Citrus Sinensis ID: 024144

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270--
Protein Sequence
MADTICRTLRDGGLEGEHAPALTIKDSKASPFGFDVFNYVLTQLSNYILAGKSQSRGLVVVAYSRSPSFYVDLLKRRGIDIASSHDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNLDKLYSLIIEQGKGLIGQGKDRFSIAIDSVSEMVRHASISSVAGILSNLRSHDQVSSIFWLLHSDLHEIKFTSVLEYLSSMVASVEPFNQAAFGQRVDLENLSMLEQNFRKGKFHVRFKRRNGRVRVMKYLLSWQASNLHQFCLKMK
Secondary Structure (PSIPRED)
cHHHHHHHHHcccccccccccEEEEccccccccHHHHHHHHHHHHHHHHHcccccccEEEEEccccHHHHHHHHHHHcccccccccEEEEEEcccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHccccccccccEEEEEccHHHHHHHccHHHHHHHHHHHcccccEEEEEEEEccccccHHHHHHHHHccEEEEEEEcccccccccccccccHHHHHHHccccEEEEEEEcccccEEEEEEEEEEEccccEEEEEccc
Secondary Structure Prediction (SSPRO)
cHHHHHHHHHccccccccccEEEEHccccccHHHHHHHHHHHHHHHHHHHHHHHcccEEEEEEcccHHHHHHHHHHccccccccccEEEEEEccccccccHHHHcccccccccccHHHHHHcHHHHHHHHHHHHHHHHHHccccccEEEEEEccHHHHHHHccHHHHHHHHHHHcccHHHHHHHHHHcccccHHHHHHHHHHHHHHEEEEccccccccccccccHHcHHHHHcccccEEEEEEEEccccEEEEEEEEEEEcccccEEEEccc
Coil and Loop (DISEMBL)
MADTICRTlrdgglegehapaltikdskaspfgfDVFNYVLTQLSNYILAGKSQSRGLVVVAYSRSPSFYVDLLKRRgidiasshdwIHILDcytdplgwknwlidKDISQEASSLSSFCQDVRNLDKLYSLIIEQGkgligqgkdrfsIAIDSVSEMVRHASISSVAGILSNLRSHDQVSSIFWLLHSDLHEIKFTSVLEYLSSMVasvepfnqaafgqrvdlENLSMLEQNFRKGKFHVRFKRRNGRVRVMKYLLSWQASNLHQFCLKMK
Flexible Loop (DISEMBL)
madticrtlrdgglegehapaltikdskaspFGFDVFNYVLTQLSNYILAGKSQSRGLVVVAYSRSPSFYVDLLKRRGIDIASSHDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNLDKLYSLIIEQgkgligqgkdRFSIAIDSVSEMVRHASISSVAGILSNLRSHDQVSSIFWLLHSDLHEIKFTSVLEYLSSMVASVEPFNQAAFGQRVDLENLSMLEQnfrkgkfhvrfkrrngRVRVMKYLLswqasnlhqfclkmk
Low Complexity Region (SEG)
MADTICRTLRDGGLEGEHAPALTIKDSKASPFGFDVFNYVLTQLSNYILAGKSQSRGLVVVAYSRSPSFYVDLLKRRGIDIASSHDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNLDKLYSLIIEQGKGLIGQGKDRFSIAIDSVSEMVRHASISSVAGILSNLRSHDQVSSIFWLLHSDLHEIKFTSVLEYLSSMVASVEPFNQAAFGQRVDLENLSMLEQNFRKGKFHVRFKRRNGRVRVMKYLLSWQASNLHQFCLKMK
Disordered region (IsUnstruct)
**********************TI***KASPFGFDVFNYVLTQLSNYILAGKSQSRGLVVVAYSRSPSFYVDLLKRRGIDIASSHDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNLDKLYSLIIEQGKGLIGQGKDRFSIAIDSVSEMVRHASISSVAGILSNLRSHDQVSSIFWLLHSDLHEIKFTSVLEYLSSMVASVEPFNQAAFGQRVDLENLSMLEQNFRKGKFHVRFKRRNGRVRVMKYLLSWQASNLHQFCL***
Disordered Region (DISOPRED)
***TICRTLRDGGLEGEHAPALTIKDSKASPFGFDVFNYVLTQLSNY*****SQSRGLVVVAYSRSPSFYVDLLKRRGIDIASSHDWIHILDCYTDPLGWK****************SFCQDVRNLDKLYSLIIEQ*****GQGKDRFSIAIDSVSEMVRHASISSVAGILSNLRSHDQVSSIFWLLHSDLHEIKFTSVLEYLSSMVASV********************E*NFRKGKFHVRFKRRNGRVRVMKYLLSWQASNLHQFCLKMK
Disordered Region (DISEMBL)
MADTICRTLRDGGLEGEHAPALTIKDSKASPFGFDVFNYVLTQLSNYILAGKSQSRGLVVVAYSRSPSFYVDLLKRRGIDIASSHDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNLDKLYSLIIEQGKGLIGQGKDRFSIAIDSVSEMVRHASISSVAGILSNLRSHDQVSSIFWLLHSDLHEIKFTSVLEYLSSMVASVEPFNQAAFGQRVDLENLSMLEQNFRKGKFHVRFKRRNGRVRVMKYLLSWQASNLHQFCLKMK
Disordered Region (DISPRO)
*****CRTLRDGGLEGEHAPALTIKDSKASPFGFDVFNYVLTQLSNYILAGKSQSRGLVVVAYSRSPSFYVDLLKRRGIDIASSHDWIHILDCYTDPLGWKNWLIDKDI*QEASSLSSFCQDVRNLDKLYSLIIEQGKGLIGQGKDRFSIAIDSVSEMVRHASISSVAGILSNLRSHDQVSSIFWLLHSDLHEIKFTSVLEYLSSMVASVEPFNQAAFGQRVDLENLSMLEQNFRKGKFHVRFKRRNGRVRVMKYLLSWQASNLHQFCLKMK
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MADTICRTLRDGGLEGEHAPALTIKDSKASPFGFDVFNYVLTQLSNYILAGKSQSRGLVVVAYSRSPSFYVDLLKRRGIDIASSHDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNLDKLYSLIIEQGKGLIGQGKDRFSIAIDSVSEMVRHASISSVAGILSNLRSHDQVSSIFWLLHSDLHEIKFTSVLEYLSSMVASVEPFNQAAFGQRVDLENLSMLEQNFRKGKFHVRFKRRNGRVRVMKYLLSWQASNLHQFCLKMK
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	272	2.2.26 [Sep-21-2011]
F4IQJ2	374	Elongator complex protein	no	no	0.915	0.665	0.560	2e-76
A1A5V9	296	Elongator complex protein	yes	no	0.386	0.354	0.276	0.0008

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

 Score =  286 bits (731), Expect = 2e-76,   Method: Compositional matrix adjust.
 Identities = 143/255 (56%), Positives = 193/255 (75%), Gaps = 6/255 (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 FHVRFKRRNGRVRVM 253
           FHVRFK R GRVRVM
Sbjct: 237 FHVRFKLRKGRVRVM 251

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 = 8e-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	272
255559196	376	conserved hypothetical protein [Ricinus	0.930	0.672	0.715	1e-107
118485334	379	unknown [Populus trichocarpa]	0.930	0.667	0.720	1e-106
224077180	386	predicted protein [Populus trichocarpa]	0.930	0.655	0.701	1e-103
225452057	376	PREDICTED: uncharacterized protein LOC10	0.926	0.670	0.678	8e-94
356500866	373	PREDICTED: dermal papilla-derived protei	0.922	0.672	0.634	6e-87
363814366	372	uncharacterized protein LOC100792556 [Gl	0.922	0.674	0.628	2e-86
449455826	375	PREDICTED: elongator complex protein 5-l	0.926	0.672	0.575	2e-82
297832500	378	hypothetical protein ARALYDRAFT_319792 [	0.915	0.658	0.568	3e-76
79322467	306	uncharacterized protein [Arabidopsis tha	0.915	0.813	0.560	6e-75
42569125	374	uncharacterized protein [Arabidopsis tha	0.915	0.665	0.560	9e-75

>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 = 184/257 (71%), Positives = 227/257 (88%), Gaps = 4/257 (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 GKFHVRFKRRNGRVRVM 253
           GK +VRFKRRNGRV VM
Sbjct: 241 GKLNVRFKRRNGRVSVM 257

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 =  389 bits (999), Expect = e-106,   Method: Compositional matrix adjust.
 Identities = 186/258 (72%), Positives = 223/258 (86%), Gaps = 5/258 (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 KGKFHVRFKRRNGRVRVM 253
           KGK  VRFKRRNGRVRV+
Sbjct: 241 KGKLQVRFKRRNGRVRVV 258

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 =  381 bits (979), Expect = e-103,   Method: Compositional matrix adjust.
 Identities = 186/265 (70%), Positives = 223/265 (84%), Gaps = 12/265 (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 MLEQNFRKGKFHVRFKRRNGRVRVM 253
           +LEQNF KGK  VRFKRRNGRVRV+
Sbjct: 241 LLEQNFGKGKLQVRFKRRNGRVRVV 265

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 =  349 bits (895), Expect = 8e-94,   Method: Compositional matrix adjust.
 Identities = 175/258 (67%), Positives = 206/258 (79%), Gaps = 6/258 (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 KGKFHVRFKRRNGRVRVM 253
           KGKFHVRFKRRNGRVRVM
Sbjct: 240 KGKFHVRFKRRNGRVRVM 257

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 (836), Expect = 6e-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 (831), Expect = 2e-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 =  311 bits (797), Expect = 2e-82,   Method: Compositional matrix adjust.
 Identities = 148/257 (57%), Positives = 198/257 (77%), Gaps = 5/257 (1%)

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 GKFHVRFKRRNGRVRVM 253
           G+FHVR KRRNGRVRV+
Sbjct: 240 GRFHVRMKRRNGRVRVI 256

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 =  291 bits (744), Expect = 3e-76,   Method: Compositional matrix adjust.
 Identities = 145/255 (56%), Positives = 195/255 (76%), Gaps = 6/255 (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 FHVRFKRRNGRVRVM 253
           FHVRFK R GRVRVM
Sbjct: 237 FHVRFKLRKGRVRVM 251

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 =  286 bits (732), Expect = 6e-75,   Method: Compositional matrix adjust.
 Identities = 143/255 (56%), Positives = 193/255 (75%), Gaps = 6/255 (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 FHVRFKRRNGRVRVM 253
           FHVRFK R GRVRVM
Sbjct: 237 FHVRFKLRKGRVRVM 251

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 =  286 bits (731), Expect = 9e-75,   Method: Compositional matrix adjust.
 Identities = 143/255 (56%), Positives = 193/255 (75%), Gaps = 6/255 (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 FHVRFKRRNGRVRVM 253
           FHVRFK R GRVRVM
Sbjct: 237 FHVRFKLRKGRVRVM 251

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	272
TAIR|locus:2062190	374	AT2G18410 "AT2G18410" [Arabido	0.915	0.665	0.572	1.1e-71

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

 Score = 725 (260.3 bits), Expect = 1.1e-71, P = 1.1e-71
 Identities = 146/255 (57%), Positives = 195/255 (76%)

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 FHVRFKRRNGRVRVM 253
             FHVRFK R GRVRVM
Sbjct:   237 FHVRFKLRKGRVRVM 251


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   0.402    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      272       272   0.00099  114 3  11 22  0.44    33
                                                     32  0.40    37


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:  608 (65 KB)
  Total size of DFA:  207 KB (2116 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:  23.83u 0.09s 23.92t   Elapsed:  00:00:01
  Total cpu time:  23.83u 0.09s 23.92t   Elapsed:  00:00:01
  Start:  Tue May 21 01:31:01 2013   End:  Tue May 21 01:31:02 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	272
PF10483	280	Elong_Iki1: Elongator subunit Iki1; InterPro: IPR0	99.94
PF09807	249	DUF2348: Uncharacterized conserved protein (DUF234	99.18
PF06745	226	KaiC: KaiC; InterPro: IPR014774 This entry represe	98.28
TIGR03877	237	thermo_KaiC_1 KaiC domain protein, Ph0284 family.	97.92
PRK04328	249	hypothetical protein; Provisional	97.75
PRK06067	234	flagellar accessory protein FlaH; Validated	97.73
COG2874	235	FlaH Predicted ATPases involved in biogenesis of a	97.29
PRK09302	509	circadian clock protein KaiC; Reviewed	97.27
PRK09302	509	circadian clock protein KaiC; Reviewed	96.75
TIGR02655	484	circ_KaiC circadian clock protein KaiC. Members of	96.68
TIGR03881	229	KaiC_arch_4 KaiC domain protein, PAE1156 family. M	96.17
COG0467	260	RAD55 RecA-superfamily ATPases implicated in signa	96.03
cd01124	187	KaiC KaiC is a circadian clock protein primarily f	95.94
TIGR02655	484	circ_KaiC circadian clock protein KaiC. Members of	95.66
TIGR03878	259	thermo_KaiC_2 KaiC domain protein, AF_0795 family.	95.5
TIGR03880	224	KaiC_arch_3 KaiC domain protein, AF_0351 family. T	94.81
KOG4723	248	consensus Uncharacterized conserved protein [Funct	94.77
PF05625	363	PAXNEB: PAXNEB protein; InterPro: IPR008728 The RN	94.62
PRK08533	230	flagellar accessory protein FlaH; Reviewed	94.4
PRK05973	237	replicative DNA helicase; Provisional	93.45
cd00984	242	DnaB_C DnaB helicase C terminal domain. The hexame	93.05
TIGR02237	209	recomb_radB DNA repair and recombination protein R	92.55
PRK09361	225	radB DNA repair and recombination protein RadB; Pr	92.41
PRK04301	317	radA DNA repair and recombination protein RadA; Va	91.1
PRK11823	446	DNA repair protein RadA; Provisional	90.97
cd01121	372	Sms Sms (bacterial radA) DNA repair protein. This	90.05
TIGR02236	310	recomb_radA DNA repair and recombination protein R	89.08
cd01393	226	recA_like RecA is a bacterial enzyme which has rol	88.05
PTZ00035	337	Rad51 protein; Provisional	87.63
cd01123	235	Rad51_DMC1_radA Rad51_DMC1_radA,B. This group of r	87.4
PF03192	210	DUF257: Pyrococcus protein of unknown function, DU	86.16
TIGR02238	313	recomb_DMC1 meiotic recombinase Dmc1. This model d	84.69
cd01394	218	radB RadB. The archaeal protein radB shares simila	81.91
PLN03187	344	meiotic recombination protein DMC1 homolog; Provis	80.48

>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=99.94  E-value=5.5e-26  Score=209.35  Aligned_cols=194  Identities=21%  Similarity=0.231  Sum_probs=118.6

Q ss_pred             CCCCceeecccCCCCchhhHHHHHHHHHHHHHHhhccccceeEEEEeecChHHHHHHHhhcCcCccCCCCeEEEEeccCC
Q 024144           17 EHAPALTIKDSKASPFGFDVFNYVLTQLSNYILAGKSQSRGLVVVAYSRSPSFYVDLLKRRGIDIASSHDWIHILDCYTD   96 (272)
Q Consensus        17 e~ap~l~i~Dsl~~~~g~~v~~h~~~~l~s~i~a~~~q~~~Vhvl~fe~Spe~y~~~lk~~G~d~~s~~~ri~i~D~ysD   96 (272)
                      |..|+++|.||++.|+ ..++++       +|+..+.++..||+|+||.+++  .+     |+|... +.+         
T Consensus        10 d~spl~Li~DSl~q~a-~~Ll~e-------~i~~a~~~~~~V~~lsfEt~~~--~~-----~~d~~~-~~~---------   64 (280)
T PF10483_consen   10 DASPLTLILDSLEQSA-RPLLKE-------FIRRAKSRNEKVHFLSFETLNK--PE-----YADSFI-NAR---------   64 (280)
T ss_dssp             S--SEEEEEEBTTB-S-HHHHHH-------HHHHHTS----EEEEESS--S----T-----T-SEEE-ETT---------
T ss_pred             CCCCeEEEEEcccccC-HHHHHH-------HHHHHHcCCCeEEEEEeEeCCC--cc-----cCCeec-ccc---------
Confidence            3789999999999985 665555       4456688999999999999888  44     666444 222         


Q ss_pred             CCCCcccccCCccccccccccccccchhhhhHHHHHHHHhccCccCCCCCcEEEEEechhHHHHhcChHHHHHHHHhhhc
Q 024144           97 PLGWKNWLIDKDISQEASSLSSFCQDVRNLDKLYSLIIEQGKGLIGQGKDRFSIAIDSVSEMVRHASISSVAGILSNLRS  176 (272)
Q Consensus        97 PLGW~~~~~~~~~~~~~s~~~~~~~~v~~L~sl~~~i~e~~~~~~~~~k~~~tVaIDSLS~LL~h~s~~~vc~lL~~Lr~  176 (272)
                        +|+-                        .+++..+.........+++.+++|+||||+||++|+++ .++++|++|.+
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              2221                        11112333321111223344699999999999999999 99999999998


Q ss_pred             CCceeEEEeeecccc-------cchhhHhHHhhhheeEEEeecCCccccccccccchhhhhh------ccccceEEEEEE
Q 024144          177 HDQVSSIFWLLHSDL-------HEIKFTSVLEYLSSMVASVEPFNQAAFGQRVDLENLSMLE------QNFRKGKFHVRF  243 (272)
Q Consensus       177 ~~~vssVl~LLHsDL-------He~~~v~ALe~LSstvvtv~P~~~~~~~~~~~~~~~~~l~------~n~~k~~~~vr~  243 (272)
                      +++ ++|+|++|+|+       |+|+++++|+|||||+++|+|........+..-+++.-++      .|..+.+++++.
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            787 78999999999       9999999999999999999999988766666555555443      556689999999


Q ss_pred             eccCCcEEEEEEEEEecccc
Q 024144          244 KRRNGRVRVMKYLLSWQASN  263 (272)
Q Consensus       244 KrRnGRV~~~~~~~~~~~~~  263 (272)
                      |||+||+..+.|++.+....
T Consensus       197 RrksGR~~~e~~~~~~~~~~  216 (280)
T PF10483_consen  197 RRKSGRVVSEWFVIDINSHI  216 (280)
T ss_dssp             E-TTS-EEEEEEEEETTTTE
T ss_pred             EcCCCCcEeEEEEEecCCCc
Confidence            99999999999999876543

