan----~~~cFlaf~k~fshy~i~~rKlG~~l~t~k~rgqlvF~dg   87 (248)
T KOG4723|consen   16 PEQGKLTLLLDTRETPG-SFLFHYYLY---HALKAN----ESTCFLAFSKTFSHYAISMRKLGMDLKTKKNRGQLVFIDG   87 (248)
T ss_pred             CCCccEEEEeecccCCc-eeeHHHHHH---HHHhcC----CcEEEEEeecchhHHHHHHHHhCCceeecccCCcEEEEhh
Confidence            46667899999999985 666666442   222222    8999999999999999999999998776  2335999998


Q ss_pred             cC
Q 024646           94 YT   95 (265)
Q Consensus        94 ys   95 (265)
                      ++
T Consensus        88 l~   89 (248)
T KOG4723|consen   88 LS   89 (248)
T ss_pred             hh
Confidence            87

>PRK05973 replicative DNA helicase; Provisional

Probab=93.33  E-value=1.8  Score=39.75  Aligned_cols=62  Identities=13%  Similarity=-0.025  Sum_probs=40.1

Q ss_pred             cCCCCCceeeccCCCCCchhhHHHHHHHHHHHHHHhhccccceeEEEEeeCChHHHHHHHhhcCCCccC
Q 024646           15 EGEHAPALTIKDSKASPFGFDVFNYVLTQLSNYILAGKSQSRGLVVVAYSRSPSFYVDLLKRRGIDIAS   83 (265)
Q Consensus        15 ~ge~ap~l~i~Dsl~~~~g~~~~~h~~~~l~s~i~a~~~q~~~Vhvl~fe~spe~y~~~lk~~G~d~~~   83 (265)
                      .|=.++.+++---=...|=+.+..+++.       .+..+++.|.++.||-+++++.+=++..|+|.+.
T Consensus        59 GGl~~Gsl~LIaG~PG~GKT~lalqfa~-------~~a~~Ge~vlyfSlEes~~~i~~R~~s~g~d~~~  120 (237)
T PRK05973         59 SQLKPGDLVLLGARPGHGKTLLGLELAV-------EAMKSGRTGVFFTLEYTEQDVRDRLRALGADRAQ  120 (237)
T ss_pred             CCCCCCCEEEEEeCCCCCHHHHHHHHHH-------HHHhcCCeEEEEEEeCCHHHHHHHHHHcCCChHH
Confidence            4555554444322233333444444332       2345688999999999999999999999988655

>TIGR02237 recomb_radB DNA repair and recombination protein RadB

Probab=93.02  E-value=0.89  Score=39.09  Aligned_cols=38  Identities=13%  Similarity=0.261  Sum_probs=26.5

Q ss_pred             cccceeEEEEeeC-ChHHHHHHHhhcCCCccCCCCeEEEEec
Q 024646           53 SQSRGLVVVAYSR-SPSFYVDLLKRRGIDIASSHDWIHILDC   93 (265)
Q Consensus        53 ~q~~~Vhvl~fe~-spe~y~~~lk~~G~d~~~~~~~v~i~D~   93 (265)
                      .+++.+..+.+|. +++.+.+.++.. ++  ....+++++++
T Consensus        38 ~~g~~v~yi~~e~~~~~rl~~~~~~~-~~--~~~~~i~~~~~   76 (209)
T TIGR02237        38 RQGKKVVYIDTEGLSPERFKQIAEDR-PE--RALSNFIVFEV   76 (209)
T ss_pred             hCCCeEEEEECCCCCHHHHHHHHHhC-hH--HHhcCEEEEEC
Confidence            3478899999996 888888866643 11  11456888776

This family consists exclusively of archaeal RadB protein, a homolog of bacterial RecA (TIGR02012), eukaryotic RAD51 (TIGR02239) and DMC1 (TIGR02238), and archaeal RadA (TIGR02236).

>PF05625 PAXNEB: PAXNEB protein; InterPro: IPR008728 The RNA polymerase II elongator complex is a major histone acetyltransferase component of the RNA polymerase II (RNAPII) holoenzyme and is involved in transcriptional elongation [, ]

Probab=91.66  E-value=0.39  Score=46.42  Aligned_cols=69  Identities=23%  Similarity=0.228  Sum_probs=49.1

Q ss_pred             EEEEEechhHHHHhcC----hHHHHHHHHhhhc----CCceeEEEEeeccccc--chhHHHHHHhhheeEEEeeeCCcc
Q 024646          148 FSIAIDSVSEMVRHAS----ISSVAGILSNLRS----HDQVSSIFWLLHSDLH--EIKFTSVLEYLSSMVASVEPFNQA  216 (265)
Q Consensus       148 ~~VaIDSLS~LL~h~s----~~~vc~lL~~Lr~----~~~vssVl~LLHsDLH--e~~vv~ALe~LAs~vv~v~P~~~~  216 (265)
                      .=|+|-||..-+-..+    ...+.+||+.||.    +..-..++.-+=.+|-  .+..+..|++++-++|.|+|....
T Consensus       202 ~RI~I~sl~SP~w~~~~~~~~~~ll~FL~~LR~LlR~~~s~~v~~iTlP~~L~~~~~~~~~~l~~l~D~vi~Le~F~~~  280 (363)
T PF05625_consen  202 LRIVIPSLGSPLWYPPSASQPSELLRFLHSLRALLRKYSSNAVAMITLPSHLYPRSPSLVRRLEHLADGVIELESFAGS  280 (363)
T ss_dssp             EEEEETTTT-TTTS-GGGGBHHHHHHHHHHHHHHHHHTTTTEEEEEEEEGTTS---HHHHHHHHHHSSEEEEEEE--HH
T ss_pred             EEEEEcCCCCcccCCcccccHHHHHHHHHHHHHHHhccCCCEEEEEEECHHHhccChHHHHHHHHhCCEEEEeecCCCc
Confidence            6788887766443322    2248999999987    3445555556678887  799999999999999999999876

It may also play some role in wobble uridine tRNA modification []. This entry represents the ELP4 subunit. ELP4 is not required for the association of the complex with nascent RNA transcript, but is required for complex integrity and histone acetyltransferase activity. It is also required for an early step in synthesis of 5-methoxycarbonylmethyl (mcm5) and 5-carbamoylmethyl (ncm5) groups present on uridines at the wobble position in tRNA in yeast species.; GO: 0006357 regulation of transcription from RNA polymerase II promoter, 0033588 Elongator holoenzyme complex; PDB: 4EJS_A 4A8J_A.

>PRK04301 radA DNA repair and recombination protein RadA; Validated

Probab=90.71  E-value=3.9  Score=38.17  Aligned_cols=39  Identities=21%  Similarity=0.269  Sum_probs=30.4

Q ss_pred             ceeEEEEeeC--ChHHHHHHHhhcCCCccCCCCeEEEEecc
Q 024646           56 RGLVVVAYSR--SPSFYVDLLKRRGIDIASSHDWIHILDCY   94 (265)
Q Consensus        56 ~~Vhvl~fe~--spe~y~~~lk~~G~d~~~~~~~v~i~D~y   94 (265)
                      ..+..+.+|.  +|+.+.+.+++.|+|.+..-+++++++++
T Consensus       137 ~~~~yi~te~~f~~~rl~~~~~~~g~~~~~~l~~i~~~~~~  177 (317)
T PRK04301        137 GKAVYIDTEGTFRPERIEQMAEALGLDPDEVLDNIHVARAY  177 (317)
T ss_pred             ceEEEEeCCCCcCHHHHHHHHHHcCCChHhhhccEEEEeCC
Confidence            5889999998  68999999988888865544567777654

>cd01121 Sms Sms (bacterial radA) DNA repair protein

Probab=90.22  E-value=9.1  Score=37.27  Aligned_cols=115  Identities=21%  Similarity=0.177  Sum_probs=62.6

Q ss_pred             ccceeEEEEeeCChHHHHHHHhhcCCCccCCCCeEEEEeccCCCCCCcccccCccccccccccccccccchhhhHHHHHH
Q 024646           54 QSRGLVVVAYSRSPSFYVDLLKRRGIDIASSHDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNLDKLYSLI  133 (265)
Q Consensus        54 q~~~Vhvl~fe~spe~y~~~lk~~G~d~~~~~~~v~i~D~ysDPlgW~~~~~~~~~~~~~s~~~~~~~~v~~L~sl~~~~  133 (265)
                      +++.|..+.+|-+++....-.++-|++.    .++.+.+.                              .++..++..+
T Consensus       109 ~g~~VlYvs~EEs~~qi~~Ra~rlg~~~----~~l~l~~e------------------------------~~le~I~~~i  154 (372)
T cd01121         109 RGGKVLYVSGEESPEQIKLRADRLGIST----ENLYLLAE------------------------------TNLEDILASI  154 (372)
T ss_pred             cCCeEEEEECCcCHHHHHHHHHHcCCCc----ccEEEEcc------------------------------CcHHHHHHHH
Confidence            4568888999999888776666666652    23333210                              0122222222


Q ss_pred             HHhccCccCCCCCcEEEEEechhHHHHhc------ChHHHHHHHHhhhc---CCceeEE-EEeecccccchhHHHHHHhh
Q 024646          134 IEQGKGLIGQGKDRFSIAIDSVSEMVRHA------SISSVAGILSNLRS---HDQVSSI-FWLLHSDLHEIKFTSVLEYL  203 (265)
Q Consensus       134 ~e~~~~~~~~~k~r~~VaIDSLS~LL~h~------s~~~vc~lL~~Lr~---~~~vssV-l~LLHsDLHe~~vv~ALe~L  203 (265)
                      .+        .++ -.|+|||++.+....      +..++-..+..|.+   ...+.-+ ++-+..|-+-.+ .+.|+|+
T Consensus       155 ~~--------~~~-~lVVIDSIq~l~~~~~~~~~g~~~qvr~~~~~L~~lak~~~itvilvghvtk~g~~aG-~~~leh~  224 (372)
T cd01121         155 EE--------LKP-DLVIIDSIQTVYSSELTSAPGSVSQVRECTAELMRFAKERNIPIFIVGHVTKEGSIAG-PKVLEHM  224 (372)
T ss_pred             Hh--------cCC-cEEEEcchHHhhccccccCCCCHHHHHHHHHHHHHHHHHcCCeEEEEeeccCCCcccC-cccchhh
Confidence            21        234 479999999986532      23444444444433   2223322 222333322222 2579999


Q ss_pred             heeEEEeee
Q 024646          204 SSMVASVEP  212 (265)
Q Consensus       204 As~vv~v~P  212 (265)
                      +.+++.++-
T Consensus       225 vD~Vi~le~  233 (372)
T cd01121         225 VDTVLYFEG  233 (372)
T ss_pred             ceEEEEEEc
Confidence            999998874

This protein is not related to archael radA any more than is to other RecA-like NTPases. Sms has a role in recombination and recombinational repair and is responsible for the stabilization or processing of branched DNA molecules.