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=2.5e-09  Score=97.87  Aligned_cols=183  Identities=19%  Similarity=0.245  Sum_probs=127.9

Q ss_pred             CCCceeecccCCCCchhhHHHHHHHHHHHHHHhhccccceeEEEEeecChHHHHHHHhhcCcCccCC--CCeEEEEeccC
Q 024144           18 HAPALTIKDSKASPFGFDVFNYVLTQLSNYILAGKSQSRGLVVVAYSRSPSFYVDLLKRRGIDIASS--HDWIHILDCYT   95 (272)
Q Consensus        18 ~ap~l~i~Dsl~~~~g~~v~~h~~~~l~s~i~a~~~q~~~Vhvl~fe~Spe~y~~~lk~~G~d~~s~--~~ri~i~D~ys   95 (272)
                      ..-.++|+|+ .+++ .=+..|++.   .+++    .+..|.+|+|..+.+.|...++|-|++-...  +.+++++|+.+
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 556667553   3333    5668999999999999999999999997752  34799999999


Q ss_pred             CCCCCcccccCCccccccccccccccchhhhhHHHHHHHHhccCccCCCCCcEEEEEechhHHHH-hcChHHHHHHHHhh
Q 024144           96 DPLGWKNWLIDKDISQEASSLSSFCQDVRNLDKLYSLIIEQGKGLIGQGKDRFSIAIDSVSEMVR-HASISSVAGILSNL  174 (272)
Q Consensus        96 DPLGW~~~~~~~~~~~~~s~~~~~~~~v~~L~sl~~~i~e~~~~~~~~~k~~~tVaIDSLS~LL~-h~s~~~vc~lL~~L  174 (272)
                      ++++|--....++...  +..+.--.+...|.+++..|.+..+...+ .++ ++|+||-||.|+- ..+..+|..+++.+
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            8887742111000100  11111111234578888887776663233 233 8999999999997 34455788889888


Q ss_pred             hc---CCceeEEEeeeccccc---c-h-hhHhHHhhhheeEEEeecC
Q 024144          175 RS---HDQVSSIFWLLHSDLH---E-I-KFTSVLEYLSSMVASVEPF  213 (272)
Q Consensus       175 r~---~~~vssVl~LLHsDLH---e-~-~~v~ALe~LSstvvtv~P~  213 (272)
                      +.   ...-.+++.|+|.|--   + . .....|+|+|..+|+++|+
T Consensus       165 ra~l~~~~~~~lVvl~h~d~~~~~e~~~~l~~~L~h~a~l~i~v~~L  211 (249)
T PF09807_consen  165 RATLCSESNGSLVVLVHCDIDDEDEENDLLLNSLAHMADLVITVEPL  211 (249)
T ss_pred             HHHhccccCCCEEEEEecCCCCccchHHHHHHHHHHHhcEEEEecCC
Confidence            84   2234588899998865   2 2 2789999999999999995

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

Probab=98.28  E-value=1.4e-05  Score=70.02  Aligned_cols=137  Identities=20%  Similarity=0.243  Sum_probs=89.9

Q ss_pred             hhccc-cceeEEEEeecChHHHHHHHhhcCcCccCC--CCeEEEEeccCCCCCCcccccCCccccccccccccccchhhh
Q 024144           50 AGKSQ-SRGLVVVAYSRSPSFYVDLLKRRGIDIASS--HDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNL  126 (272)
Q Consensus        50 a~~~q-~~~Vhvl~fe~Spe~y~~~lk~~G~d~~s~--~~ri~i~D~ysDPLGW~~~~~~~~~~~~~s~~~~~~~~v~~L  126 (272)
                      ++..+ ++.+..+.+|-+|+++.+-++..|+|.+..  +.++.++|+++...+|.. .                 ++..+
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            46677 999999999999999999999999876542  335999999999988872 1                 22233


Q ss_pred             hHHHHHHHHhccCccCCCCCcEEEEEechhHHHHhcChHHHHHHHHhhhcC---CceeEEEeeecccccchhhHhHHhh-
Q 024144          127 DKLYSLIIEQGKGLIGQGKDRFSIAIDSVSEMVRHASISSVAGILSNLRSH---DQVSSIFWLLHSDLHEIKFTSVLEY-  202 (272)
Q Consensus       127 ~sl~~~i~e~~~~~~~~~k~~~tVaIDSLS~LL~h~s~~~vc~lL~~Lr~~---~~vssVl~LLHsDLHe~~~v~ALe~-  202 (272)
                      ...+...++..       ++ -.|+||||+.+....+...+-..|+.|.+.   ..+..++-.-..+-+++.....+++ 
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       23 589999999996666766665566665542   3455554444344555666666765 


Q ss_pred             hheeEEEeec
Q 024144          203 LSSMVASVEP  212 (272)
Q Consensus       203 LSstvvtv~P  212 (272)
                      ++.++|.+.=
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            9999999964

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=97.92  E-value=0.00031  Score=62.77  Aligned_cols=144  Identities=17%  Similarity=0.177  Sum_probs=84.1

Q ss_pred             hhccccceeEEEEeecChHHHHHHHhhcCcCccC--CCCeEEEEeccCCCCCCcccccCCccccccccccccccchhhhh
Q 024144           50 AGKSQSRGLVVVAYSRSPSFYVDLLKRRGIDIAS--SHDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNLD  127 (272)
Q Consensus        50 a~~~q~~~Vhvl~fe~Spe~y~~~lk~~G~d~~s--~~~ri~i~D~ysDPLGW~~~~~~~~~~~~~s~~~~~~~~v~~L~  127 (272)
                      .+..+++.+..|.+|-+|+++.+-++..|+|...  -..++.++|||++-.++......           -+..+..++.
T Consensus        44 ~~~~~ge~~lyvs~ee~~~~i~~~~~~~g~~~~~~~~~g~l~~~d~~~~~~~~~~~~~~-----------~~~~~~~~~~  112 (237)
T TIGR03877        44 NGLQMGEPGIYVALEEHPVQVRRNMAQFGWDVRKYEEEGKFAIVDAFTGGIGEAAEREK-----------YVVKDPTDVR  112 (237)
T ss_pred             HHHHcCCcEEEEEeeCCHHHHHHHHHHhCCCHHHHhhcCCEEEEecccccccccccccc-----------ccccCcccHH
Confidence            3456799999999999999999999999988542  13479999999985554431110           0111222344


Q ss_pred             HHHHHHHHhccCccCCCCCcEEEEEechhHHHHhcCh---HHHHHHHHhhhcCCceeEEEeeecccccchhh-HhHHhhh
Q 024144          128 KLYSLIIEQGKGLIGQGKDRFSIAIDSVSEMVRHASI---SSVAGILSNLRSHDQVSSIFWLLHSDLHEIKF-TSVLEYL  203 (272)
Q Consensus       128 sl~~~i~e~~~~~~~~~k~~~tVaIDSLS~LL~h~s~---~~vc~lL~~Lr~~~~vssVl~LLHsDLHe~~~-v~ALe~L  203 (272)
                      .++..+.+..+    +.++ -.|+||||+.++...+.   ..+-++.+.+++. .+..++ .-|.+..+... ...++|+
T Consensus       113 ~~~~~i~~~i~----~~~~-~~vVIDSls~l~~~~~~~~r~~l~~l~~~lk~~-~~t~ll-t~~~~~~~~~~~~~~~~~~  185 (237)
T TIGR03877       113 ELIDVLRQAIR----DINA-KRVVIDSVTTLYITKPAMARSIVMQLKRVLSGL-GCTSIF-VSQVSVGERGFGGPGVEHA  185 (237)
T ss_pred             HHHHHHHHHHH----HhCC-CEEEEcChhHhhcCChHHHHHHHHHHHHHHHhC-CCEEEE-EECcccccccccccceEEE
Confidence            44444444322    1223 37999999998764332   1233344445543 333333 33332222111 1246899


Q ss_pred             heeEEEee
Q 024144          204 SSMVASVE  211 (272)
Q Consensus       204 Sstvvtv~  211 (272)
                      +-++|.+.
T Consensus       186 ~D~vI~L~  193 (237)
T TIGR03877       186 VDGIIRLD  193 (237)
T ss_pred             EeEEEEEE
Confidence            99998885

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.

>PRK04328 hypothetical protein; Provisional

Probab=97.75  E-value=0.00042  Score=62.81  Aligned_cols=144  Identities=19%  Similarity=0.177  Sum_probs=83.9

Q ss_pred             hhccccceeEEEEeecChHHHHHHHhhcCcCccC--CCCeEEEEeccCCCCCCcccccCCccccccccccccccchhhhh
Q 024144           50 AGKSQSRGLVVVAYSRSPSFYVDLLKRRGIDIAS--SHDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNLD  127 (272)
Q Consensus        50 a~~~q~~~Vhvl~fe~Spe~y~~~lk~~G~d~~s--~~~ri~i~D~ysDPLGW~~~~~~~~~~~~~s~~~~~~~~v~~L~  127 (272)
                      .+..+++.+..+.+|-+|+.+++-+++.|+|...  -+.++.++|+|+.-.+.......          + +..+..++.
T Consensus        46 ~~~~~ge~~lyis~ee~~~~i~~~~~~~g~d~~~~~~~~~l~iid~~~~~~~~~~~~~~----------~-~~~~~~~~~  114 (249)
T PRK04328         46 NGLQMGEPGVYVALEEHPVQVRRNMRQFGWDVRKYEEEGKFAIVDAFTGGIGSAAKREK----------Y-VVKDPDDVR  114 (249)
T ss_pred             HHHhcCCcEEEEEeeCCHHHHHHHHHHcCCCHHHHhhcCCEEEEecccccccccccccc----------c-cccCcccHH
Confidence            4567799999999999999999999999987543  13479999999987765431110          1 111223344


Q ss_pred             HHHHHHHHhccCccCCCCCcEEEEEechhHHHHhcCh---HHHHHHHHhhhcCCceeEEEeeecccccchhh-HhHHhhh
Q 024144          128 KLYSLIIEQGKGLIGQGKDRFSIAIDSVSEMVRHASI---SSVAGILSNLRSHDQVSSIFWLLHSDLHEIKF-TSVLEYL  203 (272)
Q Consensus       128 sl~~~i~e~~~~~~~~~k~~~tVaIDSLS~LL~h~s~---~~vc~lL~~Lr~~~~vssVl~LLHsDLHe~~~-v~ALe~L  203 (272)
                      .++..+.+..+    +.++ -.|+||||+.|.+..+-   ..+.++.+.|++.+ +..++- .|.+..+... -..++|+
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            44344333222    1233 37999999998764321   12344445555433 333322 2333222111 1236888


Q ss_pred             heeEEEee
Q 024144          204 SSMVASVE  211 (272)
Q Consensus       204 Sstvvtv~  211 (272)
                      +-++|.+.
T Consensus       188 ~D~vI~L~  195 (249)
T PRK04328        188 VDGIIRLD  195 (249)
T ss_pred             EEEEEEEE
Confidence            88888875

>PRK06067 flagellar accessory protein FlaH; Validated

Probab=97.73  E-value=0.0012  Score=58.34  Aligned_cols=136  Identities=17%  Similarity=0.247  Sum_probs=93.4

Q ss_pred             hccccceeEEEEeecChHHHHHHHhhcCcCccCC--CCeEEEEeccCCCCCCcccccCCccccccccccccccchhhhhH
Q 024144           51 GKSQSRGLVVVAYSRSPSFYVDLLKRRGIDIASS--HDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNLDK  128 (272)
Q Consensus        51 ~~~q~~~Vhvl~fe~Spe~y~~~lk~~G~d~~s~--~~ri~i~D~ysDPLGW~~~~~~~~~~~~~s~~~~~~~~v~~L~s  128 (272)
                      +..+++.+..+.+|.+|+++.+-+++.|+|....  ...+.++|.+..+..|...                  +.+++-.
T Consensus        49 ~~~~g~~~~y~~~e~~~~~~~~~~~~~g~~~~~~~~~g~l~i~~~~~~~~~~~~~------------------~~~~ll~  110 (234)
T PRK06067         49 ALKQGKKVYVITTENTSKSYLKQMESVKIDISDFFLWGYLRIFPLNTEGFEWNST------------------LANKLLE  110 (234)
T ss_pred             HHhCCCEEEEEEcCCCHHHHHHHHHHCCCChhHHHhCCCceEEeccccccccCcc------------------hHHHHHH
Confidence            4457999999999999999999999999886541  3357778877666655431                  1222222


Q ss_pred             HHHHHHHhccCccCCCCCcEEEEEechhHHHHhcChHHHHHHHHhhhcC-CceeEEEeeecccccchhhHhHHhhhheeE
Q 024144          129 LYSLIIEQGKGLIGQGKDRFSIAIDSVSEMVRHASISSVAGILSNLRSH-DQVSSIFWLLHSDLHEIKFTSVLEYLSSMV  207 (272)
Q Consensus       129 l~~~i~e~~~~~~~~~k~~~tVaIDSLS~LL~h~s~~~vc~lL~~Lr~~-~~vssVl~LLHsDLHe~~~v~ALe~LSstv  207 (272)
                      .+...++.       .++ -.|+|||++.++...+...+..++..|+.. ..=..++...|.+.+.+.....+++++-.+
T Consensus       111 ~l~~~i~~-------~~~-~~iviDs~t~~~~~~~~~~~~~~l~~l~~l~~~g~tvllt~~~~~~~~~~~~~~~~l~Dgv  182 (234)
T PRK06067        111 LIIEFIKS-------KRE-DVIIIDSLTIFATYAEEDDILNFLTEAKNLVDLGKTILITLHPYAFSEELLSRIRSICDVY  182 (234)
T ss_pred             HHHHHHHh-------cCC-CEEEEecHHHHHhcCCHHHHHHHHHHHHHHHhCCCEEEEEecCCcCCHHHHHHHHhheEEE
Confidence            22222221       233 379999999998878887777775555331 112456777787777677778899999999


Q ss_pred             EEeec
Q 024144          208 ASVEP  212 (272)
Q Consensus       208 vtv~P  212 (272)
                      +.+.-
T Consensus       183 I~L~~  187 (234)
T PRK06067        183 LKLRA  187 (234)
T ss_pred             EEEEe
Confidence            98875

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

Probab=97.29  E-value=0.0093  Score=55.12  Aligned_cols=137  Identities=17%  Similarity=0.196  Sum_probs=108.4

Q ss_pred             hhccccceeEEEEeecChHHHHHHHhhcCcCccC--CCCeEEEEeccCCCCCCcccccCCccccccccccccccchhhhh
Q 024144           50 AGKSQSRGLVVVAYSRSPSFYVDLLKRRGIDIAS--SHDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNLD  127 (272)
Q Consensus        50 a~~~q~~~Vhvl~fe~Spe~y~~~lk~~G~d~~s--~~~ri~i~D~ysDPLGW~~~~~~~~~~~~~s~~~~~~~~v~~L~  127 (272)
                      ..-.++..|..|.-|.+--+|..-|..-|.|..-  ++.++.|.-...+|..|+....                     +
T Consensus        51 G~L~~g~~v~yvsTe~T~refi~qm~sl~ydv~~~~l~G~l~~~~~~~~~~~~~~~~~---------------------~  109 (235)
T COG2874          51 GFLMNGYRVTYVSTELTVREFIKQMESLSYDVSDFLLSGRLLFFPVNLEPVNWGRRSA---------------------R  109 (235)
T ss_pred             HHHhCCceEEEEEechhHHHHHHHHHhcCCCchHHHhcceeEEEEecccccccChHHH---------------------H
Confidence            3556788999999999999999999988877554  5667777777779999998433                     2


Q ss_pred             HHHHHHHHhccCccCCCCCcEEEEEechhHHHHhcChHHHHHHHHhhhc-CCceeEEEeeecccccchhhHhHHhhhhee
Q 024144          128 KLYSLIIEQGKGLIGQGKDRFSIAIDSVSEMVRHASISSVAGILSNLRS-HDQVSSIFWLLHSDLHEIKFTSVLEYLSSM  206 (272)
Q Consensus       128 sl~~~i~e~~~~~~~~~k~~~tVaIDSLS~LL~h~s~~~vc~lL~~Lr~-~~~vssVl~LLHsDLHe~~~v~ALe~LSst  206 (272)
                      +++..+++..|   ..-+.  +|.|||||..+.+.+..+|-+++..+|+ ++.=.-|+--+|.+.-.+.++.-++..+++
T Consensus       110 ~~L~~l~~~~k---~~~~d--ViIIDSls~~~~~~~~~~vl~fm~~~r~l~d~gKvIilTvhp~~l~e~~~~rirs~~d~  184 (235)
T COG2874         110 KLLDLLLEFIK---RWEKD--VIIIDSLSAFATYDSEDAVLNFMTFLRKLSDLGKVIILTVHPSALDEDVLTRIRSACDV  184 (235)
T ss_pred             HHHHHHHhhHH---hhcCC--EEEEecccHHhhcccHHHHHHHHHHHHHHHhCCCEEEEEeChhhcCHHHHHHHHHhhhe
Confidence            22233333322   11244  8999999999999999999999999998 456677888999999999999999999999


Q ss_pred             EEEeec
Q 024144          207 VASVEP  212 (272)
Q Consensus       207 vvtv~P  212 (272)
                      -+.++-
T Consensus       185 ~l~L~~  190 (235)
T COG2874         185 YLRLRL  190 (235)
T ss_pred             eEEEEh
Confidence            888854

>PRK09302 circadian clock protein KaiC; Reviewed

Probab=97.27  E-value=0.0045  Score=61.33  Aligned_cols=131  Identities=18%  Similarity=0.243  Sum_probs=83.9

Q ss_pred             hhccccceeEEEEeecChHHHHHHHhhcCcCccC--CCCeEEEEeccCCCCCCcccccCCccccccccccccccchhhhh
Q 024144           50 AGKSQSRGLVVVAYSRSPSFYVDLLKRRGIDIAS--SHDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNLD  127 (272)
Q Consensus        50 a~~~q~~~Vhvl~fe~Spe~y~~~lk~~G~d~~s--~~~ri~i~D~ysDPLGW~~~~~~~~~~~~~s~~~~~~~~v~~L~  127 (272)
                      .+..+++.+..+.||-+|+.+.+-++..|+|.+.  -+..+.+++.+.++.+++.                      .+.
T Consensus       296 ~~~~~g~~~~yis~e~~~~~i~~~~~~~g~~~~~~~~~g~l~i~~~~~~~~~~~~----------------------~~~  353 (509)
T PRK09302        296 AACRRGERCLLFAFEESRAQLIRNARSWGIDLEKMEEKGLLKIICARPESYGLED----------------------HLI  353 (509)
T ss_pred             HHHhCCCcEEEEEecCCHHHHHHHHHHcCCChHHHhhcCCceeecCCcccCCHHH----------------------HHH
Confidence            3456799999999999999999999988887544  1235778887776665543                      111


Q ss_pred             HHHHHHHHhccCccCCCCCcEEEEEechhHHHHhcChHHHHHHHHhhhcC---CceeEEEeee-cccc-cchhhHhHHhh
Q 024144          128 KLYSLIIEQGKGLIGQGKDRFSIAIDSVSEMVRHASISSVAGILSNLRSH---DQVSSIFWLL-HSDL-HEIKFTSVLEY  202 (272)
Q Consensus       128 sl~~~i~e~~~~~~~~~k~~~tVaIDSLS~LL~h~s~~~vc~lL~~Lr~~---~~vssVl~LL-HsDL-He~~~v~ALe~  202 (272)
                      .+ ...++.       .++ -.|+||||+.+....+...+-+.|..|.+.   -.+..++-.. +.+. +.+.....++|
T Consensus       354 ~i-~~~i~~-------~~~-~~vVIDslt~l~~~~~~~~~~~~l~~l~~~~k~~~~t~l~t~~~~~~~g~~~~~~~~~~~  424 (509)
T PRK09302        354 II-KREIEE-------FKP-SRVAIDPLSALARGGSLNEFRQFVIRLTDYLKSEEITGLFTNLTPDFMGSHSITESHISS  424 (509)
T ss_pred             HH-HHHHHH-------cCC-CEEEEcCHHHHHHhCCHHHHHHHHHHHHHHHHhCCCeEEEEeccccccCCCCCCcCceEE
Confidence            11 222221       234 379999999999877766555555544331   3455555432 2221 23333345899


Q ss_pred             hheeEEEee
Q 024144          203 LSSMVASVE  211 (272)
Q Consensus       203 LSstvvtv~  211 (272)
                      ++.++|.+.
T Consensus       425 l~D~vI~L~  433 (509)
T PRK09302        425 LTDTWILLQ  433 (509)
T ss_pred             eeeEEEEEE
Confidence            999999986

>PRK09302 circadian clock protein KaiC; Reviewed

Probab=96.75  E-value=0.036  Score=55.02  Aligned_cols=137  Identities=18%  Similarity=0.191  Sum_probs=85.6

Q ss_pred             hhccc-cceeEEEEeecChHHHHHHHhhcCcCccCC--CCeEEEEeccCCCCCCcccccCCccccccccccccccchhhh
Q 024144           50 AGKSQ-SRGLVVVAYSRSPSFYVDLLKRRGIDIASS--HDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNL  126 (272)
Q Consensus        50 a~~~q-~~~Vhvl~fe~Spe~y~~~lk~~G~d~~s~--~~ri~i~D~ysDPLGW~~~~~~~~~~~~~s~~~~~~~~v~~L  126 (272)
                      .+..+ ++.+..+.+|-+|+++.+-++..|+|.+..  +.++.+.|.|.+|..|.. ...          .       ++
T Consensus        54 ~~~~~~ge~~lyis~ee~~~~i~~~~~~~g~d~~~~~~~g~l~~~~~~~~~~~~~~-~~~----------~-------~~  115 (509)
T PRK09302         54 NGIKRFDEPGVFVTFEESPEDIIRNVASFGWDLQKLIDEGKLFILDASPDPSEQEE-AGE----------Y-------DL  115 (509)
T ss_pred             HHHHhcCCCEEEEEccCCHHHHHHHHHHcCCCHHHHhhCCeEEEEecCcccccccc-ccc----------c-------cH
Confidence            35555 899999999999999999999999986552  346999999999988864 110          1       23


Q ss_pred             hHHHHHHHHhccCccCCCCCcEEEEEechhHHHHhcChH-----HHHHHHHhhhcCCceeEEEeeeccccc-c-hhhHhH
Q 024144          127 DKLYSLIIEQGKGLIGQGKDRFSIAIDSVSEMVRHASIS-----SVAGILSNLRSHDQVSSIFWLLHSDLH-E-IKFTSV  199 (272)
Q Consensus       127 ~sl~~~i~e~~~~~~~~~k~~~tVaIDSLS~LL~h~s~~-----~vc~lL~~Lr~~~~vssVl~LLHsDLH-e-~~~v~A  199 (272)
                      ..++..+.+..+    +.++ -.|+|||++.+.......     .+.+++..|++. .+..++. -|..-. + ....+.
T Consensus       116 ~~l~~~l~~~i~----~~~~-~~vVIDSls~l~~~~d~~~~~r~~l~~L~~~Lk~~-g~TvLlt-~~~~~~~~~~~~~~~  188 (509)
T PRK09302        116 EALFIRIEYAID----KIGA-KRVVLDSIEALFSGFSNEAVVRRELRRLFAWLKQK-GVTAVIT-GERGDEYGPLTRYGV  188 (509)
T ss_pred             HHHHHHHHHHHH----hhCC-CEEEECCHHHHHhhccCHHHHHHHHHHHHHHHHhC-CCEEEEE-ECCccCcCCccccCc
Confidence            333334333222    1233 469999999987654332     344455555543 3333333 343321 1 111224


Q ss_pred             HhhhheeEEEee
Q 024144          200 LEYLSSMVASVE  211 (272)
Q Consensus       200 Le~LSstvvtv~  211 (272)
                      .+|++..++.|.
T Consensus       189 ~~~laDgVI~L~  200 (509)
T PRK09302        189 EEFVSDCVIILR  200 (509)
T ss_pred             eEEEeeEEEEEe
Confidence            588999999887

>TIGR02655 circ_KaiC circadian clock protein KaiC

Probab=96.68  E-value=0.13  Score=51.24  Aligned_cols=94  Identities=22%  Similarity=0.306  Sum_probs=60.4

Q ss_pred             hhccccceeEEEEeecChHHHHHHHhhcCcCccC--CCCeEEEEeccCCCCCCcccccCCccccccccccccccchhhhh
Q 024144           50 AGKSQSRGLVVVAYSRSPSFYVDLLKRRGIDIAS--SHDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNLD  127 (272)
Q Consensus        50 a~~~q~~~Vhvl~fe~Spe~y~~~lk~~G~d~~s--~~~ri~i~D~ysDPLGW~~~~~~~~~~~~~s~~~~~~~~v~~L~  127 (272)
                      +++.+++.+..+.||=|++++..=+++-|+|.+.  ...++.+++.+....+..+                      .+.
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            4556889999999999999999999999988543  1235888887643332111                      122


Q ss_pred             HHHHHHHHhccCccCCCCCcEEEEEechhHHHHhcChHHHHHHHHhh
Q 024144          128 KLYSLIIEQGKGLIGQGKDRFSIAIDSVSEMVRHASISSVAGILSNL  174 (272)
Q Consensus       128 sl~~~i~e~~~~~~~~~k~~~tVaIDSLS~LL~h~s~~~vc~lL~~L  174 (272)
                      .+...+.+        .++ -.|+||||+.+....+..++-..++.|
T Consensus       344 ~i~~~i~~--------~~~-~~vvIDsi~~~~~~~~~~~~r~~~~~l  381 (484)
T TIGR02655       344 IIKSEIAD--------FKP-ARIAIDSLSALARGVSNNAFRQFVIGV  381 (484)
T ss_pred             HHHHHHHH--------cCC-CEEEEcCHHHHHHhcCHHHHHHHHHHH
Confidence            22222322        233 379999999998766655544333333

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=96.17  E-value=0.25  Score=43.26  Aligned_cols=138  Identities=12%  Similarity=0.089  Sum_probs=75.2

Q ss_pred             hccccceeEEEEeecChHHHHHHHhhcCcCccCC--CCeEEEEeccCCCC--CCcccccCCccccccccccccccchhhh
Q 024144           51 GKSQSRGLVVVAYSRSPSFYVDLLKRRGIDIASS--HDWIHILDCYTDPL--GWKNWLIDKDISQEASSLSSFCQDVRNL  126 (272)
Q Consensus        51 ~~~q~~~Vhvl~fe~Spe~y~~~lk~~G~d~~s~--~~ri~i~D~ysDPL--GW~~~~~~~~~~~~~s~~~~~~~~v~~L  126 (272)
                      +..+++.+..+.+|.+++.+.+-+++.|++....  +.++.+.|.++...  .|.- .           ..    ++.++
T Consensus        44 ~~~~g~~~~~is~e~~~~~i~~~~~~~g~~~~~~~~~~~l~i~d~~~~~~~~~~~~-~-----------~~----~~~~~  107 (229)
T TIGR03881        44 GLRDGDPVIYVTTEESRESIIRQAAQFGMDFEKAIEEGKLVIIDALMKEKEDEWSL-R-----------EL----SIEEL  107 (229)
T ss_pred             HHhcCCeEEEEEccCCHHHHHHHHHHhCCCHHHHhhcCCEEEEEcccccccccccc-c-----------cC----CHHHH
Confidence            3346889999999999999998888899886642  34688888775431  1221 0           01    23333


Q ss_pred             hHHHHHHHHhccCccCCCCCcEEEEEechhHHHHhcChHHHHHHHHhhhc---CCceeEEEeeecccc-cchhhHhHHhh
Q 024144          127 DKLYSLIIEQGKGLIGQGKDRFSIAIDSVSEMVRHASISSVAGILSNLRS---HDQVSSIFWLLHSDL-HEIKFTSVLEY  202 (272)
Q Consensus       127 ~sl~~~i~e~~~~~~~~~k~~~tVaIDSLS~LL~h~s~~~vc~lL~~Lr~---~~~vssVl~LLHsDL-He~~~v~ALe~  202 (272)
                      ..-+....+..    + .++ -.|+|||++.++...+.. .-..+..|.+   ...+..++ .-|-.. -++.....++|
T Consensus       108 ~~~i~~~~~~~----~-~~~-~~vvIDsl~~l~~~~~~~-~r~~~~~l~~~l~~~~~tvil-~~~~~~~~~~~~~~~~~~  179 (229)
T TIGR03881       108 LNKVIEAKKYL----G-YGH-ARLVIDSMSAFWLDKPAM-ARKYSYYLKRVLNRWNFTILL-TSQYAITTSQAFGFGIEH  179 (229)
T ss_pred             HHHHHHHHHhh----c-cCc-eEEEecCchhhhccChHH-HHHHHHHHHHHHHhCCCEEEE-EecccccCCCCcccceEE
Confidence            32222222211    0 122 478999999998755432 1222222222   12333333 334222 12222235788


Q ss_pred             hheeEEEeec
Q 024144          203 LSSMVASVEP  212 (272)
Q Consensus       203 LSstvvtv~P  212 (272)
                      ++-.+|.+.-
T Consensus       180 l~D~vI~L~~  189 (229)
T TIGR03881       180 VADGIIRFRK  189 (229)
T ss_pred             EEeEEEEEEE
Confidence            8888888763

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.

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

Probab=96.03  E-value=0.064  Score=48.37  Aligned_cols=142  Identities=20%  Similarity=0.254  Sum_probs=87.1

Q ss_pred             hhccccceeEEEEeecChHHHHHHHhhcCcCccC--CCCeEEEEeccCCCCCCcccccCCccccccccccccccchhhhh
Q 024144           50 AGKSQSRGLVVVAYSRSPSFYVDLLKRRGIDIAS--SHDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNLD  127 (272)
Q Consensus        50 a~~~q~~~Vhvl~fe~Spe~y~~~lk~~G~d~~s--~~~ri~i~D~ysDPLGW~~~~~~~~~~~~~s~~~~~~~~v~~L~  127 (272)
                      .++..++.+..+.+|-+|++.++-+++.|.|.+.  -+..+.++|.|+.+.+=.. .              .-.+..++.
T Consensus        46 ~~~~~ge~vlyvs~~e~~~~l~~~~~~~g~d~~~~~~~g~l~i~d~~~~~~~~~~-~--------------~~~~~~~~~  110 (260)
T COG0467          46 EGAREGEPVLYVSTEESPEELLENARSFGWDLEVYIEKGKLAILDAFLSEKGLVS-I--------------VVGDPLDLE  110 (260)
T ss_pred             HHHhcCCcEEEEEecCCHHHHHHHHHHcCCCHHHHhhcCCEEEEEcccccccccc-c--------------cccCCccHH
Confidence            4666699999999999999999999999998753  2345889998888774221 0              000112333


Q ss_pred             HHHHHHHHhccCccCCCCCcEEEEEechhHHHHhcChHHHH-HHHHhhhcC-CceeEEEeeecccccchhhH--hHHhhh
Q 024144          128 KLYSLIIEQGKGLIGQGKDRFSIAIDSVSEMVRHASISSVA-GILSNLRSH-DQVSSIFWLLHSDLHEIKFT--SVLEYL  203 (272)
Q Consensus       128 sl~~~i~e~~~~~~~~~k~~~tVaIDSLS~LL~h~s~~~vc-~lL~~Lr~~-~~vssVl~LLHsDLHe~~~v--~ALe~L  203 (272)
                      ++...+.+..+    .-++ ..++|||++.+......+... ..+..+.+. ..-. +.+++.+|.......  +-.+|+
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            33334444322    1222 689999999776666666554 444444442 1222 444555554332111  456668


Q ss_pred             heeEEEeec
Q 024144          204 SSMVASVEP  212 (272)
Q Consensus       204 Sstvvtv~P  212 (272)
                      +..++.+..
T Consensus       185 vdgvI~l~~  193 (260)
T COG0467         185 VDGVIRLDL  193 (260)
T ss_pred             EEEEEEEee
Confidence            888888876

>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=95.94  E-value=0.16  Score=42.46  Aligned_cols=135  Identities=20%  Similarity=0.151  Sum_probs=79.6

Q ss_pred             hccccceeEEEEeecChHHHHHHHhhcCcCccCC--CCeEEEEeccCCCCCCcccccCCccccccccccccccchhhhhH
Q 024144           51 GKSQSRGLVVVAYSRSPSFYVDLLKRRGIDIASS--HDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNLDK  128 (272)
Q Consensus        51 ~~~q~~~Vhvl~fe~Spe~y~~~lk~~G~d~~s~--~~ri~i~D~ysDPLGW~~~~~~~~~~~~~s~~~~~~~~v~~L~s  128 (272)
                      +..+++.+.++.+|-+++.+.+-+++.|++.+.+  ...+.+.|.+...+...+              .   +...++..
T Consensus        23 ~~~~g~~v~~~s~e~~~~~~~~~~~~~g~~~~~l~~~g~l~~~d~~~~~~s~~~--------------~---~~~~~~~~   85 (187)
T cd01124          23 GLARGEPGLYVTLEESPEELIENAESLGWDLERLEDEGLLAIVDADPDEIGPAE--------------S---SLRLELIQ   85 (187)
T ss_pred             HHHCCCcEEEEECCCCHHHHHHHHHHcCCChHHHHhcCCeEEEecCccccchhh--------------h---hhhHHHHH
Confidence            4467899999999999999999999889885531  234677775554442111              0   00001111


Q ss_pred             HHHHHHHhccCccCCCCCcEEEEEechhHHHH---hcChHHHHHHHHhhhcCCceeEEEeeeccccc-c-hhhHhHHhhh
Q 024144          129 LYSLIIEQGKGLIGQGKDRFSIAIDSVSEMVR---HASISSVAGILSNLRSHDQVSSIFWLLHSDLH-E-IKFTSVLEYL  203 (272)
Q Consensus       129 l~~~i~e~~~~~~~~~k~~~tVaIDSLS~LL~---h~s~~~vc~lL~~Lr~~~~vssVl~LLHsDLH-e-~~~v~ALe~L  203 (272)
                      .+...+..       .++ -.|+||+++.++.   ......+-+++..|++. .+. ++..-|..-. + ......++|+
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            11222111       233 5899999999987   44445556677777754 333 3333343221 1 2333567888


Q ss_pred             heeEEEeec
Q 024144          204 SSMVASVEP  212 (272)
Q Consensus       204 Sstvvtv~P  212 (272)
                      +..++.++-
T Consensus       156 aD~ii~l~~  164 (187)
T cd01124         156 VDGVIRLRL  164 (187)
T ss_pred             eeEEEEEEE
Confidence            888887764

A related protein is found in archaea.