>PRK11823 DNA repair protein RadA; Provisional

Probab=90.12  E-value=8.2  Score=38.29  Aligned_cols=116  Identities=22%  Similarity=0.176  Sum_probs=63.6

Q ss_pred             cccceeEEEEeeCChHHHHHHHhhcCCCccCCCCeEEEEeccCCCCCCcccccCccccccccccccccccchhhhHHHHH
Q 024646           53 SQSRGLVVVAYSRSPSFYVDLLKRRGIDIASSHDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNLDKLYSL  132 (265)
Q Consensus        53 ~q~~~Vhvl~fe~spe~y~~~lk~~G~d~~~~~~~v~i~D~ysDPlgW~~~~~~~~~~~~~s~~~~~~~~v~~L~sl~~~  132 (265)
                      .+++.|..+.+|-+++.+..-.++.|++.    +++.+.+    +                          .++..+...
T Consensus       106 ~~g~~vlYvs~Ees~~qi~~ra~rlg~~~----~~l~~~~----e--------------------------~~l~~i~~~  151 (446)
T PRK11823        106 AAGGKVLYVSGEESASQIKLRAERLGLPS----DNLYLLA----E--------------------------TNLEAILAT  151 (446)
T ss_pred             hcCCeEEEEEccccHHHHHHHHHHcCCCh----hcEEEeC----C--------------------------CCHHHHHHH
Confidence            35778999999999988877677777752    2333211    0                          012222222


Q ss_pred             HHHhccCccCCCCCcEEEEEechhHHHHh------cChHHHHHHHHhhhc---CCceeEEE-EeecccccchhHHHHHHh
Q 024646          133 IIEQGKGLIGQGKDRFSIAIDSVSEMVRH------ASISSVAGILSNLRS---HDQVSSIF-WLLHSDLHEIKFTSVLEY  202 (265)
Q Consensus       133 ~~e~~~~~~~~~k~r~~VaIDSLS~LL~h------~s~~~vc~lL~~Lr~---~~~vssVl-~LLHsDLHe~~vv~ALe~  202 (265)
                      +.+        .++ -.|+|||++.+...      .+..++-..+..|.+   ...+.-++ +-+..|-+-.+. ..++|
T Consensus       152 i~~--------~~~-~lVVIDSIq~l~~~~~~~~~g~~~qvr~~~~~L~~~ak~~~itvilv~hvtk~~~~ag~-~~leh  221 (446)
T PRK11823        152 IEE--------EKP-DLVVIDSIQTMYSPELESAPGSVSQVRECAAELMRLAKQRGIAVFLVGHVTKEGAIAGP-RVLEH  221 (446)
T ss_pred             HHh--------hCC-CEEEEechhhhccccccCCCCCHHHHHHHHHHHHHHHHHcCCEEEEEeeccCCCCcCCc-chhhh
Confidence            222        234 47999999998652      123444444444443   12233222 223333222222 56999


Q ss_pred             hheeEEEeee
Q 024646          203 LSSMVASVEP  212 (265)
Q Consensus       203 LAs~vv~v~P  212 (265)
                      ++.+++.++-
T Consensus       222 lvD~Vi~le~  231 (446)
T PRK11823        222 MVDTVLYFEG  231 (446)
T ss_pred             hCeEEEEEEc
Confidence            9999998873

>cd01393 recA_like RecA is a bacterial enzyme which has roles in homologous recombination, DNA repair, and the induction of the SOS response

Probab=89.31  E-value=9.7  Score=32.90  Aligned_cols=127  Identities=15%  Similarity=0.114  Sum_probs=67.0

Q ss_pred             ceeEEEEeeCC--hHHHHHHHhhcCCCccCCCCeEEEEeccCCCCCCcccccCccccccccccccccccchhhhHHHHHH
Q 024646           56 RGLVVVAYSRS--PSFYVDLLKRRGIDIASSHDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNLDKLYSLI  133 (265)
Q Consensus        56 ~~Vhvl~fe~s--pe~y~~~lk~~G~d~~~~~~~v~i~D~ysDPlgW~~~~~~~~~~~~~s~~~~~~~~v~~L~sl~~~~  133 (265)
                      ..|..+..|.+  ++.+.+.....+.+.+...+++.+.++++ +                          .++...+..+
T Consensus        54 ~~v~yi~~e~~~~~~rl~~~~~~~~~~~~~~~~~i~~~~~~~-~--------------------------~~~~~~l~~~  106 (226)
T cd01393          54 GKVVYIDTEGAFRPERLVQLAVRFGLDPEEVLDNIYVARPYN-G--------------------------EQQLEIVEEL  106 (226)
T ss_pred             ceEEEEecCCCCCHHHHHHHHHHhccchhhhhccEEEEeCCC-H--------------------------HHHHHHHHHH
Confidence            67888888876  66777767776666544345677777631 1                          1222222222


Q ss_pred             HHhccCccCCCCCcEEEEEechhHHHHhc--Ch-------HHHHHHHHhhhc----CCceeEEEEeeccccc-----chh
Q 024646          134 IEQGKGLIGQGKDRFSIAIDSVSEMVRHA--SI-------SSVAGILSNLRS----HDQVSSIFWLLHSDLH-----EIK  195 (265)
Q Consensus       134 ~e~~~~~~~~~k~r~~VaIDSLS~LL~h~--s~-------~~vc~lL~~Lr~----~~~vssVl~LLHsDLH-----e~~  195 (265)
                      .+..    ...+. -.|+||||+.+.+..  +-       ..+.++++.|++    +....=++.-+..+.-     ...
T Consensus       107 ~~~~----~~~~~-~lvVIDsis~l~~~~~~~~~~~~~~~~~l~~~~~~L~~~a~~~~~~vi~tnq~~~~~~~~~~~~~~  181 (226)
T cd01393         107 ERIM----SSGRV-DLVVVDSVAALFRKEFIGRGMLAERARLLSQALRKLLRLADKFNVAVVFTNQVRAKVDVMFGDPET  181 (226)
T ss_pred             HHHh----hcCCe-eEEEEcCcchhhhhhhcCCchHHHHHHHHHHHHHHHHHHHHHhCcEEEEEEEEeeecccccCCCcc
Confidence            2211    11233 589999999987642  11       233444444443    2211111222222221     122


Q ss_pred             HH--HHHHhhheeEEEeeeCC
Q 024646          196 FT--SVLEYLSSMVASVEPFN  214 (265)
Q Consensus       196 vv--~ALe~LAs~vv~v~P~~  214 (265)
                      +.  .+++|.+++.+.++...
T Consensus       182 p~~G~~~~~~~~~ri~l~~~~  202 (226)
T cd01393         182 PAGGNALAHASTTRLDLRKGR  202 (226)
T ss_pred             ccCchhhhCcccEEEEEEecC
Confidence            33  68899999988887533

RecA couples ATP hydrolysis to DNA strand exchange. While prokaryotes have a single RecA protein, eukaryotes have multiple RecA homologs such as Rad51, DMC1 and Rad55/57. Archaea have the RecA-like homologs radA and radB.

>TIGR02236 recomb_radA DNA repair and recombination protein RadA

Probab=88.80  E-value=5.1  Score=37.04  Aligned_cols=38  Identities=18%  Similarity=0.279  Sum_probs=28.9

Q ss_pred             eeEEEEeeC--ChHHHHHHHhhcCCCccCCCCeEEEEecc
Q 024646           57 GLVVVAYSR--SPSFYVDLLKRRGIDIASSHDWIHILDCY   94 (265)
Q Consensus        57 ~Vhvl~fe~--spe~y~~~lk~~G~d~~~~~~~v~i~D~y   94 (265)
                      .++.+.+|-  +|+.+.+.++..|++.+...+++.+..++
T Consensus       131 ~~~yi~te~~f~~~rl~~~~~~~gl~~~~~~~~i~i~~~~  170 (310)
T TIGR02236       131 KAVYIDTENTFRPERIMQMAEARGLDPDEVLKNIYVARAY  170 (310)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHcCCCHHHHhhceEEEecC
Confidence            788888888  78899999988888764434567776653

This family consists exclusively of archaeal RadA protein, a homolog of bacterial RecA (TIGR02012), eukaryotic RAD51 (TIGR02239), and archaeal RadB (TIGR02237). This protein is involved in DNA repair and recombination. The member from Pyrococcus horikoshii contains an intein.

>PRK09361 radB DNA repair and recombination protein RadB; Provisional

Probab=88.23  E-value=9.5  Score=33.24  Aligned_cols=65  Identities=23%  Similarity=0.176  Sum_probs=38.1

Q ss_pred             EEEEEechhHHHHhc-----C----hHHHHHHHHhhhc----CCceeEEEEeecccccc----hhHHHHHHhhheeEEEe
Q 024646          148 FSIAIDSVSEMVRHA-----S----ISSVAGILSNLRS----HDQVSSIFWLLHSDLHE----IKFTSVLEYLSSMVASV  210 (265)
Q Consensus       148 ~~VaIDSLS~LL~h~-----s----~~~vc~lL~~Lr~----~~~vssVl~LLHsDLHe----~~vv~ALe~LAs~vv~v  210 (265)
                      =.|+||||+.+.+..     .    ...+.+.++.|++    +....=+..-++.+.+.    +---..++|++++++.+
T Consensus       109 ~lvVIDsi~al~~~~~~~~~~~~~~~~~l~~~l~~L~~~a~~~~v~vi~tnq~~~~~~~~~~~~~gg~~~~~~~d~ii~l  188 (225)
T PRK09361        109 GLIVLDSATSLYRLELEDEEDNSKLNRELGRQLTHLLKLARKHDLAVVITNQVYSDIDSDGLRPLGGHTLEHWSKTILRL  188 (225)
T ss_pred             cEEEEeCcHHHhHHHhcCCccHHHHHHHHHHHHHHHHHHHHHhCCEEEEEccceecCCCCcccCCCcchhhhhccEEEEE
Confidence            489999999987642     1    1234554444433    33333333444445442    21123789999999999


Q ss_pred             ee
Q 024646          211 EP  212 (265)
Q Consensus       211 ~P  212 (265)
                      +.
T Consensus       189 ~~  190 (225)
T PRK09361        189 EK  190 (225)
T ss_pred             EE
Confidence            76

>cd01123 Rad51_DMC1_radA Rad51_DMC1_radA,B

Probab=87.26  E-value=5.4  Score=34.69  Aligned_cols=40  Identities=23%  Similarity=0.284  Sum_probs=30.6

Q ss_pred             cceeEEEEeeC--ChHHHHHHHhhcCCCccCCCCeEEEEecc
Q 024646           55 SRGLVVVAYSR--SPSFYVDLLKRRGIDIASSHDWIHILDCY   94 (265)
Q Consensus        55 ~~~Vhvl~fe~--spe~y~~~lk~~G~d~~~~~~~v~i~D~y   94 (265)
                      .+++..+.+|.  +++.+.+.+++.|.+....-+++++.++|
T Consensus        53 ~~~viyi~~e~~~~~~rl~~~~~~~~~~~~~~~~~i~~~~~~   94 (235)
T cd01123          53 EGKAVYIDTEGTFRPERLVQIAERFGLDPEEVLDNIYVARAY   94 (235)
T ss_pred             CccEEEEeCCCCcCHHHHHHHHHHhccChHhHhcCEEEEecC
Confidence            36888888888  57888888888888766556678877764

This group of recombinases includes the eukaryotic proteins RAD51, RAD55/57 and the meiosis-specific protein DMC1, and the archaeal proteins radA and radB. They are closely related to the bacterial RecA group. Rad51 proteins catalyze a similiar recombination reaction as RecA, using ATP-dependent DNA binding activity and a DNA-dependent ATPase. However, this reaction is less efficient and requires accessory proteins such as RAD55/57 .