>TIGR02655 circ_KaiC circadian clock protein KaiC

Probab=95.66  E-value=0.17  Score=50.35  Aligned_cols=137  Identities=19%  Similarity=0.192  Sum_probs=82.5

Q ss_pred             hhccc-cceeEEEEeecChHHHHHHHhhcCcCccCC--CCeEEEEeccCCCCCCcccccCCccccccccccccccchhhh
Q 024144           50 AGKSQ-SRGLVVVAYSRSPSFYVDLLKRRGIDIASS--HDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNL  126 (272)
Q Consensus        50 a~~~q-~~~Vhvl~fe~Spe~y~~~lk~~G~d~~s~--~~ri~i~D~ysDPLGW~~~~~~~~~~~~~s~~~~~~~~v~~L  126 (272)
                      +++.+ ++.+..|.||=+|+++.+-+++.|+|-+..  ..++.++|.+..+  |.....         ..+       ++
T Consensus        44 ~g~~~~ge~~lyvs~eE~~~~l~~~~~~~G~~~~~~~~~g~l~~~~~~~~~--~~~~~~---------~~~-------~l  105 (484)
T TIGR02655        44 NGIIHFDEPGVFVTFEESPQDIIKNARSFGWDLQKLVDEGKLFILDASPDP--EGQDVV---------GGF-------DL  105 (484)
T ss_pred             HHHHhCCCCEEEEEEecCHHHHHHHHHHcCCCHHHHhhcCceEEEecCchh--cccccc---------ccC-------CH
Confidence            46666 899999999999999999999999986531  3468888875433  222110         001       22


Q ss_pred             hHHHHHHHHhccCccCCCCCcEEEEEechhHHHHhcChH-----HHHHHHHhhhcCCceeEEEeeec-ccccch-hhHhH
Q 024144          127 DKLYSLIIEQGKGLIGQGKDRFSIAIDSVSEMVRHASIS-----SVAGILSNLRSHDQVSSIFWLLH-SDLHEI-KFTSV  199 (272)
Q Consensus       127 ~sl~~~i~e~~~~~~~~~k~~~tVaIDSLS~LL~h~s~~-----~vc~lL~~Lr~~~~vssVl~LLH-sDLHe~-~~v~A  199 (272)
                      ..++..+.+...    .+++ --|+|||++.+....+..     .+.++++.|++. .+..++- -| .+...+ ...+.
T Consensus       106 ~~~l~~i~~~ls----~g~~-qRVvIDSl~aL~~~~~~~~~~r~~l~~Li~~L~~~-g~TvLLt-sh~~~~~~~~~~~~~  178 (484)
T TIGR02655       106 SALIERINYAIR----KYKA-KRVSIDSVTAVFQQYDAVSVVRREIFRLVARLKQI-GVTTVMT-TERIEEYGPIARYGV  178 (484)
T ss_pred             HHHHHHHHHHHH----HhCC-cEEEEeehhHhhhhcCchHHHHHHHHHHHHHHHHC-CCEEEEE-ecCcccccccccCCc
Confidence            333333333211    1233 479999999987655542     345566666642 3444443 34 232221 12223


Q ss_pred             HhhhheeEEEee
Q 024144          200 LEYLSSMVASVE  211 (272)
Q Consensus       200 Le~LSstvvtv~  211 (272)
                      .+|++-.+|.+.
T Consensus       179 ~e~laDgVI~L~  190 (484)
T TIGR02655       179 EEFVSDNVVILR  190 (484)
T ss_pred             eeEeeeeEEEEE
Confidence            599999999886

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.

>TIGR03878 thermo_KaiC_2 KaiC domain protein, AF_0795 family

Probab=95.50  E-value=0.17  Score=46.32  Aligned_cols=133  Identities=14%  Similarity=0.126  Sum_probs=70.3

Q ss_pred             hccccceeEEEEeecChHH----HHHHHhhcCcCccCCCCeEEEEeccCCCCCCcccccCCccccccccccccccchhhh
Q 024144           51 GKSQSRGLVVVAYSRSPSF----YVDLLKRRGIDIASSHDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNL  126 (272)
Q Consensus        51 ~~~q~~~Vhvl~fe~Spe~----y~~~lk~~G~d~~s~~~ri~i~D~ysDPLGW~~~~~~~~~~~~~s~~~~~~~~v~~L  126 (272)
                      ++.+++.+..+.+|-++++    +..-.++.|+|.+...++++++|..+.+-     ..                  .++
T Consensus        60 ~a~~Ge~vlyis~Ee~~~~~~~~l~~~a~~~g~d~~~~~~~l~~id~~~~~~-----~~------------------~~~  116 (259)
T TIGR03878        60 QASRGNPVLFVTVESPANFVYTSLKERAKAMGVDFDKIEENIILIDAASSTE-----LR------------------ENV  116 (259)
T ss_pred             HHhCCCcEEEEEecCCchHHHHHHHHHHHHcCCCHHHHhCCEEEEECCCchh-----hh------------------hhH
Confidence            5567999999999976653    33334566777655456788888765321     00                  012


Q ss_pred             hHHHHHHHHhccCccCCCCCcEEEEEechhHHHHhcChH---HHHHHHHhhhcCCceeEEEeeecccc---cc-hhhHhH
Q 024144          127 DKLYSLIIEQGKGLIGQGKDRFSIAIDSVSEMVRHASIS---SVAGILSNLRSHDQVSSIFWLLHSDL---HE-IKFTSV  199 (272)
Q Consensus       127 ~sl~~~i~e~~~~~~~~~k~~~tVaIDSLS~LL~h~s~~---~vc~lL~~Lr~~~~vssVl~LLHsDL---He-~~~v~A  199 (272)
                      ..++..+.+..+    +.++ =.|+||||+.+.+.....   .+-+++..|++.+.-.-++.-.+.+.   .. +..-..
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            222233322211    1233 379999999876543211   12334444454333222333233322   11 111125


Q ss_pred             HhhhheeEEEee
Q 024144          200 LEYLSSMVASVE  211 (272)
Q Consensus       200 Le~LSstvvtv~  211 (272)
                      ++|++-.+|.+.
T Consensus       192 ~~~l~D~vI~L~  203 (259)
T TIGR03878       192 VSHIVDGTIVLA  203 (259)
T ss_pred             eeEeeccEEEEe
Confidence            799999988886

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

>TIGR03880 KaiC_arch_3 KaiC domain protein, AF_0351 family

Probab=94.81  E-value=0.45  Score=41.70  Aligned_cols=130  Identities=14%  Similarity=0.194  Sum_probs=75.9

Q ss_pred             hccccceeEEEEeecChHHHHHHHhhcCcCccC-CCCeEEEEeccCCCCCCcccccCCccccccccccccccchhhhhHH
Q 024144           51 GKSQSRGLVVVAYSRSPSFYVDLLKRRGIDIAS-SHDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNLDKL  129 (272)
Q Consensus        51 ~~~q~~~Vhvl~fe~Spe~y~~~lk~~G~d~~s-~~~ri~i~D~ysDPLGW~~~~~~~~~~~~~s~~~~~~~~v~~L~sl  129 (272)
                      +..+++.+..+.+|-+++.+.+-++..|++... .++++.++|....-.                     ...++.+...
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            445789999999999999999999988887543 122466776321100                     0012222221


Q ss_pred             HHHHHHhccCccCCCCCcEEEEEechhHHHHhcCh-----HHHHHHHHhhhcCCceeEEEeeecccccch--hhHhHHhh
Q 024144          130 YSLIIEQGKGLIGQGKDRFSIAIDSVSEMVRHASI-----SSVAGILSNLRSHDQVSSIFWLLHSDLHEI--KFTSVLEY  202 (272)
Q Consensus       130 ~~~i~e~~~~~~~~~k~~~tVaIDSLS~LL~h~s~-----~~vc~lL~~Lr~~~~vssVl~LLHsDLHe~--~~v~ALe~  202 (272)
                      +...++.       .++ -.|+|||++.+-.-.+.     ..+..++..|++. .+ .++-.-|.+-..+  ...+.+++
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            1122221       223 36789999987222222     3556777777754 33 3444456543332  22456899


Q ss_pred             hheeEEEee
Q 024144          203 LSSMVASVE  211 (272)
Q Consensus       203 LSstvvtv~  211 (272)
                      ++..++.+.
T Consensus       169 l~D~vI~L~  177 (224)
T TIGR03880       169 LADGVIILK  177 (224)
T ss_pred             EEeEEEEEe
Confidence            999999984

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=94.77  E-value=0.17  Score=46.73  Aligned_cols=73  Identities=21%  Similarity=0.378  Sum_probs=56.9

Q ss_pred             CCCCCceeecccCCCCchhhHHHHHHHHHHHHHHhhccccceeEEEEeecChHHHHHHHhhcCcCccC--CCCeEEEEec
Q 024144           16 GEHAPALTIKDSKASPFGFDVFNYVLTQLSNYILAGKSQSRGLVVVAYSRSPSFYVDLLKRRGIDIAS--SHDWIHILDC   93 (272)
Q Consensus        16 ge~ap~l~i~Dsl~~~~g~~v~~h~~~~l~s~i~a~~~q~~~Vhvl~fe~Spe~y~~~lk~~G~d~~s--~~~ri~i~D~   93 (272)
                      .|+--+++++|+..+| |.-+|-|++.   -..+++    +.+.+++|.++.+.|--.+++-|.|-..  .+.+++++|.
T Consensus        16 ~EqgkltLl~d~~eT~-gsFl~H~~l~---~~Lkan----~~~cFlaf~k~fshy~i~~rKlG~~l~t~k~rgqlvF~dg   87 (248)
T KOG4723|consen   16 PEQGKLTLLLDTRETP-GSFLFHYYLY---HALKAN----ESTCFLAFSKTFSHYAISMRKLGMDLKTKKNRGQLVFIDG   87 (248)
T ss_pred             CCCccEEEEeecccCC-ceeeHHHHHH---HHHhcC----CcEEEEEeecchhHHHHHHHHhCCceeecccCCcEEEEhh
Confidence            4666789999999998 5777777542   222222    8999999999999999999999999877  2335999998


Q ss_pred             cCC
Q 024144           94 YTD   96 (272)
Q Consensus        94 ysD   96 (272)
                      ++=
T Consensus        88 l~~   90 (248)
T KOG4723|consen   88 LSM   90 (248)
T ss_pred             hhh
Confidence            873

>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=94.62  E-value=0.32  Score=47.15  Aligned_cols=69  Identities=23%  Similarity=0.232  Sum_probs=49.7

Q ss_pred             EEEEEechhHHHHhcCh----HHHHHHHHhhhc----CCceeEEEeeeccccc--chhhHhHHhhhheeEEEeecCCcc
Q 024144          148 FSIAIDSVSEMVRHASI----SSVAGILSNLRS----HDQVSSIFWLLHSDLH--EIKFTSVLEYLSSMVASVEPFNQA  216 (272)
Q Consensus       148 ~tVaIDSLS~LL~h~s~----~~vc~lL~~Lr~----~~~vssVl~LLHsDLH--e~~~v~ALe~LSstvvtv~P~~~~  216 (272)
                      .=|+|-||..-+-..+-    ..+.++|+.||.    +..-..++--+=.+|-  .+..+..||+++-++|.|+|....
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            67899887765543322    248999999987    3555555556677877  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.

>PRK08533 flagellar accessory protein FlaH; Reviewed

Probab=94.40  E-value=0.45  Score=42.81  Aligned_cols=127  Identities=14%  Similarity=0.201  Sum_probs=71.1

Q ss_pred             cccceeEEEEeecChHHHHHHHhhcCcCccC--CCCeEEEEeccCCCCCCcccccCCccccccccccccccchhhhhHHH
Q 024144           53 SQSRGLVVVAYSRSPSFYVDLLKRRGIDIAS--SHDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNLDKLY  130 (272)
Q Consensus        53 ~q~~~Vhvl~fe~Spe~y~~~lk~~G~d~~s--~~~ri~i~D~ysDPLGW~~~~~~~~~~~~~s~~~~~~~~v~~L~sl~  130 (272)
                      .+++.+..+.+|.+++++.+.+++.|+|.+.  ....+.++++|..-.+.                       .+.+..+
T Consensus        50 ~~g~~~~yi~~e~~~~~~~~~~~~~g~~~~~~~~~~~l~~~~~~~~~~~~-----------------------~~~~~~l  106 (230)
T PRK08533         50 QNGYSVSYVSTQLTTTEFIKQMMSLGYDINKKLISGKLLYIPVYPLLSGN-----------------------SEKRKFL  106 (230)
T ss_pred             hCCCcEEEEeCCCCHHHHHHHHHHhCCchHHHhhcCcEEEEEecccccCh-----------------------HHHHHHH
Confidence            4678889999999999999999998987653  23467777776321111                       0111122


Q ss_pred             HHHHHhccCccCCCCCcEEEEEechhHHHHhcCh----HHHHHHHHhhhcCCceeEEEeeecccccc--hhhHhHHhhhh
Q 024144          131 SLIIEQGKGLIGQGKDRFSIAIDSVSEMVRHASI----SSVAGILSNLRSHDQVSSIFWLLHSDLHE--IKFTSVLEYLS  204 (272)
Q Consensus       131 ~~i~e~~~~~~~~~k~~~tVaIDSLS~LL~h~s~----~~vc~lL~~Lr~~~~vssVl~LLHsDLHe--~~~v~ALe~LS  204 (272)
                      ..+.+..+    ..++ -.++||+++.++....-    ..+.++|..|++...  .++- .| |...  .....-++|++
T Consensus       107 ~~il~~~~----~~~~-~~lVIDe~t~~l~~~~d~~~~~~l~~~l~~l~~~g~--tvi~-t~-~~~~~~~~~~~~~~~~~  177 (230)
T PRK08533        107 KKLMNTRR----FYEK-DVIIIDSLSSLISNDASEVAVNDLMAFFKRISSLNK--VIIL-TA-NPKELDESVLTILRTAA  177 (230)
T ss_pred             HHHHHHHH----hcCC-CEEEEECccHHhcCCcchHHHHHHHHHHHHHHhCCC--EEEE-Ee-cccccccccceeEEEee
Confidence            22232211    1123 37999999999854322    345666666654322  2222 22 2221  11223467777


Q ss_pred             eeEEEee
Q 024144          205 SMVASVE  211 (272)
Q Consensus       205 stvvtv~  211 (272)
                      -++|.+.
T Consensus       178 DgvI~L~  184 (230)
T PRK08533        178 TMLIRLE  184 (230)
T ss_pred             eEEEEEE
Confidence            7777665

>PRK05973 replicative DNA helicase; Provisional

Probab=93.45  E-value=1.6  Score=40.16  Aligned_cols=62  Identities=13%  Similarity=-0.025  Sum_probs=40.4

Q ss_pred             cCCCCCceeecccCCCCchhhHHHHHHHHHHHHHHhhccccceeEEEEeecChHHHHHHHhhcCcCccC
Q 024144           15 EGEHAPALTIKDSKASPFGFDVFNYVLTQLSNYILAGKSQSRGLVVVAYSRSPSFYVDLLKRRGIDIAS   83 (272)
Q Consensus        15 ~ge~ap~l~i~Dsl~~~~g~~v~~h~~~~l~s~i~a~~~q~~~Vhvl~fe~Spe~y~~~lk~~G~d~~s   83 (272)
                      .|=.++.+++---=...+=+.+..+|+.       .+..+++.|.++.||-+|++..+=++..|+|.+.
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       3445789999999999999999999999988666

>cd00984 DnaB_C DnaB helicase C terminal domain

Probab=93.05  E-value=0.5  Score=41.43  Aligned_cols=93  Identities=19%  Similarity=0.134  Sum_probs=51.4

Q ss_pred             EEEEEechhHHHHhc----ChHHHHHHHHhhhcC-CceeEEEeeecc------c-------ccchhhHhHHhhhheeEEE
Q 024144          148 FSIAIDSVSEMVRHA----SISSVAGILSNLRSH-DQVSSIFWLLHS------D-------LHEIKFTSVLEYLSSMVAS  209 (272)
Q Consensus       148 ~tVaIDSLS~LL~h~----s~~~vc~lL~~Lr~~-~~vssVl~LLHs------D-------LHe~~~v~ALe~LSstvvt  209 (272)
                      -.|+||+|+.+-...    ....+...+..|+.- .+.-..+.+++.      +       ++.-+-.+++++.|.+++.
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            489999999664322    113344555555531 223333444441      1       2333445788999999999


Q ss_pred             eecCCccccccccccchhhhhhccccceEEEEE-EeccCCcEEEE
Q 024144          210 VEPFNQAAFGQRVDLENLSMLEQNFRKGKFHVR-FKRRNGRVRVM  253 (272)
Q Consensus       210 v~P~~~~~~~~~~~~~~~~~l~~n~~k~~~~vr-~KrRnGRV~~~  253 (272)
                      +.+......             .+..++.+.|+ .|.|+|..-..
T Consensus       205 l~~~~~~~~-------------~~~~~~~~~l~v~KnR~G~~g~~  236 (242)
T cd00984         205 LYRDEYYNK-------------ESESKGIAEIIVAKNRNGPTGTV  236 (242)
T ss_pred             Eeccccccc-------------ccCCCCceEEEEECCCCCCCeeE
Confidence            987532110             11223334443 58899987764

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.