>cd01122 GP4d_helicase GP4d_helicase is a homohexameric 5'-3' helicases

Probab=85.63  E-value=26  Score=31.27  Aligned_cols=21  Identities=5%  Similarity=-0.113  Sum_probs=17.7

Q ss_pred             cceeEEEEeeCChHHHHHHHh
Q 024646           55 SRGLVVVAYSRSPSFYVDLLK   75 (265)
Q Consensus        55 ~~~Vhvl~fe~spe~y~~~lk   75 (265)
                      +..|.++.+|-++++...-+.
T Consensus        59 g~~vl~iS~E~~~~~~~~r~~   79 (271)
T cd01122          59 GVRVGTISLEEPVVRTARRLL   79 (271)
T ss_pred             CceEEEEEcccCHHHHHHHHH
Confidence            789999999999988877553

Helicases couple NTP hydrolysis to the unwinding of nucleic acid duplexes into their component strands.

>PTZ00035 Rad51 protein; Provisional

Probab=83.76  E-value=23  Score=33.93  Aligned_cols=40  Identities=20%  Similarity=0.272  Sum_probs=28.4

Q ss_pred             cceeEEEEeeC--ChHHHHHHHhhcCCCccCCCCeEEEEecc
Q 024646           55 SRGLVVVAYSR--SPSFYVDLLKRRGIDIASSHDWIHILDCY   94 (265)
Q Consensus        55 ~~~Vhvl~fe~--spe~y~~~lk~~G~d~~~~~~~v~i~D~y   94 (265)
                      +..+..+..|.  +|+...+..++.|++.+..-.++.+.++|
T Consensus       152 ~g~vvyIdtE~~f~~eri~~ia~~~g~~~~~~l~nI~~~~~~  193 (337)
T PTZ00035        152 EGKVLYIDTEGTFRPERIVQIAERFGLDPEDVLDNIAYARAY  193 (337)
T ss_pred             CceEEEEEccCCCCHHHHHHHHHHhCCChHhHhhceEEEccC
Confidence            44677888887  48888888888888766544566666544

>cd00984 DnaB_C DnaB helicase C terminal domain

Probab=83.26  E-value=1.6  Score=38.29  Aligned_cols=67  Identities=18%  Similarity=0.119  Sum_probs=39.1

Q ss_pred             EEEEEechhHHHHhc----ChHHHHHHHHhhhcC-CceeEEEEeecc------c-------ccchhHHHHHHhhheeEEE
Q 024646          148 FSIAIDSVSEMVRHA----SISSVAGILSNLRSH-DQVSSIFWLLHS------D-------LHEIKFTSVLEYLSSMVAS  209 (265)
Q Consensus       148 ~~VaIDSLS~LL~h~----s~~~vc~lL~~Lr~~-~~vssVl~LLHs------D-------LHe~~vv~ALe~LAs~vv~  209 (265)
                      -.|+||+|+.+-...    .-..+..++..|+.- .+....+++++.      +       ++.-+-.+++++.|.+++.
T Consensus       125 ~~vvID~l~~l~~~~~~~~~~~~~~~~~~~L~~la~~~~~~ii~~~q~~r~~~~~~~~~~~~~~~~gS~~i~~~aD~vi~  204 (242)
T cd00984         125 GLIVIDYLQLMSGSKKKGNRQQEVAEISRSLKLLAKELNVPVIALSQLSRGVESRADKRPMLSDLRESGSIEQDADVVMF  204 (242)
T ss_pred             CEEEEcCchhcCCCCCCCCHHHHHHHHHHHHHHHHHHhCCeEEEecccChhhhccCCCCCCHHHHhhhcccccCCCEEEE
Confidence            489999999664332    123445556666641 223333444441      1       2233344788999999999


Q ss_pred             eeeCC
Q 024646          210 VEPFN  214 (265)
Q Consensus       210 v~P~~  214 (265)
                      +.+..
T Consensus       205 l~~~~  209 (242)
T cd00984         205 LYRDE  209 (242)
T ss_pred             Eeccc
Confidence            98753

The hexameric helicase DnaB unwinds the DNA duplex at the chromosome replication fork. Although the mechanism by which DnaB both couples ATP hydrolysis to translocation along DNA and denatures the duplex is unknown, a change in the quaternary structure of the protein involving dimerization of the N-terminal domain has been observed and may occur during the enzymatic cycle. This C-terminal domain contains an ATP-binding site and is therefore probably the site of ATP hydrolysis.

>PF03192 DUF257: Pyrococcus protein of unknown function, DUF257; InterPro: IPR005489 This family of proteins is of unknown function

Probab=81.67  E-value=34  Score=30.91  Aligned_cols=153  Identities=17%  Similarity=0.265  Sum_probs=89.6

Q ss_pred             ceeeccCCCCCchhhHHHHHHHHHHHHHHhhccccceeEEEEeeCChHHHHHHHhhcCCCccCCCCeEEE----------
Q 024646           21 ALTIKDSKASPFGFDVFNYVLTQLSNYILAGKSQSRGLVVVAYSRSPSFYVDLLKRRGIDIASSHDWIHI----------   90 (265)
Q Consensus        21 ~l~i~Dsl~~~~g~~~~~h~~~~l~s~i~a~~~q~~~Vhvl~fe~spe~y~~~lk~~G~d~~~~~~~v~i----------   90 (265)
                      +++||-+-.++  +.++      ++..+..++.++-.|.|..+=-+-..|..-|+..|+|.+. -+++.+          
T Consensus        13 ~VLVEy~S~~~--~el~------~~~li~~~~~~~~~vlI~DilDtl~i~~~~l~~~Gi~~~~-l~~~~VIKiGG~~~~G   83 (210)
T PF03192_consen   13 TVLVEYSSSSP--PELL------FYELIKWAREKGYPVLIDDILDTLHIYKKHLELMGIDTDI-LDNIKVIKIGGRIEVG   83 (210)
T ss_dssp             EEEEEE-TTS---THHH------HHHHHH---T-SS-BEEEEETTHHHHHHHHHHHTT---HH-HHCSEEEEES-S---S
T ss_pred             EEEEEeCCCCc--HHHH------HHHHHHHhhhcCCCEEEEEcCCCHHHHHHHHHHcCCCccc-ccCceEEEecCeeeee
Confidence            56787766333  3333      4455666777888899988888888999999999999765 122333          


Q ss_pred             -----EeccCCCCCCcccccCccccccccccccccccchhhhHHHHHHHHhccCccCCCCCcEEEEEechhHHH--HhcC
Q 024646           91 -----LDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNLDKLYSLIIEQGKGLIGQGKDRFSIAIDSVSEMV--RHAS  163 (265)
Q Consensus        91 -----~D~ysDPlgW~~~~~~~~~~~~~s~~~~~~~~v~~L~sl~~~~~e~~~~~~~~~k~r~~VaIDSLS~LL--~h~s  163 (265)
                           ++..+||--|.                          +.+..+.+..   ..  +.+++..+=-+.-++  ...+
T Consensus        84 nVv~ri~~~~d~~~~~--------------------------k~Y~~~~~~~---~~--~~~~i~ivlGiekl~~~~~~~  132 (210)
T PF03192_consen   84 NVVGRIPITSDPSVYL--------------------------KEYEEILEKV---LE--KEKVINIVLGIEKLFYFFENS  132 (210)
T ss_dssp             EEEEEE-----BBTTB--------------------------HHHHHHHTT--------S-SEEEEEE-HHHHH-HH-S-
T ss_pred             eEEEEEecccChHHHH--------------------------HHHHHHHHHH---hc--cCCeEEEEecHHHHHHHHhcc
Confidence                 33333333222                          2223333321   11  222455555666666  4478


Q ss_pred             hHHHHHHHHhhhcC--CceeEEEEeecccccch---hHHHHHHhhheeEEEeeeC
Q 024646          164 ISSVAGILSNLRSH--DQVSSIFWLLHSDLHEI---KFTSVLEYLSSMVASVEPF  213 (265)
Q Consensus       164 ~~~vc~lL~~Lr~~--~~vssVl~LLHsDLHe~---~vv~ALe~LAs~vv~v~P~  213 (265)
                      ..++..++..+.+.  ..=..-|..++.|+-+.   .+...||-+||+|+.++..
T Consensus       133 ~~e~~~~~~~i~~~lg~~~r~a~yfiN~dvl~~~~~~~l~~LEeiattVi~i~~~  187 (210)
T PF03192_consen  133 PRELILFFNSISRFLGNERRIAFYFINRDVLEKISPEVLPLLEEIATTVIEIEKE  187 (210)
T ss_dssp             HHHHHHHHHHHHCCTT-TTEEEEEEEEHHHHHHHHHHHHHHHHHHSSEEEEEETT
T ss_pred             HHHHHHHHHHHHHhcCCCceEEEEEEchHHhcccCchHHHHHHHHhhheEEEecC
Confidence            99999999999875  23345688999999986   8888999999999999875

; PDB: 2EKD_C.

>TIGR02238 recomb_DMC1 meiotic recombinase Dmc1

Probab=81.14  E-value=22  Score=33.72  Aligned_cols=41  Identities=17%  Similarity=0.208  Sum_probs=31.8

Q ss_pred             ccceeEEEEeeCC--hHHHHHHHhhcCCCccCCCCeEEEEecc
Q 024646           54 QSRGLVVVAYSRS--PSFYVDLLKRRGIDIASSHDWIHILDCY   94 (265)
Q Consensus        54 q~~~Vhvl~fe~s--pe~y~~~lk~~G~d~~~~~~~v~i~D~y   94 (265)
                      .+..+..+..|-+  |+.+.+.+++.|+|++..-+++.+.++|
T Consensus       129 ~~~~vvYIdtE~~f~~eRi~~~a~~~g~d~~~~l~~i~~~~~~  171 (313)
T TIGR02238       129 GNGKVAYIDTEGTFRPDRIRAIAERFGVDPDAVLDNILYARAY  171 (313)
T ss_pred             CCCeEEEEEcCCCCCHHHHHHHHHHcCCChHHhcCcEEEecCC
Confidence            3568899999995  9999999999999876645667766554

This model describes DMC1, a subfamily of a larger family of DNA repair and recombination proteins. It is eukaryotic only and most closely related to eukaryotic RAD51. It also resembles archaeal RadA (TIGR02236) and RadB (TIGR02237) and bacterial RecA (TIGR02012). It has been characterized for human as a recombinase active only in meiosis.