>TIGR02237 recomb_radB DNA repair and recombination protein RadB

Probab=92.55  E-value=1.2  Score=38.25  Aligned_cols=39  Identities=13%  Similarity=0.298  Sum_probs=27.3

Q ss_pred             cccceeEEEEeec-ChHHHHHHHhhcCcCccCCCCeEEEEecc
Q 024144           53 SQSRGLVVVAYSR-SPSFYVDLLKRRGIDIASSHDWIHILDCY   94 (272)
Q Consensus        53 ~q~~~Vhvl~fe~-Spe~y~~~lk~~G~d~~s~~~ri~i~D~y   94 (272)
                      .+++.+..+.+|. +|+.+.+.++.. ++  ....++++++++
T Consensus        38 ~~g~~v~yi~~e~~~~~rl~~~~~~~-~~--~~~~~i~~~~~~   77 (209)
T TIGR02237        38 RQGKKVVYIDTEGLSPERFKQIAEDR-PE--RALSNFIVFEVF   77 (209)
T ss_pred             hCCCeEEEEECCCCCHHHHHHHHHhC-hH--HHhcCEEEEECC
Confidence            4578999999996 899888866643 12  113568888763

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

>PRK09361 radB DNA repair and recombination protein RadB; Provisional

Probab=92.41  E-value=7  Score=34.14  Aligned_cols=65  Identities=23%  Similarity=0.176  Sum_probs=37.9

Q ss_pred             EEEEEechhHHHHhc-----C----hHHHHHHHHhhhc----CCceeEEEeeecccccc----hhhHhHHhhhheeEEEe
Q 024144          148 FSIAIDSVSEMVRHA-----S----ISSVAGILSNLRS----HDQVSSIFWLLHSDLHE----IKFTSVLEYLSSMVASV  210 (272)
Q Consensus       148 ~tVaIDSLS~LL~h~-----s----~~~vc~lL~~Lr~----~~~vssVl~LLHsDLHe----~~~v~ALe~LSstvvtv  210 (272)
                      =.|+|||++.+.+..     .    ...+.+.++.|++    +....=+..-++.+.+.    +---..++|++++++.+
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            379999999987642     1    1234554444433    33333333444455542    21123789999999998


Q ss_pred             ec
Q 024144          211 EP  212 (272)
Q Consensus       211 ~P  212 (272)
                      ..
T Consensus       189 ~~  190 (225)
T PRK09361        189 EK  190 (225)
T ss_pred             EE
Confidence            66

>PRK04301 radA DNA repair and recombination protein RadA; Validated

Probab=91.10  E-value=3.7  Score=38.45  Aligned_cols=39  Identities=21%  Similarity=0.269  Sum_probs=31.1

Q ss_pred             ceeEEEEeec--ChHHHHHHHhhcCcCccCCCCeEEEEecc
Q 024144           56 RGLVVVAYSR--SPSFYVDLLKRRGIDIASSHDWIHILDCY   94 (272)
Q Consensus        56 ~~Vhvl~fe~--Spe~y~~~lk~~G~d~~s~~~ri~i~D~y   94 (272)
                      ..+..+.+|.  +|+.+.+.+++.|+|.+..-+++++++++
T Consensus       137 ~~~~yi~te~~f~~~rl~~~~~~~g~~~~~~l~~i~~~~~~  177 (317)
T PRK04301        137 GKAVYIDTEGTFRPERIEQMAEALGLDPDEVLDNIHVARAY  177 (317)
T ss_pred             ceEEEEeCCCCcCHHHHHHHHHHcCCChHhhhccEEEEeCC
Confidence            5788999998  69999999998888876545567777764

>PRK11823 DNA repair protein RadA; Provisional

Probab=90.97  E-value=15  Score=36.68  Aligned_cols=115  Identities=22%  Similarity=0.177  Sum_probs=62.9

Q ss_pred             cccceeEEEEeecChHHHHHHHhhcCcCccCCCCeEEEEeccCCCCCCcccccCCccccccccccccccchhhhhHHHHH
Q 024144           53 SQSRGLVVVAYSRSPSFYVDLLKRRGIDIASSHDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNLDKLYSL  132 (272)
Q Consensus        53 ~q~~~Vhvl~fe~Spe~y~~~lk~~G~d~~s~~~ri~i~D~ysDPLGW~~~~~~~~~~~~~s~~~~~~~~v~~L~sl~~~  132 (272)
                      .+++.|..+.+|-+++.+..-.++.|++.    +++.+.+    +                          .++..+...
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            35788899999999998877677777762    2333221    0                          012222222


Q ss_pred             HHHhccCccCCCCCcEEEEEechhHHHHh------cChHHHHHHHHhhhc---CCceeEE-EeeecccccchhhHhHHhh
Q 024144          133 IIEQGKGLIGQGKDRFSIAIDSVSEMVRH------ASISSVAGILSNLRS---HDQVSSI-FWLLHSDLHEIKFTSVLEY  202 (272)
Q Consensus       133 i~e~~~~~~~~~k~~~tVaIDSLS~LL~h------~s~~~vc~lL~~Lr~---~~~vssV-l~LLHsDLHe~~~v~ALe~  202 (272)
                      +.+        .++ -.|+|||++.+..-      .+..++-..+..|.+   ...+.-+ ++-+..|-.-.+. ..++|
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      123334333333333   1223222 2223233222222 56999


Q ss_pred             hheeEEEee
Q 024144          203 LSSMVASVE  211 (272)
Q Consensus       203 LSstvvtv~  211 (272)
                      ++.+++.++
T Consensus       222 lvD~Vi~le  230 (446)
T PRK11823        222 MVDTVLYFE  230 (446)
T ss_pred             hCeEEEEEE
Confidence            999999775

>cd01121 Sms Sms (bacterial radA) DNA repair protein

Probab=90.05  E-value=20  Score=35.06  Aligned_cols=115  Identities=21%  Similarity=0.178  Sum_probs=62.6

Q ss_pred             ccceeEEEEeecChHHHHHHHhhcCcCccCCCCeEEEEeccCCCCCCcccccCCccccccccccccccchhhhhHHHHHH
Q 024144           54 QSRGLVVVAYSRSPSFYVDLLKRRGIDIASSHDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNLDKLYSLI  133 (272)
Q Consensus        54 q~~~Vhvl~fe~Spe~y~~~lk~~G~d~~s~~~ri~i~D~ysDPLGW~~~~~~~~~~~~~s~~~~~~~~v~~L~sl~~~i  133 (272)
                      +++.|..+.+|-+++....-.++.|++    ..++.+.+.                              .++..++..+
T Consensus       109 ~g~~VlYvs~EEs~~qi~~Ra~rlg~~----~~~l~l~~e------------------------------~~le~I~~~i  154 (372)
T cd01121         109 RGGKVLYVSGEESPEQIKLRADRLGIS----TENLYLLAE------------------------------TNLEDILASI  154 (372)
T ss_pred             cCCeEEEEECCcCHHHHHHHHHHcCCC----cccEEEEcc------------------------------CcHHHHHHHH
Confidence            457888889999998887766666666    233433220                              0122222222


Q ss_pred             HHhccCccCCCCCcEEEEEechhHHHHhc------ChHHHHHHHHhhhc---CCceeEE-EeeecccccchhhHhHHhhh
Q 024144          134 IEQGKGLIGQGKDRFSIAIDSVSEMVRHA------SISSVAGILSNLRS---HDQVSSI-FWLLHSDLHEIKFTSVLEYL  203 (272)
Q Consensus       134 ~e~~~~~~~~~k~~~tVaIDSLS~LL~h~------s~~~vc~lL~~Lr~---~~~vssV-l~LLHsDLHe~~~v~ALe~L  203 (272)
                      .+        .++ -.|+|||++.+....      +..++-..+..|.+   ...+.-+ ++-+..|-+-.+ .+.|+|+
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            22        234 479999999996532      13444333333333   2223222 222333332222 2579999


Q ss_pred             heeEEEeec
Q 024144          204 SSMVASVEP  212 (272)
Q Consensus       204 Sstvvtv~P  212 (272)
                      +.+++.++-
T Consensus       225 vD~Vi~le~  233 (372)
T cd01121         225 VDTVLYFEG  233 (372)
T ss_pred             ceEEEEEEc
Confidence            999998764

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.

>TIGR02236 recomb_radA DNA repair and recombination protein RadA

Probab=89.08  E-value=17  Score=33.63  Aligned_cols=38  Identities=18%  Similarity=0.279  Sum_probs=29.7

Q ss_pred             eeEEEEeec--ChHHHHHHHhhcCcCccCCCCeEEEEecc
Q 024144           57 GLVVVAYSR--SPSFYVDLLKRRGIDIASSHDWIHILDCY   94 (272)
Q Consensus        57 ~Vhvl~fe~--Spe~y~~~lk~~G~d~~s~~~ri~i~D~y   94 (272)
                      .+..+.+|-  +|+.+.+.++..|++.+...+++.+..++
T Consensus       131 ~~~yi~te~~f~~~rl~~~~~~~gl~~~~~~~~i~i~~~~  170 (310)
T TIGR02236       131 KAVYIDTENTFRPERIMQMAEARGLDPDEVLKNIYVARAY  170 (310)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHcCCCHHHHhhceEEEecC
Confidence            788888888  79999999998888865545667777654

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.

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

Probab=88.05  E-value=9.9  Score=32.92  Aligned_cols=39  Identities=26%  Similarity=0.281  Sum_probs=27.6

Q ss_pred             ceeEEEEeecC--hHHHHHHHhhcCcCccCCCCeEEEEecc
Q 024144           56 RGLVVVAYSRS--PSFYVDLLKRRGIDIASSHDWIHILDCY   94 (272)
Q Consensus        56 ~~Vhvl~fe~S--pe~y~~~lk~~G~d~~s~~~ri~i~D~y   94 (272)
                      ..|..+..|.+  ++.+.+.....+.+.....+++++.+++
T Consensus        54 ~~v~yi~~e~~~~~~rl~~~~~~~~~~~~~~~~~i~~~~~~   94 (226)
T cd01393          54 GKVVYIDTEGAFRPERLVQLAVRFGLDPEEVLDNIYVARPY   94 (226)
T ss_pred             ceEEEEecCCCCCHHHHHHHHHHhccchhhhhccEEEEeCC
Confidence            77888888876  6677777777776655445677777763

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.

>PTZ00035 Rad51 protein; Provisional

Probab=87.63  E-value=27  Score=33.54  Aligned_cols=40  Identities=20%  Similarity=0.272  Sum_probs=29.4

Q ss_pred             cceeEEEEeec--ChHHHHHHHhhcCcCccCCCCeEEEEecc
Q 024144           55 SRGLVVVAYSR--SPSFYVDLLKRRGIDIASSHDWIHILDCY   94 (272)
Q Consensus        55 ~~~Vhvl~fe~--Spe~y~~~lk~~G~d~~s~~~ri~i~D~y   94 (272)
                      +..+..+..|.  +|+...+..++.|++.+..-.++.+.++|
T Consensus       152 ~g~vvyIdtE~~f~~eri~~ia~~~g~~~~~~l~nI~~~~~~  193 (337)
T PTZ00035        152 EGKVLYIDTEGTFRPERIVQIAERFGLDPEDVLDNIAYARAY  193 (337)
T ss_pred             CceEEEEEccCCCCHHHHHHHHHHhCCChHhHhhceEEEccC
Confidence            45677888887  48888888888888876655667666654

>cd01123 Rad51_DMC1_radA Rad51_DMC1_radA,B

Probab=87.40  E-value=6  Score=34.48  Aligned_cols=40  Identities=23%  Similarity=0.284  Sum_probs=31.3

Q ss_pred             cceeEEEEeec--ChHHHHHHHhhcCcCccCCCCeEEEEecc
Q 024144           55 SRGLVVVAYSR--SPSFYVDLLKRRGIDIASSHDWIHILDCY   94 (272)
Q Consensus        55 ~~~Vhvl~fe~--Spe~y~~~lk~~G~d~~s~~~ri~i~D~y   94 (272)
                      .+++..+.+|.  +++.+.+.+++.|.+.....+++++.++|
T Consensus        53 ~~~viyi~~e~~~~~~rl~~~~~~~~~~~~~~~~~i~~~~~~   94 (235)
T cd01123          53 EGKAVYIDTEGTFRPERLVQIAERFGLDPEEVLDNIYVARAY   94 (235)
T ss_pred             CccEEEEeCCCCcCHHHHHHHHHHhccChHhHhcCEEEEecC
Confidence            46788888888  57888888888888776656778887764

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 .

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

Probab=86.16  E-value=22  Score=32.22  Aligned_cols=153  Identities=17%  Similarity=0.278  Sum_probs=90.8

Q ss_pred             ceeecccCCCCchhhHHHHHHHHHHHHHHhhccccceeEEEEeecChHHHHHHHhhcCcCccCCCCeEEEEe--------
Q 024144           21 ALTIKDSKASPFGFDVFNYVLTQLSNYILAGKSQSRGLVVVAYSRSPSFYVDLLKRRGIDIASSHDWIHILD--------   92 (272)
Q Consensus        21 ~l~i~Dsl~~~~g~~v~~h~~~~l~s~i~a~~~q~~~Vhvl~fe~Spe~y~~~lk~~G~d~~s~~~ri~i~D--------   92 (272)
                      +++|+-+-.++  +.++      ++..++.++.++-.|.|..+==+-..|..-|+..|+|.+. -+++-++-        
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            56777665333  3333      4556667888888999998888888999999999999775 12233332        


Q ss_pred             -------ccCCCCCCcccccCCccccccccccccccchhhhhHHHHHHHHhccCccCCCCCcEEEEEechhHHH--HhcC
Q 024144           93 -------CYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNLDKLYSLIIEQGKGLIGQGKDRFSIAIDSVSEMV--RHAS  163 (272)
Q Consensus        93 -------~ysDPLGW~~~~~~~~~~~~~s~~~~~~~~v~~L~sl~~~i~e~~~~~~~~~k~~~tVaIDSLS~LL--~h~s  163 (272)
                             ..+||--|.                          +.+..+.+.   ...  +.++...+=-+.-++  ...+
T Consensus        84 nVv~ri~~~~d~~~~~--------------------------k~Y~~~~~~---~~~--~~~~i~ivlGiekl~~~~~~~  132 (210)
T PF03192_consen   84 NVVGRIPITSDPSVYL--------------------------KEYEEILEK---VLE--KEKVINIVLGIEKLFYFFENS  132 (210)
T ss_dssp             EEEEEE-----BBTTB--------------------------HHHHHHHTT--------S-SEEEEEE-HHHHH-HH-S-
T ss_pred             eEEEEEecccChHHHH--------------------------HHHHHHHHH---Hhc--cCCeEEEEecHHHHHHHHhcc
Confidence                   222222222                          222333332   111  222555555677777  4468


Q ss_pred             hHHHHHHHHhhhcC--CceeEEEeeecccccch---hhHhHHhhhheeEEEeecC
Q 024144          164 ISSVAGILSNLRSH--DQVSSIFWLLHSDLHEI---KFTSVLEYLSSMVASVEPF  213 (272)
Q Consensus       164 ~~~vc~lL~~Lr~~--~~vssVl~LLHsDLHe~---~~v~ALe~LSstvvtv~P~  213 (272)
                      ...+..++..+.+.  ..=..-|..+..|+-+.   .++..||-+||+|+.+...
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  33445788999999986   8888999999999999874

; PDB: 2EKD_C.

>TIGR02238 recomb_DMC1 meiotic recombinase Dmc1

Probab=84.69  E-value=23  Score=33.75  Aligned_cols=41  Identities=17%  Similarity=0.208  Sum_probs=32.5

Q ss_pred             ccceeEEEEeecC--hHHHHHHHhhcCcCccCCCCeEEEEecc
Q 024144           54 QSRGLVVVAYSRS--PSFYVDLLKRRGIDIASSHDWIHILDCY   94 (272)
Q Consensus        54 q~~~Vhvl~fe~S--pe~y~~~lk~~G~d~~s~~~ri~i~D~y   94 (272)
                      .+..+..+.+|-+  |+.+.+.+++.|+|++..-+++.+.++|
T Consensus       129 ~~~~vvYIdtE~~f~~eRi~~~a~~~g~d~~~~l~~i~~~~~~  171 (313)
T TIGR02238       129 GNGKVAYIDTEGTFRPDRIRAIAERFGVDPDAVLDNILYARAY  171 (313)
T ss_pred             CCCeEEEEEcCCCCCHHHHHHHHHHcCCChHHhcCcEEEecCC
Confidence            3568889999994  9999999999999977655677766655

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.

>cd01394 radB RadB

Probab=81.91  E-value=28  Score=30.14  Aligned_cols=64  Identities=23%  Similarity=0.127  Sum_probs=35.1

Q ss_pred             EEEEEechhHHHHhcCh---------HHHHHHHHhhhc----CCceeEEEeeeccccc----chhhHhHHhhhheeEEEe
Q 024144          148 FSIAIDSVSEMVRHASI---------SSVAGILSNLRS----HDQVSSIFWLLHSDLH----EIKFTSVLEYLSSMVASV  210 (272)
Q Consensus       148 ~tVaIDSLS~LL~h~s~---------~~vc~lL~~Lr~----~~~vssVl~LLHsDLH----e~~~v~ALe~LSstvvtv  210 (272)
                      -.|+|||++.+.+....         ..+.+.++.|+.    +....=+.+-+..+..    .|.--..++|++.+++.+
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            48999999999753221         134555444443    2322222333333332    122122689999999988


Q ss_pred             e
Q 024144          211 E  211 (272)
Q Consensus       211 ~  211 (272)
                      .
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.

>PLN03187 meiotic recombination protein DMC1 homolog; Provisional

Probab=80.48  E-value=14  Score=35.81  Aligned_cols=39  Identities=21%  Similarity=0.256  Sum_probs=31.9

Q ss_pred             ceeEEEEeec--ChHHHHHHHhhcCcCccCCCCeEEEEecc
Q 024144           56 RGLVVVAYSR--SPSFYVDLLKRRGIDIASSHDWIHILDCY   94 (272)
Q Consensus        56 ~~Vhvl~fe~--Spe~y~~~lk~~G~d~~s~~~ri~i~D~y   94 (272)
                      ..+..+.+|.  +|+-+.+..++.|+|++..-++|.+.++|
T Consensus       161 ~~vvyIdTE~tF~peRl~~ia~~~g~d~~~~l~~I~~~~~~  201 (344)
T PLN03187        161 GKVAYIDTEGTFRPDRIVPIAERFGMDADAVLDNIIYARAY  201 (344)
T ss_pred             ceEEEEEcCCCCCHHHHHHHHHHcCCChhhhcCeEEEecCC
Confidence            5788999998  79999999999999977655677766654

---

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	272
4a8j_B	270	Elongator complex protein 5; transcription; 2.10A	98.77
3bs4_A	260	Uncharacterized protein PH0321; structural genomic	98.0
4a8j_C	280	Elongator complex protein 6; transcription; 2.10A	97.93
2zts_A	251	Putative uncharacterized protein PH0186; KAIC like	95.77
2dr3_A	247	UPF0273 protein PH0284; RECA superfamily ATPase, h	94.84
3bh0_A	315	DNAB-like replicative helicase; ATPase, replicatio	94.47
2i1q_A	322	DNA repair and recombination protein RADA; ATPase,	94.39
2z43_A	324	DNA repair and recombination protein RADA; archaea	93.14
2w0m_A	235	SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus	92.71
2cvh_A	220	DNA repair and recombination protein RADB; filamen	90.3
1q57_A	503	DNA primase/helicase; dntpase, DNA replication, tr	88.52
4a8j_A	361	Elongator complex protein 4; transcription; 2.10A	88.17
3bgw_A	444	DNAB-like replicative helicase; ATPase, replicatio	86.63
1v5w_A	343	DMC1, meiotic recombination protein DMC1/LIM15 hom	83.59
2q6t_A	444	DNAB replication FORK helicase; hydrolase; 2.90A {	83.46
3cmu_A	2050	Protein RECA, recombinase A; homologous recombinat	80.81

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

Probab=98.77  E-value=7.4e-08  Score=88.48  Aligned_cols=106  Identities=15%  Similarity=0.243  Sum_probs=81.9

Q ss_pred             cEEEEEechhHHHHhcChHHHHHHHHhhhcCCceeEEEeeeccccc-------------chhhHhHHhhhheeEEEeecC
Q 024144          147 RFSIAIDSVSEMVRHASISSVAGILSNLRSHDQVSSIFWLLHSDLH-------------EIKFTSVLEYLSSMVASVEPF  213 (272)
Q Consensus       147 ~~tVaIDSLS~LL~h~s~~~vc~lL~~Lr~~~~vssVl~LLHsDLH-------------e~~~v~ALe~LSstvvtv~P~  213 (272)
                      +..|+||||..++.    ..+.++|+.+-. | -.++++--|.|+.             .|....-|.|||+++++|.|.
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            48999999999986    578888888885 5 4589999999974             566778899999999999999


Q ss_pred             Cccccccccccchhhhh----hccccceEEEEEEeccCCcEEEEEEEEE
Q 024144          214 NQAAFGQRVDLENLSML----EQNFRKGKFHVRFKRRNGRVRVMKYLLS  258 (272)
Q Consensus       214 ~~~~~~~~~~~~~~~~l----~~n~~k~~~~vr~KrRnGRV~~~~~~~~  258 (272)
                      .....-.|.--+.++-+    .-|...=++++..||++||=-.--|.|.
T Consensus       175 ~~~~~deE~l~~~l~k~~~P~glN~~~f~l~ltnrRKSGRsl~y~f~id  223 (270)
T 4a8j_B          175 LTGTLDTEEVSELLNEFRIPRGLNNDIFQLRLVNKRKSGRSLEYDFIVN  223 (270)
T ss_dssp             CCSSCCHHHHHHHHHTTCCCSSCSCSEEEEEEEEECTTSCEEEEEEEEE
T ss_pred             CCCCccHHHHHHHhhheecccccCCCeEEEEEEeccccCcceEEEEEEc
Confidence            88765554322222222    3466777888899999999877777664

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

Probab=98.00  E-value=0.00017  Score=65.20  Aligned_cols=163  Identities=13%  Similarity=0.114  Sum_probs=99.6

Q ss_pred             chhhHHHHHHHHHHHHHHhhccccceeEEEEeecChHHHHHHHhhcCcCccCC--CCeEEEEeccCCCCCCcccccCCcc
Q 024144           32 FGFDVFNYVLTQLSNYILAGKSQSRGLVVVAYSRSPSFYVDLLKRRGIDIASS--HDWIHILDCYTDPLGWKNWLIDKDI  109 (272)
Q Consensus        32 ~g~~v~~h~~~~l~s~i~a~~~q~~~Vhvl~fe~Spe~y~~~lk~~G~d~~s~--~~ri~i~D~ysDPLGW~~~~~~~~~  109 (272)
                      +|..+..+|+       .++..+++.+.+++||-+|++++.-++..|+|.+..  +.++.++|.|++..+......    
T Consensus        33 ~~~~l~~qfl-------~~g~~~Ge~~~~~~~~e~~~~l~~~~~~~G~dl~~~~~~g~l~i~d~~~~~~~~~~~~~----  101 (260)
T 3bs4_A           33 RGKDILFYIL-------SRKLKSDNLVGMFSISYPLQLIIRILSRFGVDVIKYLENHRLAIVDTFGSFHGIKATMP----  101 (260)
T ss_dssp             CHHHHHHHHH-------HHHHHTTCEEEEEECSSCHHHHHHHHHHTTCCHHHHHHTTSEEEECHHHHHHTC---CT----
T ss_pred             cHHHHHHHHH-------HHHHHCCCcEEEEEEeCCHHHHHHHHHHcCCCHHHHhhCCcEEEEEccccccccccccc----
Confidence            4565445544       367888999999999999999999999999997641  357999999885554333110    


Q ss_pred             ccccccccccc--cchhhhhHHHHHHHHhccC---ccC-CCCCcEEEEEechhHHHHhcChHHHHHHHHhhh--------
Q 024144          110 SQEASSLSSFC--QDVRNLDKLYSLIIEQGKG---LIG-QGKDRFSIAIDSVSEMVRHASISSVAGILSNLR--------  175 (272)
Q Consensus       110 ~~~~s~~~~~~--~~v~~L~sl~~~i~e~~~~---~~~-~~k~~~tVaIDSLS~LL~h~s~~~vc~lL~~Lr--------  175 (272)
                           ..+...  -++..+-.....+++..|.   ... -+..|+.++||||+.+..-.+....-+.+.++.        
T Consensus       102 -----~v~~~~~e~d~~~l~~~i~~iv~~~~~~~~i~~~~~~~rvv~vidsldsl~~~~~~~~~~~~~~~ll~~~~~~~~  176 (260)
T 3bs4_A          102 -----GVWYLEGMLSSETLPIKYAKAVEDHKKVWMDLNLFEGRELYGFAISMSGYLEVFTPEETLRYLETSAEVRYGHPA  176 (260)
T ss_dssp             -----TEECCCSCCCTTTHHHHHHHHHHHHHHHHHHTTCSTTCCEEEEEETGGGGGGTSCHHHHHHHHHHHHHHHHHCHH
T ss_pred             -----ceecccccCCHHHHHHHHHHHHHhhccccchhhccCCceEEEEEeecchHHHHhChhhHHHHHHHHHHhhhhHHH
Confidence                 000000  0233332212344443100   001 123457788888887777666655544444442        


Q ss_pred             --cCCceeEEEeeecccccchhhHhHHhhhheeEEEeec
Q 024144          176 --SHDQVSSIFWLLHSDLHEIKFTSVLEYLSSMVASVEP  212 (272)
Q Consensus       176 --~~~~vssVl~LLHsDLHe~~~v~ALe~LSstvvtv~P  212 (272)
                        +...+..++ ++. |.+.+.....+.++|-.||.+.-
T Consensus       177 ~~~~~~~ttil-~~~-~~~~~~~~~~l~~laD~VI~lr~  213 (260)
T 3bs4_A          177 YKKYPRGTNFW-LWE-GVKDKRVLLSVYRRADYVLKTRS  213 (260)
T ss_dssp             HHSSCCCEEEE-EEE-SCSCHHHHHHHHHHCSEEEEEEE
T ss_pred             HhccCCcEEEE-EEC-CCcccccccceEEEeeEEEEEEE
Confidence              214454444 455 77777777889999999999854

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

Probab=97.93  E-value=0.00028  Score=65.28  Aligned_cols=169  Identities=13%  Similarity=0.150  Sum_probs=110.1

Q ss_pred             cC-CCCCceeecccCCCCchhhHHHHHHHHHHHHHHhhc-------------cccceeEEEEeecChHHHHHHHhhcCcC
Q 024144           15 EG-EHAPALTIKDSKASPFGFDVFNYVLTQLSNYILAGK-------------SQSRGLVVVAYSRSPSFYVDLLKRRGID   80 (272)
Q Consensus        15 ~g-e~ap~l~i~Dsl~~~~g~~v~~h~~~~l~s~i~a~~-------------~q~~~Vhvl~fe~Spe~y~~~lk~~G~d   80 (272)
                      ++ +..-+++|...+.+..-=.+-.+    +.+.+....             .....|+++.|-+.+++|.+.+||-|+|
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            56 67788889999855432333333    223332111             1335799999999999999999999999


Q ss_pred             ccCCCCeEEEEeccCCCCCCccc-ccCCccccccccccccccchhhhhHHHHHHHHhccCccCCCCCcEEEEEechhHHH
Q 024144           81 IASSHDWIHILDCYTDPLGWKNW-LIDKDISQEASSLSSFCQDVRNLDKLYSLIIEQGKGLIGQGKDRFSIAIDSVSEMV  159 (272)
Q Consensus        81 ~~s~~~ri~i~D~ysDPLGW~~~-~~~~~~~~~~s~~~~~~~~v~~L~sl~~~i~e~~~~~~~~~k~~~tVaIDSLS~LL  159 (272)
                      .    .++.|+|||||..  .++ ..  .+   ..   .   ..+++.+++..++...      ++ +.+|+||..-.||
T Consensus       107 l----~~f~fvD~~tdl~--~~~~~~--kp---~~---~---~l~~v~~~f~~~i~~~------~~-~~vlIldqpdlLL  162 (280)
T 4a8j_C          107 S----NNYNVLDFLSDFI--VNNIHN--KP---RD---K---ILSDVLAKFSAAIQNN------PT-DTIVIIEQPELLL  162 (280)
T ss_dssp             G----GGEEEEESSTTHH--HHHTTT--CC---HH---H---HHHHHHHHHHHHHHTS------TT-SEEEEEECGGGHH
T ss_pred             h----hheeEEEecchhh--hhcccC--Cc---ch---h---hhHHHHHHHhhhhhcc------CC-CeEEEEcChHHHH
Confidence            5    5799999999998  111 01  00   00   0   1245555555554421      12 3799999998887


Q ss_pred             Hh---cChHHH-HHHHHhhhcCCceeEEEeeecccc---cc----------hhhHhHHhhhheeEEEeecC
Q 024144          160 RH---ASISSV-AGILSNLRSHDQVSSIFWLLHSDL---HE----------IKFTSVLEYLSSMVASVEPF  213 (272)
Q Consensus       160 ~h---~s~~~v-c~lL~~Lr~~~~vssVl~LLHsDL---He----------~~~v~ALe~LSstvvtv~P~  213 (272)
                      --   ....++ -..|..|++... ..|+.+ -.|.   |+          ..++-.+-|.|.++++|.|+
T Consensus       163 a~t~~it~~~L~~~~I~~L~k~~~-~lvvt~-saD~pli~~~~~t~~~~e~a~f~~~l~H~A~~visLrpL  231 (280)
T 4a8j_C          163 SLVSGLTCSELNNKFITPLLRQCK-VLIIVS-NSDIFNIDEYDASVHSSNLQNFYKSSFIKSMINLNLNPL  231 (280)
T ss_dssp             HHSTTCCHHHHHHHTHHHHHHTCS-EEEEEE-ECGGGCCSSCCHHHHTHHHHHHHHHHHHHCSEEEEEECC
T ss_pred             HhccCCCHHHHHHHHHHHHHHhcc-eEEEEe-ccCccccccCCCCchHHHHHHHHHHHHHHhheEEeeccc
Confidence            74   456666 888899987432 233332 3333   31          35778899999999999997

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

Probab=95.77  E-value=0.3  Score=40.39  Aligned_cols=172  Identities=11%  Similarity=0.044  Sum_probs=81.7

Q ss_pred             CCCCCceeecccCCCCchhhHHHHHHHHHHHHHHhhccccceeEEEEeecChHHHHHHHhhcCcCccC--CCCeEEEEec
Q 024144           16 GEHAPALTIKDSKASPFGFDVFNYVLTQLSNYILAGKSQSRGLVVVAYSRSPSFYVDLLKRRGIDIAS--SHDWIHILDC   93 (272)
Q Consensus        16 ge~ap~l~i~Dsl~~~~g~~v~~h~~~~l~s~i~a~~~q~~~Vhvl~fe~Spe~y~~~lk~~G~d~~s--~~~ri~i~D~   93 (272)
                      |=+++.+++-=--...+=+.+..+++.      .+.+..++.|.++.+|-+++.+.+-+.+.|.+.+.  ...++.+.|.
T Consensus        26 Gl~~G~l~~i~G~pG~GKT~l~l~~~~------~~~~~~~~~v~~~s~E~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~   99 (251)
T 2zts_A           26 GFPEGTTVLLTGGTGTGKTTFAAQFIY------KGAEEYGEPGVFVTLEERARDLRREMASFGWDFEKYEKEGKIAIVDG   99 (251)
T ss_dssp             SEETTCEEEEECCTTSSHHHHHHHHHH------HHHHHHCCCEEEEESSSCHHHHHHHHHTTTCCHHHHHHTTSEEEEC-
T ss_pred             CCCCCeEEEEEeCCCCCHHHHHHHHHH------HHHHhcCCCceeecccCCHHHHHHHHHHcCCChHHHHhcCcchhhhh
Confidence            444554444333333333444444332      12334577899999999999999988887776443  2346889998


Q ss_pred             cCCCCCCcccccCCccccccccccccccchhhhhHHHHHHHHhccCccCCCCCcEEEEEechhHHHHhcC-hHHHHHHHH
Q 024144           94 YTDPLGWKNWLIDKDISQEASSLSSFCQDVRNLDKLYSLIIEQGKGLIGQGKDRFSIAIDSVSEMVRHAS-ISSVAGILS  172 (272)
Q Consensus        94 ysDPLGW~~~~~~~~~~~~~s~~~~~~~~v~~L~sl~~~i~e~~~~~~~~~k~~~tVaIDSLS~LL~h~s-~~~vc~lL~  172 (272)
                      ++...+-.......         ........++.......++.       .++ -.|+||+++.+....+ ...+...++
T Consensus       100 ~~~~~~~~~~~~~~---------~~~~~~~~~~~~~~~~~~~~-------~~~-~~vviD~~~~l~~~~~~~~~~~~~~~  162 (251)
T 2zts_A          100 VSSVVGLPSEEKFV---------LEDRFNVDNFLRYIYRVVKA-------INA-KRLVIDSIPSIALRLEEERKIREVLL  162 (251)
T ss_dssp             ---------------------------CCHHHHHHHHHHHHHH-------TTC-SEEEEECHHHHHHHSSSGGGHHHHHH
T ss_pred             HHHHhhcccchhcc---------ccccccHHHHHHHHHHHHHh-------cCC-cEEEEEcHHHHhhhccChHHHHHHHH
Confidence            87765433311100         00000122222221222221       233 4789999999987553 233344444


Q ss_pred             hhhcC---CceeEEEeeecc---cccchhhHhHHhhhheeEEEee
Q 024144          173 NLRSH---DQVSSIFWLLHS---DLHEIKFTSVLEYLSSMVASVE  211 (272)
Q Consensus       173 ~Lr~~---~~vssVl~LLHs---DLHe~~~v~ALe~LSstvvtv~  211 (272)
                      .|.+.   -.+. ++.+-|.   +.-.....+.++++|.+++.+.
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            44431   1111 2222221   1112233456789999988874

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

Probab=94.84  E-value=0.53  Score=38.94  Aligned_cols=140  Identities=14%  Similarity=0.153  Sum_probs=72.6

Q ss_pred             cccceeEEEEeecChHHHHHHHhhcCcCccCC--CCeEEEEeccCCCCCCcccccCCcccccccccccc--ccchhhhhH
Q 024144           53 SQSRGLVVVAYSRSPSFYVDLLKRRGIDIASS--HDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSF--CQDVRNLDK  128 (272)
Q Consensus        53 ~q~~~Vhvl~fe~Spe~y~~~lk~~G~d~~s~--~~ri~i~D~ysDPLGW~~~~~~~~~~~~~s~~~~~--~~~v~~L~s  128 (272)
                      .+++.+.++.+|.++++..+-+++.|++....  ..++.+.|+|.+-++.......          +..  +.++.++..
T Consensus        49 ~~~~~v~~~~~e~~~~~~~~~~~~~g~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~----------~~~~~~~~~~~~~~  118 (247)
T 2dr3_A           49 KMGEPGIYVALEEHPVQVRQNMAQFGWDVKPYEEKGMFAMVDAFTAGIGKSKEYEK----------YIVHDLTDIREFIE  118 (247)
T ss_dssp             HTTCCEEEEESSSCHHHHHHHHHTTTCCCHHHHHHTSEEEEECSTTTTCC--CCCS----------CBCSCCSSHHHHHH
T ss_pred             hcCCeEEEEEccCCHHHHHHHHHHcCCCHHHHhhCCcEEEEecchhhccccccccc----------ccccCccCHHHHHH
Confidence            35789999999999999988888888875431  2368999987654432110000          000  012222222


Q ss_pred             HHHHHHHhccCccCCCCCcEEEEEechhHHHHhcChHHHHHHHHhhhc---CCceeEEEeeecccccchhh-HhHHhhhh
Q 024144          129 LYSLIIEQGKGLIGQGKDRFSIAIDSVSEMVRHASISSVAGILSNLRS---HDQVSSIFWLLHSDLHEIKF-TSVLEYLS  204 (272)
Q Consensus       129 l~~~i~e~~~~~~~~~k~~~tVaIDSLS~LL~h~s~~~vc~lL~~Lr~---~~~vssVl~LLHsDLHe~~~-v~ALe~LS  204 (272)
                      ......+.       .++ -.|+||+++.++. ......-+.+..|.+   ... ..|+..-|..-.+... -.++++.+
T Consensus       119 ~i~~~~~~-------~~~-~~vviD~~~~l~~-~~~~~~~~~l~~l~~~~~~~~-~~vi~~~h~~~~~~~~~~~~~~~~~  188 (247)
T 2dr3_A          119 VLRQAIRD-------INA-KRVVVDSVTTLYI-NKPAMARSIILQLKRVLAGTG-CTSIFVSQVSVGERGFGGPGVEHGV  188 (247)
T ss_dssp             HHHHHHHH-------HTC-CEEEEETSGGGTT-TCGGGHHHHHHHHHHHHHHTT-CEEEEEEECC----CCC-CCHHHHS
T ss_pred             HHHHHHHH-------hCC-CEEEECCchHhhc-CCHHHHHHHHHHHHHHHHHCC-CeEEEEecCCCCcccccccccceeE
Confidence            22222221       123 3799999998872 222223333333332   122 2455455543221100 00367777


Q ss_pred             eeEEEeec
Q 024144          205 SMVASVEP  212 (272)
Q Consensus       205 stvvtv~P  212 (272)
                      .+++.+..
T Consensus       189 D~vi~L~~  196 (247)
T 2dr3_A          189 DGIIRLDL  196 (247)
T ss_dssp             SEEEEEEE
T ss_pred             EEEEEEEE
Confidence            88888864

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

Probab=94.47  E-value=0.61  Score=41.93  Aligned_cols=92  Identities=15%  Similarity=0.174  Sum_probs=48.9

Q ss_pred             EEEEEechhHHHHhcC----hHHHHHHHHhhhc---CCceeEEEeeec--ccc----------cchhhHhHHhhhheeEE
Q 024144          148 FSIAIDSVSEMVRHAS----ISSVAGILSNLRS---HDQVSSIFWLLH--SDL----------HEIKFTSVLEYLSSMVA  208 (272)
Q Consensus       148 ~tVaIDSLS~LL~h~s----~~~vc~lL~~Lr~---~~~vssVl~LLH--sDL----------He~~~v~ALe~LSstvv  208 (272)
                      ..|+||+|+.|-...+    ...+...++.|+.   .-.+ .|+.+-|  .+.          ..-+-.+++|++|.+++
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    1345555555543   1122 2444434  111          11223478999999999