>TIGR02239 recomb_RAD51 DNA repair protein RAD51

Probab=80.31  E-value=49  Score=31.33  Aligned_cols=125  Identities=12%  Similarity=0.113  Sum_probs=67.8

Q ss_pred             ceeEEEEeeC--ChHHHHHHHhhcCCCccCCCCeEEEEeccCCCCCCcccccCccccccccccccccccchhhhHHHHHH
Q 024646           56 RGLVVVAYSR--SPSFYVDLLKRRGIDIASSHDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNLDKLYSLI  133 (265)
Q Consensus        56 ~~Vhvl~fe~--spe~y~~~lk~~G~d~~~~~~~v~i~D~ysDPlgW~~~~~~~~~~~~~s~~~~~~~~v~~L~sl~~~~  133 (265)
                      ..+..+.+|.  +|+-+.+..++.|++++..-.++++.++|+ +                          .++..++...
T Consensus       131 ~~vvyIdtE~~f~~~Rl~~ia~~~~~~~~~~l~~i~~~~~~~-~--------------------------~~~~~~l~~~  183 (316)
T TIGR02239       131 GKALYIDTEGTFRPERLLAIAERYGLNPEDVLDNVAYARAYN-T--------------------------DHQLQLLQQA  183 (316)
T ss_pred             ceEEEEECCCCCCHHHHHHHHHHcCCChHHhhccEEEEecCC-h--------------------------HHHHHHHHHH
Confidence            3677888888  687788888888887655445566665431 0                          1111111222


Q ss_pred             HHhccCccCCCCCcEEEEEechhHHHHhcC-----h----HHHHHHHHhhhc----CCceeEEEEeeccccc--------
Q 024646          134 IEQGKGLIGQGKDRFSIAIDSVSEMVRHAS-----I----SSVAGILSNLRS----HDQVSSIFWLLHSDLH--------  192 (265)
Q Consensus       134 ~e~~~~~~~~~k~r~~VaIDSLS~LL~h~s-----~----~~vc~lL~~Lr~----~~~vssVl~LLHsDLH--------  192 (265)
                      .+...    ..+. -.|+|||++.+.+..-     .    ..+.++++.|++    +....=+..-+.+|.-        
T Consensus       184 ~~~~~----~~~~-~LvVIDSI~al~r~~~~~~~~~~~rq~~l~~~~~~L~~la~~~~vavv~tNqv~~~~~~~~~~~~g  258 (316)
T TIGR02239       184 AAMMS----ESRF-ALLIVDSATALYRTDFSGRGELSARQMHLARFLRSLQRLADEFGVAVVITNQVVAQVDGAGSMFAG  258 (316)
T ss_pred             HHhhc----cCCc-cEEEEECcHHHhhhhcCCcchHHHHHHHHHHHHHHHHHHHHHhCCEEEEECceEEecCCccccccC
Confidence            22111    1233 4799999999976421     1    123455556654    2222222222222222        


Q ss_pred             ---chhHHHHHHhhheeEEEeee
Q 024646          193 ---EIKFTSVLEYLSSMVASVEP  212 (265)
Q Consensus       193 ---e~~vv~ALe~LAs~vv~v~P  212 (265)
                         .|--=.+++|.+++.+.++-
T Consensus       259 ~~~~p~gG~~~~h~~~~ri~l~k  281 (316)
T TIGR02239       259 DPKKPIGGNIMAHASTTRLSLRK  281 (316)
T ss_pred             CCCcCCchHHHHhhccEEEEEEe
Confidence               12223588999999999984

This eukaryotic sequence family consists of RAD51, a protein involved in DNA homologous recombination and repair. It is similar in sequence the exclusively meiotic recombinase DMC1 (TIGR02238), to archaeal families RadA (TIGR02236) and RadB (TIGR02237), and to bacterial RecA (TIGR02012).

>cd01394 radB RadB

Probab=80.04  E-value=31  Score=29.77  Aligned_cols=64  Identities=23%  Similarity=0.127  Sum_probs=35.9

Q ss_pred             EEEEEechhHHHHhcCh---------HHHHHHHHhhhc----CCceeEEEEeeccccc----chhHHHHHHhhheeEEEe
Q 024646          148 FSIAIDSVSEMVRHASI---------SSVAGILSNLRS----HDQVSSIFWLLHSDLH----EIKFTSVLEYLSSMVASV  210 (265)
Q Consensus       148 ~~VaIDSLS~LL~h~s~---------~~vc~lL~~Lr~----~~~vssVl~LLHsDLH----e~~vv~ALe~LAs~vv~v  210 (265)
                      -.|+|||++.+.+..-.         ..+.+.++.|+.    +....=+.+-+..+..    .|.--..++|++.+++.+
T Consensus       105 ~lvvIDsi~~l~~~~~~~~~~~~~~~~~l~~~~~~L~~~a~~~~~~vi~t~q~~~~~~~~~~~p~~g~~~~~~~d~~i~l  184 (218)
T cd01394         105 DLVVVDSATALYRLELGDDDTTIKNYRELAKQLTFLLWLARKHDVAVVITNQVYSDVGSGSVRPLGGHTLEHWSKVILRL  184 (218)
T ss_pred             cEEEEechHHhhhHHhcCccchHHHHHHHHHHHHHHHHHHHHhCCEEEEecCCEEcCCCCcccccCCcchhcceeEEEEE
Confidence            48999999999653211         144555544443    3333323333333332    122223689999999999


Q ss_pred             e
Q 024646          211 E  211 (265)
Q Consensus       211 ~  211 (265)
                      +
T Consensus       185 ~  185 (218)
T cd01394         185 E  185 (218)
T ss_pred             E
Confidence            6

The archaeal protein radB shares similarity radA, the archaeal functional homologue to the bacterial RecA. The precise function of radB is unclear.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

No hit with e-value below 0.005

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	265
4a8j_B	270	Elongator complex protein 5; transcription; 2.10A	98.96
4a8j_C	280	Elongator complex protein 6; transcription; 2.10A	98.01
3bs4_A	260	Uncharacterized protein PH0321; structural genomic	97.8
2zts_A	251	Putative uncharacterized protein PH0186; KAIC like	94.51
2w0m_A	235	SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus	92.31
2dr3_A	247	UPF0273 protein PH0284; RECA superfamily ATPase, h	92.2
2i1q_A	322	DNA repair and recombination protein RADA; ATPase,	91.59
4a8j_A	361	Elongator complex protein 4; transcription; 2.10A	89.95
3bh0_A	315	DNAB-like replicative helicase; ATPase, replicatio	89.59
2z43_A	324	DNA repair and recombination protein RADA; archaea	88.93
2q6t_A	444	DNAB replication FORK helicase; hydrolase; 2.90A {	82.2
1q57_A	503	DNA primase/helicase; dntpase, DNA replication, tr	80.03

>4a8j_B Elongator complex protein 5; transcription; 2.10A {Saccharomyces cerevisiae} PDB: 4ejs_B

Probab=98.96  E-value=4.4e-09  Score=96.00  Aligned_cols=99  Identities=16%  Similarity=0.229  Sum_probs=74.5

Q ss_pred             cEEEEEechhHHHHhcChHHHHHHHHhhhcCCceeEEEEeeccccc-------------chhHHHHHHhhheeEEEeeeC
Q 024646          147 RFSIAIDSVSEMVRHASISSVAGILSNLRSHDQVSSIFWLLHSDLH-------------EIKFTSVLEYLSSMVASVEPF  213 (265)
Q Consensus       147 r~~VaIDSLS~LL~h~s~~~vc~lL~~Lr~~~~vssVl~LLHsDLH-------------e~~vv~ALe~LAs~vv~v~P~  213 (265)
                      +..|+||||+.++.    ..+.++|..+-. | -.++++--|.|+.             .|....-|.||||++++|.|.
T Consensus       101 k~LVIIDSLN~l~~----~~L~~FlsSi~s-P-~~sLv~vYH~DvP~~~~~~~~~~n~y~Ps~LtLL~ylATTIl~v~~~  174 (270)
T 4a8j_B          101 KHMVIIDSLNYIST----EYITRFLSEIAS-P-HCTMVATYHKDIKDENRTVIPDWNNNYPDKLTLLQFMATTIVDIDVV  174 (270)
T ss_dssp             CEEEEESCGGGSCG----GGHHHHHHHHCC-T-TEEEEEEEETTSCCC------CTTBCCCCHHHHHHHHCSEEEEEEEC
T ss_pred             ceEEEEecCcchhh----hhHHHHHHHhhc-C-CcEEEEEecCCCCCCCccccccccCCCCChHHHHHHhhhheEEEecC
Confidence            58999999999996    578899998885 5 4589999999974             566778899999999999999


Q ss_pred             Ccccccccchhhhhhhh----hhccccceEEEEeecCCCchh
Q 024646          214 NQAAFGQRVDLENLSML----EQNFRKGKFHVRFKRRNGRVR  251 (265)
Q Consensus       214 ~~~~~~~~~~~~~~~~l----~~n~~kg~~~vr~KrrnGRV~  251 (265)
                      .....-.|+--.+++-+    .-|.+.=++++..|||.||..
T Consensus       175 ~~~~~deE~l~~~l~k~~~P~glN~~~f~l~ltnrRKSGRsl  216 (270)
T 4a8j_B          175 LTGTLDTEEVSELLNEFRIPRGLNNDIFQLRLVNKRKSGRSL  216 (270)
T ss_dssp             CCSSCCHHHHHHHHHTTCCCSSCSCSEEEEEEEEECTTSCEE
T ss_pred             CCCCccHHHHHHHhhheecccccCCCeEEEEEEeccccCcce
Confidence            87664444322222222    234444468999999999964

>4a8j_C Elongator complex protein 6; transcription; 2.10A {Saccharomyces cerevisiae} PDB: 4ejs_C

Probab=98.01  E-value=0.00018  Score=66.18  Aligned_cols=170  Identities=13%  Similarity=0.162  Sum_probs=111.7

Q ss_pred             cC-CCCCceeeccCCCCCchhhHHHHHHHHHHHHHHhhc-------------cccceeEEEEeeCChHHHHHHHhhcCCC
Q 024646           15 EG-EHAPALTIKDSKASPFGFDVFNYVLTQLSNYILAGK-------------SQSRGLVVVAYSRSPSFYVDLLKRRGID   80 (265)
Q Consensus        15 ~g-e~ap~l~i~Dsl~~~~g~~~~~h~~~~l~s~i~a~~-------------~q~~~Vhvl~fe~spe~y~~~lk~~G~d   80 (265)
                      ++ +..-.++|...+.+..-=.+-.+    +.+.+....             .....|+++.|-.++++|...+||-|+|
T Consensus        31 ~~~~~~~L~liT~~~gTsp~WLin~l----ves~L~G~~~~~n~~~~~~~~~~~~~~Vv~~SF~~~~~fy~~~~~Klgid  106 (280)
T 4a8j_C           31 QDSNSHNLFFITHQSCTQPLWMINAL----VETHVLGSPSSLNESSSSMLPSSTRSHAVLASFIHEQNYFTNSLNKLKIP  106 (280)
T ss_dssp             TSSSCCEEEEEEECTTSCCHHHHHHH----HHHHHHSSCHHHHCC----CCCCCCCEEEEEESSSCHHHHHHHHHHTTCC
T ss_pred             CCCCCceEEEEccccCCChHHHHHHH----HHHHhcCCcccccccccccccCCCCceEEEEEeecCHHHHHHHHHHhCCC
Confidence            55 67778889999855431222333    223332111             2335799999999999999999999999


Q ss_pred             ccCCCCeEEEEeccCCCCCCccc-ccCccccccccccccccccchhhhHHHHHHHHhccCccCCCCCcEEEEEechhHHH
Q 024646           81 IASSHDWIHILDCYTDPLGWKNW-LIDKDISQEASSLSSFCQDVRNLDKLYSLIIEQGKGLIGQGKDRFSIAIDSVSEMV  159 (265)
Q Consensus        81 ~~~~~~~v~i~D~ysDPlgW~~~-~~~~~~~~~~s~~~~~~~~v~~L~sl~~~~~e~~~~~~~~~k~r~~VaIDSLS~LL  159 (265)
                      .    +++.|+|||||..  .++ ..  .+   ..      +..+++..++..++...      + .+.+|+||..-.||
T Consensus       107 l----~~f~fvD~~tdl~--~~~~~~--kp---~~------~~l~~v~~~f~~~i~~~------~-~~~vlIldqpdlLL  162 (280)
T 4a8j_C          107 S----NNYNVLDFLSDFI--VNNIHN--KP---RD------KILSDVLAKFSAAIQNN------P-TDTIVIIEQPELLL  162 (280)
T ss_dssp             G----GGEEEEESSTTHH--HHHTTT--CC---HH------HHHHHHHHHHHHHHHTS------T-TSEEEEEECGGGHH
T ss_pred             h----hheeEEEecchhh--hhcccC--Cc---ch------hhhHHHHHHHhhhhhcc------C-CCeEEEEcChHHHH
Confidence            5    5899999999988  111 01  00   00      01245666666655521      1 23899999999888


Q ss_pred             Hh---cChHHH-HHHHHhhhcCCceeEEEEeecccc---cc----------hhHHHHHHhhheeEEEeeeCC
Q 024646          160 RH---ASISSV-AGILSNLRSHDQVSSIFWLLHSDL---HE----------IKFTSVLEYLSSMVASVEPFN  214 (265)
Q Consensus       160 ~h---~s~~~v-c~lL~~Lr~~~~vssVl~LLHsDL---He----------~~vv~ALe~LAs~vv~v~P~~  214 (265)
                      --   ....++ -.+|..|++... ..|+ -+..|.   |.          ..++..+.|.|.++++|.|+.
T Consensus       163 a~t~~it~~~L~~~~I~~L~k~~~-~lvv-t~saD~pli~~~~~t~~~~e~a~f~~~l~H~A~~visLrpL~  232 (280)
T 4a8j_C          163 SLVSGLTCSELNNKFITPLLRQCK-VLII-VSNSDIFNIDEYDASVHSSNLQNFYKSSFIKSMINLNLNPLK  232 (280)
T ss_dssp             HHSTTCCHHHHHHHTHHHHHHTCS-EEEE-EEECGGGCCSSCCHHHHTHHHHHHHHHHHHHCSEEEEEECCC
T ss_pred             HhccCCCHHHHHHHHHHHHHHhcc-eEEE-EeccCccccccCCCCchHHHHHHHHHHHHHHhheEEeecccC
Confidence            74   456677 888999987433 2233 333443   21          257888999999999999973

>3bs4_A Uncharacterized protein PH0321; structural genomics, unknown function, PSI-2, protein struct initiative; 1.60A {Pyrococcus horikoshii}

Probab=97.80  E-value=0.00028  Score=63.68  Aligned_cols=154  Identities=12%  Similarity=0.083  Sum_probs=94.4

Q ss_pred             hhccccceeEEEEeeCChHHHHHHHhhcCCCccCC--CCeEEEEeccCCCCCCcccccCccccccccccccccccchhhh
Q 024646           50 AGKSQSRGLVVVAYSRSPSFYVDLLKRRGIDIASS--HDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNLD  127 (265)
Q Consensus        50 a~~~q~~~Vhvl~fe~spe~y~~~lk~~G~d~~~~--~~~v~i~D~ysDPlgW~~~~~~~~~~~~~s~~~~~~~~v~~L~  127 (265)
                      ++..+++.+.+++||-||+.+..-++..|+|.+..  +.++.++|.|++..++......   --+.+..+    ++..+-
T Consensus        44 ~g~~~Ge~~~~~~~~e~~~~l~~~~~~~G~dl~~~~~~g~l~i~d~~~~~~~~~~~~~~---v~~~~~e~----d~~~l~  116 (260)
T 3bs4_A           44 RKLKSDNLVGMFSISYPLQLIIRILSRFGVDVIKYLENHRLAIVDTFGSFHGIKATMPG---VWYLEGML----SSETLP  116 (260)
T ss_dssp             HHHHTTCEEEEEECSSCHHHHHHHHHHTTCCHHHHHHTTSEEEECHHHHHHTC---CTT---EECCCSCC----CTTTHH
T ss_pred             HHHHCCCcEEEEEEeCCHHHHHHHHHHcCCCHHHHhhCCcEEEEEcccccccccccccc---eecccccC----CHHHHH
Confidence            57788999999999999999999999999997531  3579999998855443321000   00000001    222331


Q ss_pred             HHHHHHHHhccC---ccC-CCCCcEEEEEechhHHHHhcChHHHHHHHHhhhc---------C-CceeEEEEeecccccc
Q 024646          128 KLYSLIIEQGKG---LIG-QGKDRFSIAIDSVSEMVRHASISSVAGILSNLRS---------H-DQVSSIFWLLHSDLHE  193 (265)
Q Consensus       128 sl~~~~~e~~~~---~~~-~~k~r~~VaIDSLS~LL~h~s~~~vc~lL~~Lr~---------~-~~vssVl~LLHsDLHe  193 (265)
                      .....+++..|.   +.. -+..|++++||||+.+..-.+.....+++.++..         . ..+..++ ++. |.+.
T Consensus       117 ~~i~~iv~~~~~~~~i~~~~~~~rvv~vidsldsl~~~~~~~~~~~~~~~ll~~~~~~~~~~~~~~~ttil-~~~-~~~~  194 (260)
T 3bs4_A          117 IKYAKAVEDHKKVWMDLNLFEGRELYGFAISMSGYLEVFTPEETLRYLETSAEVRYGHPAYKKYPRGTNFW-LWE-GVKD  194 (260)
T ss_dssp             HHHHHHHHHHHHHHHHTTCSTTCCEEEEEETGGGGGGTSCHHHHHHHHHHHHHHHHHCHHHHSSCCCEEEE-EEE-SCSC
T ss_pred             HHHHHHHHhhccccchhhccCCceEEEEEeecchHHHHhChhhHHHHHHHHHHhhhhHHHHhccCCcEEEE-EEC-CCcc
Confidence            112344442100   011 1224578888888888777766666555555532         2 4454444 455 7777


Q ss_pred             hhHHHHHHhhheeEEEeee
Q 024646          194 IKFTSVLEYLSSMVASVEP  212 (265)
Q Consensus       194 ~~vv~ALe~LAs~vv~v~P  212 (265)
                      +.+...+.++|-.+|.+.-
T Consensus       195 ~~~~~~l~~laD~VI~lr~  213 (260)
T 3bs4_A          195 KRVLLSVYRRADYVLKTRS  213 (260)
T ss_dssp             HHHHHHHHHHCSEEEEEEE
T ss_pred             cccccceEEEeeEEEEEEE
Confidence            7777889999999999954

>2zts_A Putative uncharacterized protein PH0186; KAIC like protein, ATP-binding, nucleotide-binding, ATP- binding protein; HET: ADP; 2.07A {Pyrococcus horikoshii}

Probab=94.51  E-value=0.48  Score=39.22  Aligned_cols=172  Identities=11%  Similarity=0.042  Sum_probs=81.5

Q ss_pred             CCCCCceeeccCCCCCchhhHHHHHHHHHHHHHHhhccccceeEEEEeeCChHHHHHHHhhcCCCccC--CCCeEEEEec
Q 024646           16 GEHAPALTIKDSKASPFGFDVFNYVLTQLSNYILAGKSQSRGLVVVAYSRSPSFYVDLLKRRGIDIAS--SHDWIHILDC   93 (265)
Q Consensus        16 ge~ap~l~i~Dsl~~~~g~~~~~h~~~~l~s~i~a~~~q~~~Vhvl~fe~spe~y~~~lk~~G~d~~~--~~~~v~i~D~   93 (265)
                      |=+++.+++-=--...+-+.+..+++..      +....++.|.++.+|-+++.+.+-+.+.|.+.+.  ...++.+.|.
T Consensus        26 Gl~~G~l~~i~G~pG~GKT~l~l~~~~~------~~~~~~~~v~~~s~E~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~   99 (251)
T 2zts_A           26 GFPEGTTVLLTGGTGTGKTTFAAQFIYK------GAEEYGEPGVFVTLEERARDLRREMASFGWDFEKYEKEGKIAIVDG   99 (251)
T ss_dssp             SEETTCEEEEECCTTSSHHHHHHHHHHH------HHHHHCCCEEEEESSSCHHHHHHHHHTTTCCHHHHHHTTSEEEEC-
T ss_pred             CCCCCeEEEEEeCCCCCHHHHHHHHHHH------HHHhcCCCceeecccCCHHHHHHHHHHcCCChHHHHhcCcchhhhh
Confidence            4445544443323343434444443321      1234567899999999999999988877765432  2346889998


Q ss_pred             cCCCCCCcccccCccccccccccccccccchhhhHHHHHHHHhccCccCCCCCcEEEEEechhHHHHhcC-hHHHHHHHH
Q 024646           94 YTDPLGWKNWLIDKDISQEASSLSSFCQDVRNLDKLYSLIIEQGKGLIGQGKDRFSIAIDSVSEMVRHAS-ISSVAGILS  172 (265)
Q Consensus        94 ysDPlgW~~~~~~~~~~~~~s~~~~~~~~v~~L~sl~~~~~e~~~~~~~~~k~r~~VaIDSLS~LL~h~s-~~~vc~lL~  172 (265)
                      +....+..........         ......++.......++.       .++ -.|+||+++.+....+ ...+...++
T Consensus       100 ~~~~~~~~~~~~~~~~---------~~~~~~~~~~~~~~~~~~-------~~~-~~vviD~~~~l~~~~~~~~~~~~~~~  162 (251)
T 2zts_A          100 VSSVVGLPSEEKFVLE---------DRFNVDNFLRYIYRVVKA-------INA-KRLVIDSIPSIALRLEEERKIREVLL  162 (251)
T ss_dssp             ---------------------------CCHHHHHHHHHHHHHH-------TTC-SEEEEECHHHHHHHSSSGGGHHHHHH
T ss_pred             HHHHhhcccchhcccc---------ccccHHHHHHHHHHHHHh-------cCC-cEEEEEcHHHHhhhccChHHHHHHHH
Confidence            8766543321110000         000112222211222221       223 4789999999987553 233444444