Q ss_pred             EeecCCccccccccccchhhhhhccccceEEEEE-EeccCCcEEEE
Q 024144          209 SVEPFNQAAFGQRVDLENLSMLEQNFRKGKFHVR-FKRRNGRVRVM  253 (272)
Q Consensus       209 tv~P~~~~~~~~~~~~~~~~~l~~n~~k~~~~vr-~KrRnGRV~~~  253 (272)
                      .+.....   +.+.          ...++...++ .|.|||..-..
T Consensus       262 ~L~r~~~---~~~~----------~~~~~~~~l~v~K~R~G~~g~~  294 (315)
T 3bh0_A          262 FLYRDDY---YDKE----------SESKNIVEVIIAKHRDGPVGTV  294 (315)
T ss_dssp             EEEEHHH---HCTT----------CTTTTEEEEEEEEETTSCCEEE
T ss_pred             EEecccc---cCcc----------ccCCCcEEEEEECCcCCCCceE
Confidence            9975321   1000          0112333443 48999987653

>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=94.39  E-value=1.1  Score=39.88  Aligned_cols=150  Identities=9%  Similarity=0.047  Sum_probs=83.6

Q ss_pred             ceeEEEEeecC--hHHHHHHHhhcCcCccCCCCeEEEEeccCCCCCCcccccCCccccccccccccccchhhhhHHHHHH
Q 024144           56 RGLVVVAYSRS--PSFYVDLLKRRGIDIASSHDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNLDKLYSLI  133 (272)
Q Consensus        56 ~~Vhvl~fe~S--pe~y~~~lk~~G~d~~s~~~ri~i~D~ysDPLGW~~~~~~~~~~~~~s~~~~~~~~v~~L~sl~~~i  133 (272)
                      ..|..+.+|.+  |+...+.+++.|+|.+..-+++.+.+.++    ..                       ++..++..+
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            78999999987  88888888888888543223566655321    10                       111111122


Q ss_pred             HHhccCccCC-CCCcEEEEEechhHHHHhcC-----h----HHHHHHHHhhhcC---CceeEEEeeec--cccc------
Q 024144          134 IEQGKGLIGQ-GKDRFSIAIDSVSEMVRHAS-----I----SSVAGILSNLRSH---DQVSSIFWLLH--SDLH------  192 (272)
Q Consensus       134 ~e~~~~~~~~-~k~~~tVaIDSLS~LL~h~s-----~----~~vc~lL~~Lr~~---~~vssVl~LLH--sDLH------  192 (272)
                      .+..+    + .++ -.|+||||+.+.+..-     .    ..+.+.++.|++.   -.+ .|+..-|  .+..      
T Consensus       196 ~~~~~----~~~~~-~lvVIDsl~~l~~~~~~~~~~~~~r~~~~~~~~~~L~~la~~~~~-~vi~~nq~~~~~~~~~g~~  269 (322)
T 2i1q_A          196 EDLIQ----EGNNI-KLVVIDSLTSTFRNEYTGRGKLAERQQKLGRHMATLNKLADLFNC-VVLVTNQVSAKPDAFFGMA  269 (322)
T ss_dssp             HHHHH----TTCEE-EEEEEECSSHHHHHHCCCTTSHHHHHHHHHHHHHHHHHHHHHTTC-EEEEEECEECC-------C
T ss_pred             HHHHh----hccCc-cEEEEECcHHHHHHHhcCCccHHHHHHHHHHHHHHHHHHHHHhCC-EEEEECceeecCCCCCCCC
Confidence            22111    1 223 5899999999986411     1    2356666666541   122 2222222  2222      


Q ss_pred             -chhhHhHHhhhheeEEEeecCCccccccccccchhhhhhccccceEEEEEEeccCCcEEEEEEEEE
Q 024144          193 -EIKFTSVLEYLSSMVASVEPFNQAAFGQRVDLENLSMLEQNFRKGKFHVRFKRRNGRVRVMKYLLS  258 (272)
Q Consensus       193 -e~~~v~ALe~LSstvvtv~P~~~~~~~~~~~~~~~~~l~~n~~k~~~~vr~KrRnGRV~~~~~~~~  258 (272)
                       .|.--.++++.+.+++.+.....                 +   -++-...|-|+|......|.|.
T Consensus       270 ~~~~g~~~~~~~~d~~i~l~~~~~-----------------~---~r~~~v~k~~~~p~~~~~f~I~  316 (322)
T 2i1q_A          270 EQAIGGHIVGHAATFRFFVRKGKG-----------------D---KRVAKLYDSPHLPDAEAIFRIT  316 (322)
T ss_dssp             CEESSHHHHHHHCSEEEEEEECST-----------------T---EEEEEEEECSSSCCEEEEEEEE
T ss_pred             cCCCCcHHHHhcCcEEEEEEecCC-----------------C---eEEEEEEECCCCCCeEEEEEEe
Confidence             23334589999999999975320                 0   0233345778887766677775

>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=93.14  E-value=0.94  Score=40.69  Aligned_cols=153  Identities=13%  Similarity=0.037  Sum_probs=74.4

Q ss_pred             cceeEEEEeecC--hHHHHHHHhhcCcCccCCCCeEEEEeccCCCCCCcccccCCccccccccccccccchhhhhHHHHH
Q 024144           55 SRGLVVVAYSRS--PSFYVDLLKRRGIDIASSHDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNLDKLYSL  132 (272)
Q Consensus        55 ~~~Vhvl~fe~S--pe~y~~~lk~~G~d~~s~~~ri~i~D~ysDPLGW~~~~~~~~~~~~~s~~~~~~~~v~~L~sl~~~  132 (272)
                      +..+..+.+|.+  |+...+.+++.|++.+..-+++.+.+.++                           ..++..++..
T Consensus       141 ~~~vlyi~~e~~~~~~~l~~~~~~~g~~~~~~~~~l~~~~~~~---------------------------~~~~~~~l~~  193 (324)
T 2z43_A          141 SGKAVYIDTEGTFRWERIENMAKALGLDIDNVMNNIYYIRAIN---------------------------TDHQIAIVDD  193 (324)
T ss_dssp             SCEEEEEESSSCCCHHHHHHHHHHTTCCHHHHHHTEEEEECCS---------------------------HHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHhCCCHHHHhccEEEEeCCC---------------------------HHHHHHHHHH
Confidence            678999999987  88888888888887543223465555321                           0111111122


Q ss_pred             HHHhccCccCCCCCcEEEEEechhHHHHhc-----Ch----HHHHHHHHhhhcC----CceeEEEeeeccccc-------
Q 024144          133 IIEQGKGLIGQGKDRFSIAIDSVSEMVRHA-----SI----SSVAGILSNLRSH----DQVSSIFWLLHSDLH-------  192 (272)
Q Consensus       133 i~e~~~~~~~~~k~~~tVaIDSLS~LL~h~-----s~----~~vc~lL~~Lr~~----~~vssVl~LLHsDLH-------  192 (272)
                      +.+..+   ...++ -.|+|||++.+.+..     ..    ..+.+.++.|++.    ....=++.-+..+..       
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            222111   00133 589999999998641     11    2356666666552    111111112222222       


Q ss_pred             chhhHhHHhhhheeEEEeecCCccccccccccchhhhhhccccceEEEEEEeccCCcEEEEEEEEE
Q 024144          193 EIKFTSVLEYLSSMVASVEPFNQAAFGQRVDLENLSMLEQNFRKGKFHVRFKRRNGRVRVMKYLLS  258 (272)
Q Consensus       193 e~~~v~ALe~LSstvvtv~P~~~~~~~~~~~~~~~~~l~~n~~k~~~~vr~KrRnGRV~~~~~~~~  258 (272)
                      .|.--.++++.+.+++.+....       .          +  + ++--..|-|+|......|.|.
T Consensus       270 ~~~gg~~l~~~~d~~l~l~r~~-------~----------~--~-r~~~v~k~~~~p~~~~~f~I~  315 (324)
T 2z43_A          270 VAVGGHTLYHVPGIRIQLKKSR-------G----------N--R-RIARVVDAPHLPEGEVVFALT  315 (324)
T ss_dssp             ------------CEEEEEEECS-------T----------T--E-EEEEEEECSSSCCEEEEEEEE
T ss_pred             CCCchHHHHhhCcEEEEEEEcC-------C----------C--e-EEEEEEECCCCCceEEEEEEe
Confidence            2233347999999999997532       0          1  1 222334778887666677775

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

Probab=92.71  E-value=3.3  Score=33.44  Aligned_cols=138  Identities=12%  Similarity=0.074  Sum_probs=73.0

Q ss_pred             ccceeEEEEeecChHHHHHHHhhcCcCccCC-CCeEEEEeccCCCCCCcccccCCccccccccccccccchhhhhHHHHH
Q 024144           54 QSRGLVVVAYSRSPSFYVDLLKRRGIDIASS-HDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNLDKLYSL  132 (272)
Q Consensus        54 q~~~Vhvl~fe~Spe~y~~~lk~~G~d~~s~-~~ri~i~D~ysDPLGW~~~~~~~~~~~~~s~~~~~~~~v~~L~sl~~~  132 (272)
                      ++..|.++++|.+++.+...++..|++.... ...+.++|.+....+ ......           ..  +..++...+..
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            4668999999999998888777778775431 225778887765543 110000           00  23333332233


Q ss_pred             HHHhccCccCCCCCcEEEEEechhHHHH--hcChHHHHHHHHhhhcCCceeEEEeeecccccchhhH-hHHhhhheeEEE
Q 024144          133 IIEQGKGLIGQGKDRFSIAIDSVSEMVR--HASISSVAGILSNLRSHDQVSSIFWLLHSDLHEIKFT-SVLEYLSSMVAS  209 (272)
Q Consensus       133 i~e~~~~~~~~~k~~~tVaIDSLS~LL~--h~s~~~vc~lL~~Lr~~~~vssVl~LLHsDLHe~~~v-~ALe~LSstvvt  209 (272)
                      .....+     ++ ...|+||+++.++.  ......+.+.|..+.+...+ .|+..-|..-.+.+.. ..+++++..++.
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            222211     22 15899999999873  22345566666666432232 4444444321222222 458888988888


Q ss_pred             eec
Q 024144          210 VEP  212 (272)
Q Consensus       210 v~P  212 (272)
                      +.-
T Consensus       189 l~~  191 (235)
T 2w0m_A          189 FRR  191 (235)
T ss_dssp             EEE
T ss_pred             EEE
Confidence            865

>2cvh_A DNA repair and recombination protein RADB; filament formation, homologous recombination, ATPase domain, hyperthermophIle; HET: DNA; 2.20A {Thermococcus kodakarensis} PDB: 2cvf_A*

Probab=90.30  E-value=2.1  Score=34.68  Aligned_cols=153  Identities=10%  Similarity=0.142  Sum_probs=81.4

Q ss_pred             cccceeEEEEeec--ChHHHHHHHhhcCcCccCCCCeEEEEeccCCCCCCcccccCCccccccccccccccchhhhhHHH
Q 024144           53 SQSRGLVVVAYSR--SPSFYVDLLKRRGIDIASSHDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNLDKLY  130 (272)
Q Consensus        53 ~q~~~Vhvl~fe~--Spe~y~~~lk~~G~d~~s~~~ri~i~D~ysDPLGW~~~~~~~~~~~~~s~~~~~~~~v~~L~sl~  130 (272)
                      .++..+.++.+|.  +++.+.+.++..|++.+....++.+.+    |.++.                       ++...+
T Consensus        43 ~~~~~v~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~-----------------------~~~~~~   95 (220)
T 2cvh_A           43 LSGKKVAYVDTEGGFSPERLVQMAETRGLNPEEALSRFILFT----PSDFK-----------------------EQRRVI   95 (220)
T ss_dssp             HHCSEEEEEESSCCCCHHHHHHHHHTTTCCHHHHHHHEEEEC----CTTTS-----------------------HHHHHH
T ss_pred             HcCCcEEEEECCCCCCHHHHHHHHHhcCCChHHHhhcEEEEe----cCCHH-----------------------HHHHHH
Confidence            4577899999988  888888877766665332122333332    22111                       111121


Q ss_pred             HHHHHhccCccCCCCCcEEEEEechhHHHHhcCh-----HH---HHHHHHhhhcCCceeEEEeeecc--cc----cchhh
Q 024144          131 SLIIEQGKGLIGQGKDRFSIAIDSVSEMVRHASI-----SS---VAGILSNLRSHDQVSSIFWLLHS--DL----HEIKF  196 (272)
Q Consensus       131 ~~i~e~~~~~~~~~k~~~tVaIDSLS~LL~h~s~-----~~---vc~lL~~Lr~~~~vssVl~LLHs--DL----He~~~  196 (272)
                      ..+....+    + ++ -.|+||+++.++...+-     ..   +.+.|.++.+...+ .|+..-|.  +.    ..|.-
T Consensus        96 ~~~~~l~~----~-~~-~lliiD~~~~~l~~~~~~~~~~~~~~~~~~~L~~l~~~~~~-~vi~~~h~~~~~~~~~~~p~~  168 (220)
T 2cvh_A           96 GSLKKTVD----S-NF-ALVVVDSITAHYRAEENRSGLIAELSRQLQVLLWIARKHNI-PVIVINQVHFDSRTEMTKPVA  168 (220)
T ss_dssp             HHHHHHCC----T-TE-EEEEEECCCCCTTGGGGSSTTHHHHHHHHHHHHHHHHHHTC-CEEEEECSSSSCTTSSCCSCC
T ss_pred             HHHHHHhh----c-CC-CEEEEcCcHHHhhhcCchHHHHHHHHHHHHHHHHHHHHcCC-EEEEEeeEEEcCCCCccccCC
Confidence            22222211    2 33 58999999998865322     33   44445555432122 24433342  11    11222


Q ss_pred             HhHHhhhheeEEEeecCCccccccccccchhhhhhccccceEEEEEEeccCCcEEE-EEEEEE
Q 024144          197 TSVLEYLSSMVASVEPFNQAAFGQRVDLENLSMLEQNFRKGKFHVRFKRRNGRVRV-MKYLLS  258 (272)
Q Consensus       197 v~ALe~LSstvvtv~P~~~~~~~~~~~~~~~~~l~~n~~k~~~~vr~KrRnGRV~~-~~~~~~  258 (272)
                      ...+++++..++.+.....                 + .+-++.| .|.|+|.... ..|.|.
T Consensus       169 ~~~~~~~~d~vi~l~~~~~-----------------~-~~r~l~v-~K~r~~~~~~~~~f~I~  212 (220)
T 2cvh_A          169 EQTLGYRCKDILRLDKLPK-----------------P-GLRVAVL-ERHRFRPEGLMAYFRIT  212 (220)
T ss_dssp             CHHHHHTSSEEEEEEECSS-----------------T-TEEEEEE-EECSSSCTTCEEEEEEE
T ss_pred             CcceeecCcEEEEEEEecC-----------------C-CEEEEEE-EeCCCCCCCceEEEEEe
Confidence            3478999999999976431                 0 1223444 4888887644 456554

>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=88.52  E-value=9.2  Score=36.18  Aligned_cols=26  Identities=8%  Similarity=0.009  Sum_probs=19.2

Q ss_pred             cceeEEEEeecChHHHHHHH--hhcCcC
Q 024144           55 SRGLVVVAYSRSPSFYVDLL--KRRGID   80 (272)
Q Consensus        55 ~~~Vhvl~fe~Spe~y~~~l--k~~G~d   80 (272)
                      ++.|.++.+|-++++...=+  ...|++
T Consensus       271 g~~vl~~s~E~s~~~l~~r~~~~~~~~~  298 (503)
T 1q57_A          271 GKKVGLAMLEESVEETAEDLIGLHNRVR  298 (503)
T ss_dssp             CCCEEEEESSSCHHHHHHHHHHHHTTSC
T ss_pred             CCcEEEEeccCCHHHHHHHHHHHHcCCC
Confidence            78899999999999876632  334554

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

Probab=88.17  E-value=0.96  Score=42.98  Aligned_cols=89  Identities=22%  Similarity=0.262  Sum_probs=64.1

Q ss_pred             hhhHHHHHHHHhccCccCCCCCcEEEEEechhHHHHhc----ChHHHHHHHHhhhc----CCceeEEEeeecccccchhh
Q 024144          125 NLDKLYSLIIEQGKGLIGQGKDRFSIAIDSVSEMVRHA----SISSVAGILSNLRS----HDQVSSIFWLLHSDLHEIKF  196 (272)
Q Consensus       125 ~L~sl~~~i~e~~~~~~~~~k~~~tVaIDSLS~LL~h~----s~~~vc~lL~~Lr~----~~~vssVl~LLHsDLHe~~~  196 (272)
                      .+.+++..+.+..+.  + ++.-.=|+|=||-.-+...    ....+-++|+.||.    +.....++--+..+|-.+..
T Consensus       199 ~y~~lL~~I~~~i~~--~-~~~ilRIvI~SLgSP~wy~~~~~~~~~ll~FL~~LRaLlR~~~~~~v~~iTlP~~l~~~~l  275 (361)
T 4a8j_A          199 PVSTILSQIEQTIKR--N-DKKLIRIVIPSLLHPAMYPPKMFESSEIIGLMHGVRSLVKKYYERVVLFASISIDIITPPL  275 (361)
T ss_dssp             CHHHHHHHHHHHHHH--T-TTSEEEEEETTTTCTTTSCGGGGBHHHHHHHHHHHHHHHHHTTTTEEEEEEEECTTSCHHH
T ss_pred             hHHHHHHHHHHHHhc--C-CCceEEEEecCCCCcccCCCcccCHHHHHHHHHHHHHHHhhcCCceEEEEEEChHHcChHH
Confidence            344555555544432  1 2333678898887665433    36778999999987    34444567779999999999


Q ss_pred             HhHHhhhheeEEEeecCCcc
Q 024144          197 TSVLEYLSSMVASVEPFNQA  216 (272)
Q Consensus       197 v~ALe~LSstvvtv~P~~~~  216 (272)
                      +.-+|+|+-+++.|+|....
T Consensus       276 ~~rle~l~D~vi~L~pF~~~  295 (361)
T 4a8j_A          276 LVLLRNMFDSVINLEPFNQE  295 (361)
T ss_dssp             HHHHHHHCSEEEEEEECCHH
T ss_pred             HHHHHHhCcEEEEeeecCCc
Confidence            99999999999999998653

>3bgw_A DNAB-like replicative helicase; ATPase, replication; 3.91A {Bacillus phage SPP1}