Q ss_pred             hhhcC---CceeEEEEeecc---cccchhHHHHHHhhheeEEEee
Q 024646          173 NLRSH---DQVSSIFWLLHS---DLHEIKFTSVLEYLSSMVASVE  211 (265)
Q Consensus       173 ~Lr~~---~~vssVl~LLHs---DLHe~~vv~ALe~LAs~vv~v~  211 (265)
                      .|.+.   -.+. |+.+-|.   +.-.....+.++++|.+++.+.
T Consensus       163 ~L~~~a~~~~i~-vi~~~q~~~~~~~~~~~~~~~~~~aD~vi~l~  206 (251)
T 2zts_A          163 KLNTILLEMGVT-TILTTEAPDPQHGKLSRYGIEEFIARGVIVLD  206 (251)
T ss_dssp             HHHHHHHHHCCE-EEEEECCC----CCSSSSSCGGGGCSEEEEEE
T ss_pred             HHHHHHHHcCCC-eEEEEEEecccccccccCCceeEEeeEEEEEE
Confidence            44442   1122 2222221   1111223456789999998885

>2w0m_A SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus solfataricus P2}

Probab=92.31  E-value=2.8  Score=33.88  Aligned_cols=139  Identities=12%  Similarity=0.089  Sum_probs=73.2

Q ss_pred             ccceeEEEEeeCChHHHHHHHhhcCCCccCC-CCeEEEEeccCCCCCCcccccCccccccccccccccccchhhhHHHHH
Q 024646           54 QSRGLVVVAYSRSPSFYVDLLKRRGIDIASS-HDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNLDKLYSL  132 (265)
Q Consensus        54 q~~~Vhvl~fe~spe~y~~~lk~~G~d~~~~-~~~v~i~D~ysDPlgW~~~~~~~~~~~~~s~~~~~~~~v~~L~sl~~~  132 (265)
                      ++..|.++++|.+++.+...++..|++.... ..++.++|.+....+ ......           ..  +..++...+..
T Consensus        50 ~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~-----------~~--~~~~~~~~~~~  115 (235)
T 2w0m_A           50 DGDPCIYVTTEESRDSIIRQAKQFNWDFEEYIEKKLIIIDALMKEKE-DQWSLV-----------NL--TPEELVNKVIE  115 (235)
T ss_dssp             HTCCEEEEESSSCHHHHHHHHHHTTCCCGGGBTTTEEEEECCC-----CTTBCS-----------SC--CHHHHHHHHHH
T ss_pred             CCCeEEEEEcccCHHHHHHHHHHhcchHHHHhhCCEEEEeccccccC-ceeeec-----------CC--CHHHHHHHHHH
Confidence            4568999999999998888777777765431 225778887765543 110000           00  22333322233


Q ss_pred             HHHhccCccCCCCCcEEEEEechhHHH--HhcChHHHHHHHHhhhcCCceeEEEEeecccccchhHH-HHHHhhheeEEE
Q 024646          133 IIEQGKGLIGQGKDRFSIAIDSVSEMV--RHASISSVAGILSNLRSHDQVSSIFWLLHSDLHEIKFT-SVLEYLSSMVAS  209 (265)
Q Consensus       133 ~~e~~~~~~~~~k~r~~VaIDSLS~LL--~h~s~~~vc~lL~~Lr~~~~vssVl~LLHsDLHe~~vv-~ALe~LAs~vv~  209 (265)
                      .....+     ++ ...|+||+++.++  .......+.+.|.++.+...+ .|+..-|..-.+.+.. ..+++++..++.
T Consensus       116 ~~~~~~-----~~-~~llilDe~~~~~~~d~~~~~~~~~~l~~~~~~~~~-~vi~~~h~~~~~~~~~~~~~~~~~d~vi~  188 (235)
T 2w0m_A          116 AKQKLG-----YG-KARLVIDSVSALFLDKPAMARKISYYLKRVLNKWNF-TIYATSQYAITTSQAFGFGVEHVADGIIR  188 (235)
T ss_dssp             HHHHHC-----SS-CEEEEEETGGGGSSSCGGGHHHHHHHHHHHHHHTTE-EEEEEEC-----------CHHHHCSEEEE
T ss_pred             HHHhhC-----CC-ceEEEEECchHhhcCCHHHHHHHHHHHHHHHHhCCC-eEEEEeccCcccccccccchheeeeEEEE
Confidence            232211     12 1589999999987  323345666777766442233 4444444331221111 458889999988


Q ss_pred             eeeC
Q 024646          210 VEPF  213 (265)
Q Consensus       210 v~P~  213 (265)
                      +.-.
T Consensus       189 l~~~  192 (235)
T 2w0m_A          189 FRRM  192 (235)
T ss_dssp             EEEE
T ss_pred             EEEE
Confidence            8653

>2dr3_A UPF0273 protein PH0284; RECA superfamily ATPase, hexamer, structural genomics; HET: ADP; 2.00A {Pyrococcus horikoshii}

Probab=92.20  E-value=0.77  Score=37.95  Aligned_cols=139  Identities=14%  Similarity=0.147  Sum_probs=72.2

Q ss_pred             ccceeEEEEeeCChHHHHHHHhhcCCCccCC--CCeEEEEeccCCCCCCcccccCccccccccccccc--cccchhhhHH
Q 024646           54 QSRGLVVVAYSRSPSFYVDLLKRRGIDIASS--HDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSF--CQDVRNLDKL  129 (265)
Q Consensus        54 q~~~Vhvl~fe~spe~y~~~lk~~G~d~~~~--~~~v~i~D~ysDPlgW~~~~~~~~~~~~~s~~~~~--~~~v~~L~sl  129 (265)
                      ++..|.++.+|.+++...+-+++.|++....  ..++.+.|+|.+-.+......          .+..  +.++.++...
T Consensus        50 ~~~~v~~~~~e~~~~~~~~~~~~~g~~~~~~~~~~~l~~~~~~~~~~~~~~~~~----------~~~~~~~~~~~~~~~~  119 (247)
T 2dr3_A           50 MGEPGIYVALEEHPVQVRQNMAQFGWDVKPYEEKGMFAMVDAFTAGIGKSKEYE----------KYIVHDLTDIREFIEV  119 (247)
T ss_dssp             TTCCEEEEESSSCHHHHHHHHHTTTCCCHHHHHHTSEEEEECSTTTTCC--CCC----------SCBCSCCSSHHHHHHH
T ss_pred             cCCeEEEEEccCCHHHHHHHHHHcCCCHHHHhhCCcEEEEecchhhcccccccc----------cccccCccCHHHHHHH
Confidence            5778999999999999988888888875321  236899998765443211000          0000  0112222222


Q ss_pred             HHHHHHhccCccCCCCCcEEEEEechhHHHHhcChHHHHHHHHhhhc---CCceeEEEEeecccccchhH-HHHHHhhhe
Q 024646          130 YSLIIEQGKGLIGQGKDRFSIAIDSVSEMVRHASISSVAGILSNLRS---HDQVSSIFWLLHSDLHEIKF-TSVLEYLSS  205 (265)
Q Consensus       130 ~~~~~e~~~~~~~~~k~r~~VaIDSLS~LL~h~s~~~vc~lL~~Lr~---~~~vssVl~LLHsDLHe~~v-v~ALe~LAs  205 (265)
                      ....++.       .++ -.|+||+++.++. ......-+.+..|.+   ...+ .|+..-|..-..... --++++.+.
T Consensus       120 i~~~~~~-------~~~-~~vviD~~~~l~~-~~~~~~~~~l~~l~~~~~~~~~-~vi~~~h~~~~~~~~~~~~~~~~~D  189 (247)
T 2dr3_A          120 LRQAIRD-------INA-KRVVVDSVTTLYI-NKPAMARSIILQLKRVLAGTGC-TSIFVSQVSVGERGFGGPGVEHGVD  189 (247)
T ss_dssp             HHHHHHH-------HTC-CEEEEETSGGGTT-TCGGGHHHHHHHHHHHHHHTTC-EEEEEEECC----CCC-CCHHHHSS
T ss_pred             HHHHHHH-------hCC-CEEEECCchHhhc-CCHHHHHHHHHHHHHHHHHCCC-eEEEEecCCCCcccccccccceeEE
Confidence            1222221       123 3799999998873 222223333333332   1222 455555543321100 003778888


Q ss_pred             eEEEeee
Q 024646          206 MVASVEP  212 (265)
Q Consensus       206 ~vv~v~P  212 (265)
                      +++.+..
T Consensus       190 ~vi~L~~  196 (247)
T 2dr3_A          190 GIIRLDL  196 (247)
T ss_dssp             EEEEEEE
T ss_pred             EEEEEEE
Confidence            8888865

>2i1q_A DNA repair and recombination protein RADA; ATPase, recombinase, ATP complex, calcium stimulation, RECA, DMC1; HET: DNA ANP; 1.90A {Methanococcus voltae} SCOP: a.60.4.1 c.37.1.11 PDB: 1xu4_A* 2b21_A* 2fpk_A* 2fpl_A* 2fpm_A* 1t4g_A* 3fyh_A* 2f1j_A* 2f1i_A* 2f1h_A* 3ntu_A* 3ewa_A* 3ew9_A* 3etl_A* 4dc9_A* 2gdj_A*

Probab=91.59  E-value=1.3  Score=39.32  Aligned_cols=126  Identities=11%  Similarity=0.056  Sum_probs=69.2

Q ss_pred             ceeEEEEeeCC--hHHHHHHHhhcCCCccCCCCeEEEEeccCCCCCCcccccCccccccccccccccccchhhhHHHHHH
Q 024646           56 RGLVVVAYSRS--PSFYVDLLKRRGIDIASSHDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNLDKLYSLI  133 (265)
Q Consensus        56 ~~Vhvl~fe~s--pe~y~~~lk~~G~d~~~~~~~v~i~D~ysDPlgW~~~~~~~~~~~~~s~~~~~~~~v~~L~sl~~~~  133 (265)
                      ..|..+.+|.+  ++...+.+++.|+|.+..-+++.+.+.++    ..                       ++..++..+
T Consensus       143 ~~v~yi~~e~~~~~~~l~~~~~~~g~~~~~~~~~l~~~~~~~----~~-----------------------~~~~~l~~l  195 (322)
T 2i1q_A          143 PKAVYIDTEGTFRPERIMQMAEHAGIDGQTVLDNTFVARAYN----SD-----------------------MQMLFAEKI  195 (322)
T ss_dssp             EEEEEEESSSCCCHHHHHHHHHHHTCCHHHHHHTEEEEECSS----HH-----------------------HHHHHHHTH
T ss_pred             ceEEEEECCCCCCHHHHHHHHHHcCCCHHHHhcCEEEEeCCC----HH-----------------------HHHHHHHHH
Confidence            68999999987  88888888888887532113466555321    10                       111111111


Q ss_pred             HHhccCccCCCCCcEEEEEechhHHHHhc-----Ch----HHHHHHHHhhhcC---CceeEEEEeec--cccc-------
Q 024646          134 IEQGKGLIGQGKDRFSIAIDSVSEMVRHA-----SI----SSVAGILSNLRSH---DQVSSIFWLLH--SDLH-------  192 (265)
Q Consensus       134 ~e~~~~~~~~~k~r~~VaIDSLS~LL~h~-----s~----~~vc~lL~~Lr~~---~~vssVl~LLH--sDLH-------  192 (265)
                      .+..+   ...++ -.|+||||+.+.+..     ..    ..+.++++.|++.   -.+ .|+..-|  .+..       
T Consensus       196 ~~~~~---~~~~~-~lvVIDsl~~l~~~~~~~~~~~~~r~~~~~~~~~~L~~la~~~~~-~vi~~nq~~~~~~~~~g~~~  270 (322)
T 2i1q_A          196 EDLIQ---EGNNI-KLVVIDSLTSTFRNEYTGRGKLAERQQKLGRHMATLNKLADLFNC-VVLVTNQVSAKPDAFFGMAE  270 (322)
T ss_dssp             HHHHH---TTCEE-EEEEEECSSHHHHHHCCCTTSHHHHHHHHHHHHHHHHHHHHHTTC-EEEEEECEECC-------CC
T ss_pred             HHHHh---hccCc-cEEEEECcHHHHHHHhcCCccHHHHHHHHHHHHHHHHHHHHHhCC-EEEEECceeecCCCCCCCCc
Confidence            11111   00123 589999999998641     11    2356666666552   122 2222222  2222       


Q ss_pred             chhHHHHHHhhheeEEEeeeC
Q 024646          193 EIKFTSVLEYLSSMVASVEPF  213 (265)
Q Consensus       193 e~~vv~ALe~LAs~vv~v~P~  213 (265)
                      .|.--.++++.+++++.+...
T Consensus       271 ~~~g~~~~~~~~d~~i~l~~~  291 (322)
T 2i1q_A          271 QAIGGHIVGHAATFRFFVRKG  291 (322)
T ss_dssp             EESSHHHHHHHCSEEEEEEEC
T ss_pred             CCCCcHHHHhcCcEEEEEEec
Confidence            233345899999999999753

>4a8j_A Elongator complex protein 4; transcription; 2.10A {Saccharomyces cerevisiae} PDB: 4ejs_A

Probab=89.95  E-value=0.64  Score=43.98  Aligned_cols=68  Identities=24%  Similarity=0.305  Sum_probs=54.9

Q ss_pred             EEEEEechhHHHHhc----ChHHHHHHHHhhhc----CCceeEEEEeecccccchhHHHHHHhhheeEEEeeeCCc
Q 024646          148 FSIAIDSVSEMVRHA----SISSVAGILSNLRS----HDQVSSIFWLLHSDLHEIKFTSVLEYLSSMVASVEPFNQ  215 (265)
Q Consensus       148 ~~VaIDSLS~LL~h~----s~~~vc~lL~~Lr~----~~~vssVl~LLHsDLHe~~vv~ALe~LAs~vv~v~P~~~  215 (265)
                      .=|+|=||-.-+...    ..+.+.+||+.||.    +.....++.-++++|-.+..+.-+++++-+++.|+|...
T Consensus       219 lRIvI~SLgSP~wy~~~~~~~~~ll~FL~~LRaLlR~~~~~~v~~iTlP~~l~~~~l~~rle~l~D~vi~L~pF~~  294 (361)
T 4a8j_A          219 IRIVIPSLLHPAMYPPKMFESSEIIGLMHGVRSLVKKYYERVVLFASISIDIITPPLLVLLRNMFDSVINLEPFNQ  294 (361)
T ss_dssp             EEEEETTTTCTTTSCGGGGBHHHHHHHHHHHHHHHHHTTTTEEEEEEEECTTSCHHHHHHHHHHCSEEEEEEECCH
T ss_pred             EEEEecCCCCcccCCCcccCHHHHHHHHHHHHHHHhhcCCceEEEEEEChHHcChHHHHHHHHhCcEEEEeeecCC
Confidence            678888876655433    46789999999988    344445666789999999999999999999999999865

>3bh0_A DNAB-like replicative helicase; ATPase, replication; 2.35A {Bacillus phage SPP1}

Probab=89.59  E-value=1.7  Score=38.91  Aligned_cols=65  Identities=12%  Similarity=0.157  Sum_probs=37.6

Q ss_pred             EEEEEechhHHHHhcC----hHHHHHHHHhhhcC---CceeEEEEeec--cccc----------chhHHHHHHhhheeEE
Q 024646          148 FSIAIDSVSEMVRHAS----ISSVAGILSNLRSH---DQVSSIFWLLH--SDLH----------EIKFTSVLEYLSSMVA  208 (265)
Q Consensus       148 ~~VaIDSLS~LL~h~s----~~~vc~lL~~Lr~~---~~vssVl~LLH--sDLH----------e~~vv~ALe~LAs~vv  208 (265)
                      ..|+||+|..|-...+    ..++...++.|++-   -.+ .|+.+-|  .+.-          .-+-.+++++.|.+++
T Consensus       183 ~lVVID~l~~l~~~~~~~~r~~~i~~~~~~Lk~lAk~~~i-~vi~lsql~r~~e~r~~~~p~l~dlr~sg~ie~~aD~vi  261 (315)
T 3bh0_A          183 VIVMIDYLQLLEPAKANDSRTNQISQISRDLKKMARELDV-VVIALSQLSRQVEQRQDKRPMLSDLRESGQLEQDADIIE  261 (315)
T ss_dssp             EEEEEECGGGSBCSCTTSCHHHHHHHHHHHHHHHHHHHTC-EEEEEECCCGGGTTSSSCCCCGGGGTTTSHHHHHCSEEE
T ss_pred             eEEEEeCchhcCCCCCCCCHHHHHHHHHHHHHHHHHHhCC-eEEEEeecCcccccCCCCCCCHHHhhhhhhhHhhCCEEE
Confidence            4899999998753211    24555555555441   122 2344433  2221          1123478999999999


Q ss_pred             EeeeC
Q 024646          209 SVEPF  213 (265)
Q Consensus       209 ~v~P~  213 (265)
                      .+...
T Consensus       262 ~L~r~  266 (315)
T 3bh0_A          262 FLYRD  266 (315)
T ss_dssp             EEEEH
T ss_pred             EEecc
Confidence            99753

>2z43_A DNA repair and recombination protein RADA; archaea, filament, DNA binding, molecular SWI RECA, DMC1; HET: DNA; 1.93A {Sulfolobus solfataricus} PDB: 2bke_A* 2dfl_A* 2zub_A* 2zuc_A* 2zud_A*

Probab=88.93  E-value=2.3  Score=38.07  Aligned_cols=128  Identities=14%  Similarity=0.030  Sum_probs=60.2

Q ss_pred             cceeEEEEeeCC--hHHHHHHHhhcCCCccCCCCeEEEEeccCCCCCCcccccCccccccccccccccccchhhhHHHHH
Q 024646           55 SRGLVVVAYSRS--PSFYVDLLKRRGIDIASSHDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNLDKLYSL  132 (265)
Q Consensus        55 ~~~Vhvl~fe~s--pe~y~~~lk~~G~d~~~~~~~v~i~D~ysDPlgW~~~~~~~~~~~~~s~~~~~~~~v~~L~sl~~~  132 (265)
                      +..+..+.+|.+  ++...+.+++.|++.+..-+++.+.+.++    .                       .++..++..
T Consensus       141 ~~~vlyi~~e~~~~~~~l~~~~~~~g~~~~~~~~~l~~~~~~~----~-----------------------~~~~~~l~~  193 (324)
T 2z43_A          141 SGKAVYIDTEGTFRWERIENMAKALGLDIDNVMNNIYYIRAIN----T-----------------------DHQIAIVDD  193 (324)
T ss_dssp             SCEEEEEESSSCCCHHHHHHHHHHTTCCHHHHHHTEEEEECCS----H-----------------------HHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHhCCCHHHHhccEEEEeCCC----H-----------------------HHHHHHHHH
Confidence            568999999987  88888888888887532113455554321    0                       011111111


Q ss_pred             HHHhccCccCCCCCcEEEEEechhHHHHhc-----Ch----HHHHHHHHhhhcC----CceeEEEEeeccccc-------
Q 024646          133 IIEQGKGLIGQGKDRFSIAIDSVSEMVRHA-----SI----SSVAGILSNLRSH----DQVSSIFWLLHSDLH-------  192 (265)
Q Consensus       133 ~~e~~~~~~~~~k~r~~VaIDSLS~LL~h~-----s~----~~vc~lL~~Lr~~----~~vssVl~LLHsDLH-------  192 (265)
                      +.+..+   ...++ -.|+|||++.+.+..     ..    ..+.++++.|++.    ....=++.-+..+..       
T Consensus       194 l~~~~~---~~~~~-~lvVIDsl~~l~~~~~~~~g~~~~r~~~~~~~l~~L~~la~~~~~~Vi~~nq~~~~~~~~~~~~~  269 (324)
T 2z43_A          194 LQELVS---KDPSI-KLIVVDSVTSHFRAEYPGRENLAVRQQKLNKHLHQLTRLAEVYDIAVIITNQVMARPDMFYGDPT  269 (324)
T ss_dssp             HHHHHH---HCTTE-EEEEETTTTHHHHHHSCTTTSHHHHHHHHHHHHHHHHHHHHHHTCEEEEEEEC------------
T ss_pred             HHHHHH---hccCC-CEEEEeCcHHHhhhhhcCcccHHHHHHHHHHHHHHHHHHHHHhCCEEEEEcceeecCCCcCCCCC
Confidence            111111   00123 689999999998641     11    2356666666652    111111122222222       


Q ss_pred             chhHHHHHHhhheeEEEeeeC
Q 024646          193 EIKFTSVLEYLSSMVASVEPF  213 (265)
Q Consensus       193 e~~vv~ALe~LAs~vv~v~P~  213 (265)
                      .|.--.++++.+++++.+...
T Consensus       270 ~~~gg~~l~~~~d~~l~l~r~  290 (324)
T 2z43_A          270 VAVGGHTLYHVPGIRIQLKKS  290 (324)
T ss_dssp             ------------CEEEEEEEC
T ss_pred             CCCchHHHHhhCcEEEEEEEc
Confidence            222334799999999999753