Probab=86.63  E-value=7.1  Score=37.06  Aligned_cols=20  Identities=0%  Similarity=-0.120  Sum_probs=17.1

Q ss_pred             ccceeEEEEeecChHHHHHH
Q 024144           54 QSRGLVVVAYSRSPSFYVDL   73 (272)
Q Consensus        54 q~~~Vhvl~fe~Spe~y~~~   73 (272)
                      +++.|.++.+|-|+++...=
T Consensus       224 ~g~~vl~fSlEms~~ql~~R  243 (444)
T 3bgw_A          224 NDDVVNLHSLEMGKKENIKR  243 (444)
T ss_dssp             TTCEEEEECSSSCTTHHHHH
T ss_pred             cCCEEEEEECCCCHHHHHHH
Confidence            47889999999999987764

>1v5w_A DMC1, meiotic recombination protein DMC1/LIM15 homolog; DNA-binding protein, ring protein, octamer, AAA ATPase; 3.20A {Homo sapiens} SCOP: c.37.1.11 PDB: 2zjb_A

Probab=83.59  E-value=15  Score=33.15  Aligned_cols=39  Identities=13%  Similarity=0.192  Sum_probs=28.0

Q ss_pred             ccceeEEEEeecC--hHHHHHHHhhcCcCccCCCCeEEEEe
Q 024144           54 QSRGLVVVAYSRS--PSFYVDLLKRRGIDIASSHDWIHILD   92 (272)
Q Consensus        54 q~~~Vhvl~fe~S--pe~y~~~lk~~G~d~~s~~~ri~i~D   92 (272)
                      ++..+..+.+|.+  |+...+.+++.|++.+..-+++.+.+
T Consensus       155 ~~~~vlyi~~E~~~~~~~l~~~~~~~g~~~~~~l~~l~~~~  195 (343)
T 1v5w_A          155 PGGKIIFIDTENTFRPDRLRDIADRFNVDHDAVLDNVLYAR  195 (343)
T ss_dssp             CCCEEEEEESSSCCCHHHHHHHHHHTTCCHHHHHHTEEEEE
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHcCCCHHHHHhceeEee
Confidence            4678999999996  88888888888887542123465554

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

Probab=83.46  E-value=20  Score=33.40  Aligned_cols=30  Identities=10%  Similarity=0.138  Sum_probs=21.3

Q ss_pred             ccceeEEEEeecChHHHHHHH--hhcCcCccC
Q 024144           54 QSRGLVVVAYSRSPSFYVDLL--KRRGIDIAS   83 (272)
Q Consensus        54 q~~~Vhvl~fe~Spe~y~~~l--k~~G~d~~s   83 (272)
                      +++.|.++.+|-+++++..-+  ...|++...
T Consensus       228 ~g~~vl~~slE~~~~~l~~R~~~~~~~i~~~~  259 (444)
T 2q6t_A          228 EGVGVGIYSLEMPAAQLTLRMMCSEARIDMNR  259 (444)
T ss_dssp             TCCCEEEEESSSCHHHHHHHHHHHHTTCCTTT
T ss_pred             CCCeEEEEECCCCHHHHHHHHHHHHcCCCHHH
Confidence            467899999999999877632  244666433

>3cmu_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 4.20A {Escherichia coli}

Probab=80.81  E-value=2  Score=48.96  Aligned_cols=120  Identities=12%  Similarity=0.164  Sum_probs=70.3

Q ss_pred             ccccceeEEEEeecChHHHHHHHhhcCcCccCCCCeEEEEeccCCCCCCcccccCCccccccccccccccchhhhhHHHH
Q 024144           52 KSQSRGLVVVAYSRSPSFYVDLLKRRGIDIASSHDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNLDKLYS  131 (272)
Q Consensus        52 ~~q~~~Vhvl~fe~Spe~y~~~lk~~G~d~~s~~~ri~i~D~ysDPLGW~~~~~~~~~~~~~s~~~~~~~~v~~L~sl~~  131 (272)
                      ..+++.+..+.+|.+++..+  ++..|+|.+    ++.+.    +|.     .                  ..++..++.
T Consensus        59 ~~~Ge~vlYI~tEes~~~~r--a~~lG~dl~----~i~v~----~p~-----~------------------~e~ll~il~  105 (2050)
T 3cmu_A           59 QREGKTCAFIDAEHALDPIY--ARKLGVDID----NLLCS----QPD-----T------------------GEQALEICD  105 (2050)
T ss_dssp             HTTTCCEEEECTTSCCCHHH--HHHTTCCTT----TCEEE----CCS-----S------------------HHHHHHHHH
T ss_pred             hccCCceEEEEccCcchhhH--HhhhccCcc----cceec----CCC-----c------------------HHHHHHHHH
Confidence            34688999999999999887  466788743    34443    341     0                  112223333


Q ss_pred             HHHHhccCccCCCCCcEEEEEechhHHHHhcCh-------------HHHHHHHHhhhc----CCceeEEE-------eee
Q 024144          132 LIIEQGKGLIGQGKDRFSIAIDSVSEMVRHASI-------------SSVAGILSNLRS----HDQVSSIF-------WLL  187 (272)
Q Consensus       132 ~i~e~~~~~~~~~k~~~tVaIDSLS~LL~h~s~-------------~~vc~lL~~Lr~----~~~vssVl-------~LL  187 (272)
                      .+.+.       +++ -.|+||||+.+.+....             ..+-+++..|.+    +....=+.       +..
T Consensus       106 ~L~~~-------~~~-~lVVIDSISaL~~~~e~~~e~~d~~~~~raR~l~~~l~~L~~~ak~~gitVVlTNQv~~~~g~~  177 (2050)
T 3cmu_A          106 ALARS-------GAV-DVIVVDSVAALTPKAEIEGEIGDSHMGLAARMMSQAMRKLAGNLKQSNTLLIFINQIRMKIGVM  177 (2050)
T ss_dssp             HHHHH-------TCC-SEEEESCGGGCCCHHHHHSCSSSCCTTHHHHHHHHHHHHHHHHHHTTTCEEEEEECCEECTTCC
T ss_pred             HHHhc-------cCC-cEEEEcChHHhhhhcccccccccchhhHHHHHHHHHHHHHHHHHHHhCCeEEEEEecccccccc
Confidence            33332       122 48999999999875321             123344444443    32111111       112


Q ss_pred             cccccchhhHhHHhhhheeEEEeec
Q 024144          188 HSDLHEIKFTSVLEYLSSMVASVEP  212 (272)
Q Consensus       188 HsDLHe~~~v~ALe~LSstvvtv~P  212 (272)
                      +++-+.+..-.+++|++.+++.++=
T Consensus       178 fg~~~~~~gG~~l~~iaD~VI~L~r  202 (2050)
T 3cmu_A          178 FGNPETTTGGNALKFYASVRLDIRR  202 (2050)
T ss_dssp             SSCCEECSSHHHHHHHEEEEEEEEE
T ss_pred             cCcccccCCcchhhhhCcEEEEEEe
Confidence            3455667778899999999999964

---

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	272
d1tf7a2	242	Circadian clock protein KaiC {Synechococcus sp. st	95.74
d1xp8a1	268	RecA protein, ATPase-domain {Deinococcus radiodura	85.48
d1mo6a1	269	RecA protein, ATPase-domain {Mycobacterium tubercu	82.67
d1tf7a1	242	Circadian clock protein KaiC {Synechococcus sp. st	80.56

>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=95.74  E-value=0.052  Score=43.44  Aligned_cols=129  Identities=16%  Similarity=0.218  Sum_probs=77.1

Q ss_pred             hccccceeEEEEeecChHHHHHHHhhcCcCccC--CCCeEEEEeccCCCCCCcccccCCccccccccccccccchhhhhH
Q 024144           51 GKSQSRGLVVVAYSRSPSFYVDLLKRRGIDIAS--SHDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNLDK  128 (272)
Q Consensus        51 ~~~q~~~Vhvl~fe~Spe~y~~~lk~~G~d~~s--~~~ri~i~D~ysDPLGW~~~~~~~~~~~~~s~~~~~~~~v~~L~s  128 (272)
                      ...+++.+..+.+|-+++.+..-+++.|++.+.  -...+.+.|.|..-                       ....+   
T Consensus        50 ~~~~~~~~~~is~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----------------------~~~~~---  103 (242)
T d1tf7a2          50 ACANKERAILFAYEESRAQLLRNAYSWGMDFEEMERQNLLKIVCAYPES-----------------------AGLED---  103 (242)
T ss_dssp             HHTTTCCEEEEESSSCHHHHHHHHHTTSCCHHHHHHTTSEEECCCCGGG-----------------------SCHHH---
T ss_pred             HHHhccccceeeccCCHHHHHHHHHHcCCChHHHhhcCceEEEEeecch-----------------------hhHHH---
Confidence            457788899999999999999988888776433  01123333322110                       01111   


Q ss_pred             HHHHHHHhccCccCCCCCcEEEEEechhHHHHhcChHHHHHHHHhhhcC---CceeEEEeeecccccc---hhhHhHHhh
Q 024144          129 LYSLIIEQGKGLIGQGKDRFSIAIDSVSEMVRHASISSVAGILSNLRSH---DQVSSIFWLLHSDLHE---IKFTSVLEY  202 (272)
Q Consensus       129 l~~~i~e~~~~~~~~~k~~~tVaIDSLS~LL~h~s~~~vc~lL~~Lr~~---~~vssVl~LLHsDLHe---~~~v~ALe~  202 (272)
                      .+..+.+..+    +.++ -.++|||++.++...+...+-..+..|.+.   ..+. ++...|...-.   ......+++
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    2344 478999999999999988887777776652   2232 34444432221   222356889


Q ss_pred             hheeEEEee
Q 024144          203 LSSMVASVE  211 (272)
Q Consensus       203 LSstvvtv~  211 (272)
                      ++.+++.+.
T Consensus       178 ~ad~vi~l~  186 (242)
T d1tf7a2         178 ITDTIILLQ  186 (242)
T ss_dssp             TCSEEEEEE
T ss_pred             ecceEEEEE
Confidence            999998884

>d1xp8a1 c.37.1.11 (A:15-282) RecA protein, ATPase-domain {Deinococcus radiodurans [TaxId: 1299]}

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: RecA protein, ATPase-domain
species: Deinococcus radiodurans [TaxId: 1299]

Probab=85.48  E-value=2.7  Score=35.54  Aligned_cols=119  Identities=14%  Similarity=0.182  Sum_probs=57.9

Q ss_pred             ccceeEEEEeecChHHHHHHHhhcCcCccCCCCeEEEEeccCCCCCCcccccCCccccccccccccccchhhhhHHHHHH
Q 024144           54 QSRGLVVVAYSRSPSFYVDLLKRRGIDIASSHDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNLDKLYSLI  133 (272)
Q Consensus        54 q~~~Vhvl~fe~Spe~y~~~lk~~G~d~~s~~~ri~i~D~ysDPLGW~~~~~~~~~~~~~s~~~~~~~~v~~L~sl~~~i  133 (272)
                      ++..+..+..|.+-+.  +.+++.|+|+    ++++|..    |.                       +..+...++...
T Consensus        84 ~g~~v~yiDtE~~~~~--~~a~~~Gvd~----d~i~~~~----~~-----------------------~~E~~~~~~~~l  130 (268)
T d1xp8a1          84 AGGTCAFIDAEHALDP--VYARALGVNT----DELLVSQ----PD-----------------------NGEQALEIMELL  130 (268)
T ss_dssp             TTCCEEEEESSCCCCH--HHHHHTTCCG----GGCEEEC----CS-----------------------SHHHHHHHHHHH
T ss_pred             CCCEEEEEECCccCCH--HHHHHhCCCc----hhEEEEc----CC-----------------------CHHHHHHHHHHH
Confidence            4556777887755432  2455779994    4566554    21                       122222333444


Q ss_pred             HHhccCccCCCCCcEEEEEechhHHHHhcCh-------------HHHHHHHHhhhc----C-------CceeEEEeeecc
Q 024144          134 IEQGKGLIGQGKDRFSIAIDSVSEMVRHASI-------------SSVAGILSNLRS----H-------DQVSSIFWLLHS  189 (272)
Q Consensus       134 ~e~~~~~~~~~k~~~tVaIDSLS~LL~h~s~-------------~~vc~lL~~Lr~----~-------~~vssVl~LLHs  189 (272)
                      ++.       ++. -+|+|||++.|.-+...             ..+...++.|..    +       .|+..-.+..++
T Consensus       131 ~~~-------~~~-~liIiDSi~al~~r~e~~~~~~~~~~~~~a~~l~~~lr~l~~~~~~~~~~vi~tNQv~~~~g~~~g  202 (268)
T d1xp8a1         131 VRS-------GAI-DVVVVDSVAALTPRAEIEGDMGDSLPGLQARLMSQALRKLTAILSKTGTAAIFINQVREKIGVMYG  202 (268)
T ss_dssp             HTT-------TCC-SEEEEECTTTCCCSTTC--------CCHHHHHHHHHHHHHHHHHTTTCCEEEEEEEC---------
T ss_pred             Hhc-------CCC-cEEEEecccccccHHHHcccccchhHHHHHHHHHHHHHHHHhhhhhcCCeEEEEeEEeeccccccC
Confidence            332       222 48999999988722211             113444444443    2       233333333343


Q ss_pred             cccchhhHhHHhhhheeEEEeecC
Q 024144          190 DLHEIKFTSVLEYLSSMVASVEPF  213 (272)
Q Consensus       190 DLHe~~~v~ALe~LSstvvtv~P~  213 (272)
                      |-=.+.==.+|.|.|++.+.+...
T Consensus       203 ~~~~~~GG~al~~~ss~rl~l~k~  226 (268)
T d1xp8a1         203 NPETTTGGRALKFYASVRLDVRKI  226 (268)
T ss_dssp             ------CHHHHHHHCSEEEEEEEE
T ss_pred             cceeecccchhhhceeEEEEEEec
Confidence            311122237999999999999654

>d1mo6a1 c.37.1.11 (A:1-269) RecA protein, ATPase-domain {Mycobacterium tuberculosis [TaxId: 1773]}

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: RecA protein, ATPase-domain
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=82.67  E-value=2  Score=36.54  Aligned_cols=15  Identities=20%  Similarity=0.359  Sum_probs=13.6

Q ss_pred             hHHhhhheeEEEeec
Q 024144          198 SVLEYLSSMVASVEP  212 (272)
Q Consensus       198 ~ALe~LSstvvtv~P  212 (272)
                      .++.|.|++.+.+..
T Consensus       214 ~al~~~ss~rl~l~k  228 (269)
T d1mo6a1         214 KALKFYASVRMDVRR  228 (269)
T ss_dssp             HHHHHHCSEEEEEEE
T ss_pred             cceeeeeeEEEEEEe
Confidence            799999999999964

>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=80.56  E-value=9.5  Score=28.57  Aligned_cols=134  Identities=21%  Similarity=0.204  Sum_probs=71.2

Q ss_pred             ccceeEEEEeecChHHHHHHHhhcCcCccC--CCCeEEEEeccCCCCCCcccccCCccccccccccccccchhhhhHHHH
Q 024144           54 QSRGLVVVAYSRSPSFYVDLLKRRGIDIAS--SHDWIHILDCYTDPLGWKNWLIDKDISQEASSLSSFCQDVRNLDKLYS  131 (272)
Q Consensus        54 q~~~Vhvl~fe~Spe~y~~~lk~~G~d~~s--~~~ri~i~D~ysDPLGW~~~~~~~~~~~~~s~~~~~~~~v~~L~sl~~  131 (272)
                      .+..+..+.+|-+++.+...+...+.+...  ...+....+.+.++.+|.....                  .+...++.
T Consensus        54 ~~~~~~~~s~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------------------~~~~~l~~  115 (242)
T d1tf7a1          54 FDEPGVFVTFEETPQDIIKNARSFGWDLAKLVDEGKLFILDASPDPEGQEVVGG------------------FDLSALIE  115 (242)
T ss_dssp             HCCCEEEEESSSCHHHHHHHHGGGTCCHHHHHHTTSEEEEECCCCSSCCSCCSS------------------HHHHHHHH
T ss_pred             cCCCcccccccCCHHHHHHHHHHcCCChHHHHHhcchhhhhhccchhhhhhhcc------------------ccHHHHHH
Confidence            445788899999999998888877666433  1223555565556665543111                  11122212


Q ss_pred             HHHHhccCccCCCCCcEEEEEechhHHHHhcChHHH-H----HHHHhhhcCCceeEEEeeec-cc-ccchhhHhHHhhhh
Q 024144          132 LIIEQGKGLIGQGKDRFSIAIDSVSEMVRHASISSV-A----GILSNLRSHDQVSSIFWLLH-SD-LHEIKFTSVLEYLS  204 (272)
Q Consensus       132 ~i~e~~~~~~~~~k~~~tVaIDSLS~LL~h~s~~~v-c----~lL~~Lr~~~~vssVl~LLH-sD-LHe~~~v~ALe~LS  204 (272)
                      .+.+..+    +.++ -.|+||+++.+.....-... -    +++..+++.. +. ++.+.| .+ .......+++++++
T Consensus       116 ~l~~~i~----~~~~-~~viiD~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~-~~-~~~~~~~~~~~~~~~~~~~~~~~~  188 (242)
T d1tf7a1         116 RINYAIQ----KYRA-RRVSIDSVTSVFQQYDASSVVRRELFRLVARLKQIG-AT-TVMTTERIEEYGPIARYGVEEFVS  188 (242)
T ss_dssp             HHHHHHH----HHTC-SEEEEECSTTTSTTTCCHHHHHHHHHHHHHHHHHHT-CE-EEEEEECSSSSSCSSTTSCHHHHC
T ss_pred             HHHHHHH----hhcc-chhhhhHHHHHHHhccChhHHHHHHHHHHHHHHhcC-Cc-eEEeecccccccccccCcceeeec
Confidence            2222111    1233 36899999988766553332 2    2233333222 22 222222 22 23344456788899


Q ss_pred             eeEEEeec
Q 024144          205 SMVASVEP  212 (272)
Q Consensus       205 stvvtv~P  212 (272)
                      .+++.+.-
T Consensus       189 d~i~~~~~  196 (242)
T d1tf7a1         189 DNVVILRN  196 (242)
T ss_dssp             SEEEEEEE
T ss_pred             cEEEEEEE
Confidence            88888754