>2q6t_A DNAB replication FORK helicase; hydrolase; 2.90A {Thermus aquaticus}

Probab=82.20  E-value=11  Score=35.21  Aligned_cols=28  Identities=11%  Similarity=0.153  Sum_probs=20.1

Q ss_pred             ccceeEEEEeeCChHHHHHHH--hhcCCCc
Q 024646           54 QSRGLVVVAYSRSPSFYVDLL--KRRGIDI   81 (265)
Q Consensus        54 q~~~Vhvl~fe~spe~y~~~l--k~~G~d~   81 (265)
                      ++..|.++.+|-|++++..-+  ...|++.
T Consensus       228 ~g~~vl~~slE~~~~~l~~R~~~~~~~i~~  257 (444)
T 2q6t_A          228 EGVGVGIYSLEMPAAQLTLRMMCSEARIDM  257 (444)
T ss_dssp             TCCCEEEEESSSCHHHHHHHHHHHHTTCCT
T ss_pred             CCCeEEEEECCCCHHHHHHHHHHHHcCCCH
Confidence            467899999999998777632  2346654

>1q57_A DNA primase/helicase; dntpase, DNA replication, transferase; HET: DNA; 3.45A {Enterobacteria phage T7} SCOP: c.37.1.11 e.13.1.2

Probab=80.03  E-value=17  Score=34.28  Aligned_cols=65  Identities=17%  Similarity=0.280  Sum_probs=36.5

Q ss_pred             EEEEEechhHHHHh----cChHHHHHHHHhhhc---CCceeEEEEeeccc---------------ccchhHHHHHHhhhe
Q 024646          148 FSIAIDSVSEMVRH----ASISSVAGILSNLRS---HDQVSSIFWLLHSD---------------LHEIKFTSVLEYLSS  205 (265)
Q Consensus       148 ~~VaIDSLS~LL~h----~s~~~vc~lL~~Lr~---~~~vssVl~LLHsD---------------LHe~~vv~ALe~LAs  205 (265)
                      -.|+||+|..|-..    ...+.+...++.|++   .-.+ .|+.+-|--               +..-+-.+++++.|-
T Consensus       356 ~lvVID~l~~l~~~~~~~~~~~~~~~~~~~Lk~lak~~~i-~vi~~~q~~r~~~~~~~~~~~~p~l~dlr~s~~ie~~aD  434 (503)
T 1q57_A          356 DVIILDHISIVVSASGESDERKMIDNLMTKLKGFAKSTGV-VLVVICHLKNPDKGKAHEEGRPVSITDLRGSGALRQLSD  434 (503)
T ss_dssp             SEEEEECTTCCCSCCSCCCHHHHHHHHHHHHHHHHHHHTC-EEEEEEECCCCSSSSCSTTCCCCCSSSCSSSSHHHHHCS
T ss_pred             CEEEEccchhcCCCCCCCCHHHHHHHHHHHHHHHHHHHCC-eEEEEEcCCchhccCccccCCCCChhhhccchHhhecCc
Confidence            48999999876321    112344555555544   1122 233333321               122223578999999


Q ss_pred             eEEEeeeC
Q 024646          206 MVASVEPF  213 (265)
Q Consensus       206 ~vv~v~P~  213 (265)
                      +++.+...
T Consensus       435 ~vi~l~r~  442 (503)
T 1q57_A          435 TIIALERN  442 (503)
T ss_dssp             EEEEEEEC
T ss_pred             EEEEEEeC
Confidence            99999764

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

No hit with e-value below 0.005

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	265
d1tf7a2	242	Circadian clock protein KaiC {Synechococcus sp. st	95.32
d1tf7a1	242	Circadian clock protein KaiC {Synechococcus sp. st	80.69

>d1tf7a2 c.37.1.11 (A:256-497) Circadian clock protein KaiC {Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Circadian clock protein KaiC
species: Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]

Probab=95.32  E-value=0.025  Score=45.39  Aligned_cols=130  Identities=15%  Similarity=0.205  Sum_probs=77.6

Q ss_pred             hccccceeEEEEeeCChHHHHHHHhhcCCCccC--CCCeEEEEeccCCCCCCcccccCccccccccccccccccchhhhH
Q 024646           51 GKSQSRGLVVVAYSRSPSFYVDLLKRRGIDIAS--SHDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNLDK  128 (265)
Q Consensus        51 ~~~q~~~Vhvl~fe~spe~y~~~lk~~G~d~~~--~~~~v~i~D~ysDPlgW~~~~~~~~~~~~~s~~~~~~~~v~~L~s  128 (265)
                      ...++..+..+.+|-+++.+..-+++.|++.+.  -...+.+.|.|..-.                       ...+   
T Consensus        50 ~~~~~~~~~~is~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----------------------~~~~---  103 (242)
T d1tf7a2          50 ACANKERAILFAYEESRAQLLRNAYSWGMDFEEMERQNLLKIVCAYPESA-----------------------GLED---  103 (242)
T ss_dssp             HHTTTCCEEEEESSSCHHHHHHHHHTTSCCHHHHHHTTSEEECCCCGGGS-----------------------CHHH---
T ss_pred             HHHhccccceeeccCCHHHHHHHHHHcCCChHHHhhcCceEEEEeecchh-----------------------hHHH---
Confidence            456788899999999999999988887776432  011233333222110                       1111   


Q ss_pred             HHHHHHHhccCccCCCCCcEEEEEechhHHHHhcChHHHHHHHHhhhcC---CceeEEEEeecccccc---hhHHHHHHh
Q 024646          129 LYSLIIEQGKGLIGQGKDRFSIAIDSVSEMVRHASISSVAGILSNLRSH---DQVSSIFWLLHSDLHE---IKFTSVLEY  202 (265)
Q Consensus       129 l~~~~~e~~~~~~~~~k~r~~VaIDSLS~LL~h~s~~~vc~lL~~Lr~~---~~vssVl~LLHsDLHe---~~vv~ALe~  202 (265)
                      .+..+.+..+    +.++ -.|+|||++.++...+..++-..+..|.+.   ..+. ++...|...-.   ......+++
T Consensus       104 ~~~~i~~~i~----~~~~-~~vviDs~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~-~i~~~~~~~~~~~~~~~~~~~~~  177 (242)
T d1tf7a2         104 HLQIIKSEIN----DFKP-ARIAIDSLSALARGVSNNAFRQFVIGVTGYAKQEEIT-GLFTNTSDQFMGAHSITDSHIST  177 (242)
T ss_dssp             HHHHHHHHHH----TTCC-SEEEEECHHHHTSSSCHHHHHHHHHHHHHHHHHTTCE-EEEEEECSSSSCCCSSCSSCCTT
T ss_pred             HHHHHHHHHH----hcCC-ceeeeecchhhhcCCCHHHHHHHHHHHHHHHHHcCCe-EEEEEeeEeeccccccCCcceee
Confidence            1122222111    1234 478999999999999998888888777663   2233 34444432222   122346889


Q ss_pred             hheeEEEeee
Q 024646          203 LSSMVASVEP  212 (265)
Q Consensus       203 LAs~vv~v~P  212 (265)
                      ++.+++.+.-
T Consensus       178 ~ad~vi~l~~  187 (242)
T d1tf7a2         178 ITDTIILLQY  187 (242)
T ss_dssp             TCSEEEEEEE
T ss_pred             ecceEEEEEE
Confidence            9999998853

>d1tf7a1 c.37.1.11 (A:14-255) Circadian clock protein KaiC {Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Circadian clock protein KaiC
species: Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]

Probab=80.69  E-value=4.5  Score=30.54  Aligned_cols=136  Identities=20%  Similarity=0.236  Sum_probs=72.0

Q ss_pred             ccceeEEEEeeCChHHHHHHHhhcCCCccC--CCCeEEEEeccCCCCCCcccccCccccccccccccccccchh-hhHHH
Q 024646           54 QSRGLVVVAYSRSPSFYVDLLKRRGIDIAS--SHDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRN-LDKLY  130 (265)
Q Consensus        54 q~~~Vhvl~fe~spe~y~~~lk~~G~d~~~--~~~~v~i~D~ysDPlgW~~~~~~~~~~~~~s~~~~~~~~v~~-L~sl~  130 (265)
                      ....+..+.+|-+++.+...+...+.+...  ...+....+.+.++.+|.....           .    +... +..+ 
T Consensus        54 ~~~~~~~~s~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----------~----~~~~l~~~l-  117 (242)
T d1tf7a1          54 FDEPGVFVTFEETPQDIIKNARSFGWDLAKLVDEGKLFILDASPDPEGQEVVGG-----------F----DLSALIERI-  117 (242)
T ss_dssp             HCCCEEEEESSSCHHHHHHHHGGGTCCHHHHHHTTSEEEEECCCCSSCCSCCSS-----------H----HHHHHHHHH-
T ss_pred             cCCCcccccccCCHHHHHHHHHHcCCChHHHHHhcchhhhhhccchhhhhhhcc-----------c----cHHHHHHHH-
Confidence            345788999999999998877777665432  1224556666666665554111           0    1111 1222 


Q ss_pred             HHHHHhccCccCCCCCcEEEEEechhHHHHhcChHHH-H----HHHHhhhcCCceeEEEEeecccccchhHHHHHHhhhe
Q 024646          131 SLIIEQGKGLIGQGKDRFSIAIDSVSEMVRHASISSV-A----GILSNLRSHDQVSSIFWLLHSDLHEIKFTSVLEYLSS  205 (265)
Q Consensus       131 ~~~~e~~~~~~~~~k~r~~VaIDSLS~LL~h~s~~~v-c----~lL~~Lr~~~~vssVl~LLHsDLHe~~vv~ALe~LAs  205 (265)
                      ...++.       .++ -.|+||+++.+.....-... -    .++..+++.....-++.-...+.....-.+++++++.
T Consensus       118 ~~~i~~-------~~~-~~viiD~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d  189 (242)
T d1tf7a1         118 NYAIQK-------YRA-RRVSIDSVTSVFQQYDASSVVRRELFRLVARLKQIGATTVMTTERIEEYGPIARYGVEEFVSD  189 (242)
T ss_dssp             HHHHHH-------HTC-SEEEEECSTTTSTTTCCHHHHHHHHHHHHHHHHHHTCEEEEEEECSSSSSCSSTTSCHHHHCS
T ss_pred             HHHHHh-------hcc-chhhhhHHHHHHHhccChhHHHHHHHHHHHHHHhcCCceEEeecccccccccccCcceeeecc
Confidence            222221       123 36899999988766553332 2    2233333322222111111222333444567889999


Q ss_pred             eEEEeeeC
Q 024646          206 MVASVEPF  213 (265)
Q Consensus       206 ~vv~v~P~  213 (265)
                      +++.+...
T Consensus       190 ~i~~~~~~  197 (242)
T d1tf7a1         190 NVVILRNV  197 (242)
T ss_dssp             EEEEEEEE
T ss_pred             EEEEEEEe
Confidence            99888653