Psyllid ID: psy17095

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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
MSSDLSSQPISEPSSPPINAGVGFAPPISLEDSARVCSRVPGLSFGQVRQCSLFADHMASVGRGAAESIAECQHQFRHHRWNCSSGGPGAGGGGGGKSESTTAPSVLPPTLHIGSREAAFTHAIATAGVVYAVARSCKDGSLPSCGCSRTARPKDLKREWLWGGCGDNLEYGYKGGKKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDEGRRR
Secondary Structure (PSIPRED)
ccccccccccccccccccccccccccccccccHHHHccccccccHHHHHHHHHcHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHccHHHHHHHHHHHHHHHHHHHHHccccccccccccccccHHHHcccccHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccHHHHHcccccccccHHHHHHHccccccccccccHHcccccccHHHHHHHHHcHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccHHHccccHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccEEccccccHHHHHHHHHHHccHHHHccccHHHHHHHHcccHHHHHHHHHHHHHHcccccccccEEHHHHHHcccHHHHHHHHHHHccccEEEEEEcccccccccccccccccccc
Coil and Loop (DISEMBL)
mssdlssqpisepssppinagvgfappisledsarvcsrvpglsfgqvrqCSLFADHMASVGRGAAESIAECQHQFrhhrwncssggpgaggggggksesttapsvlpptlhigsrEAAFTHAIATAGVVYAVARsckdgslpscgcsrtarpkdlkrewlwggcgdnleygykggkkeRRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKkkkdegrrr
Flexible Loop (DISEMBL)
mssdlssqpisepssppinAGVGFAPPISLEDSARVCSRVPGLSFGQVRQCSLFADHMASVGRGAAESIAECQHQFRHHRWNCSSGGPGAGGGGGGKSESTTAPSVLPPTLHIGSREAAFTHAIATAGVVYAVARSckdgslpscgcsrtarpkdlkrewlwggcgdnleygykggkkerrkqrrrkrkrkrkkeeeekeeekkeekkkekkkekkkekkkkekkkekkkkkkkkkekkkkkkekkkkkeekkkekkkkkkkkekkkkkdegrrr
Low Complexity Region (SEG)
MssdlssqpisepssppINAGVGFAPPISLEDSARVCSRVPGLSFGQVRQCSLFADHMASVGRGAAESIAECQHQFRHHRWNCSSggpgaggggggKSESTTAPSVLPPTLHIGSREAAFTHAIATAGVVYAVARSCKDGSLPSCGCSRTARPKDLKREWLWGGCGDNLEYGYKGGkkerrkqrrrkrkrkrkkeeeekeeekkeekkkekkkekkkekkkkekkkekkkkkkkkkekkkkkkekkkkkeekkkekkkkkkkkekkkkkDEGRRR
Disordered region (IsUnstruct)
***************************ISLEDSARVCSRVPGLSFGQVRQCSLFADHMASVGRGAAESIAECQHQFRHHRWN****************************LHIGSREAAFTHAIATAGVVYAVARSCKDGSLPSCGCSRTARPKDLKREWLWGGCGDNLEYGY******************************************************************************************************
Disordered Region (DISOPRED)
*SSDLSSQPISEPSSPPINAGVGFAPPISLEDSARVCSRVPGLSFGQVRQCSLFADHMASVGRGAAESIAECQHQFRHHRWNCSSGGPG****GGGKSESTTAPSVLPPTLHIGSREAAFTHAIATAGVVYAVARSCKDGSLPSCGCSRTARPKDLKREWLWGGCGDNLEYGYKGGK******************EEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEK******************************
Disordered Region (DISEMBL)
***************PPINAGVGFAPPISLEDSARVCSRVPGLSFGQVRQCSLFADHMASVGRGAAESIAECQHQFRHHRWNCSSGG****************PSVLPPTLHIGSREAAFTHAIATAGVVYAVARSCKDGSLPSCGCSRTARPKDLKREWLWGGCGDNLEYGYKG****************************************************************************************************
Disordered Region (DISPRO)
MSSDLSSQPISEPSSPPINAGVGFAPPISLEDSARVCSRVPGLSFGQVRQCSLFADHMASVGRGAAESIAECQHQFRHHRWNCSSG*****************PSVLPPTLHIGSREAAFTHAIATAGVVYAVARSCKDGSLPSCGCSRTARPKDLKREWLWGGCGDNLEYGYKGGKKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKKKEKK******************
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
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Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MSSDLSSQPISEPSSPPINAGVGFAPPISLEDSARVCSRVPGLSFGQVRQCSLFADHMASVGRGAAESIAECQHQFRHHRWNCSSGGPGAGGGGGGKSESTTAPSVLPPTLHIGSREAAFTHAIATAGVVYAVARSCKDGSLPSCGCSRTARPKDLKREWLWGGCGDNLEYGYKGGxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxRR
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	275	2.2.26 [Sep-21-2011]
Q9H1J7	359	Protein Wnt-5b OS=Homo sa	yes	N/A	0.567	0.434	0.488	9e-43
Q5NVK2	359	Protein Wnt-5b OS=Pongo a	yes	N/A	0.567	0.434	0.482	3e-42
P33945	360	Protein Wnt-5b OS=Xenopus	N/A	N/A	0.574	0.438	0.471	1e-41
Q06442	359	Protein Wnt-5a OS=Ambysto	N/A	N/A	0.527	0.403	0.506	2e-41
P31286	380	Protein Wnt-5a OS=Xenopus	N/A	N/A	0.563	0.407	0.476	4e-41
P22726	359	Protein Wnt-5b OS=Mus mus	yes	N/A	0.567	0.434	0.470	6e-41
Q27Q52	380	Protein Wnt-5a OS=Oryctol	no	N/A	0.589	0.426	0.437	7e-40
P41221	380	Protein Wnt-5a OS=Homo sa	no	N/A	0.589	0.426	0.437	7e-40
P22725	380	Protein Wnt-5a OS=Mus mus	no	N/A	0.589	0.426	0.437	8e-40
Q9QXQ7	380	Protein Wnt-5a OS=Rattus	no	N/A	0.589	0.426	0.437	1e-39

>sp|Q9H1J7|WNT5B_HUMAN Protein Wnt-5b OS=Homo sapiens GN=WNT5B PE=2 SV=2

 Score =  173 bits (439), Expect = 9e-43,   Method: Compositional matrix adjust.
 Identities = 84/172 (48%), Positives = 110/172 (63%), Gaps = 16/172 (9%)

Query: 26  PPISLEDSARVCSRVPGLSFGQVRQCSLFADHMASVGRGAAESIAECQHQFRHHRWNCSS 85
           P + +  +  VCS++PGLS GQ + C L+ +HMA +G GA   I ECQHQFR  RWNCS+
Sbjct: 37  PEMFIIGAQPVCSQLPGLSPGQRKLCQLYQEHMAYIGEGAKTGIKECQHQFRQRRWNCST 96

Query: 86  GGPGAGGGGGGKSESTTAPSVLPPTLHIGSREAAFTHAIATAGVVYAVARSCKDGSLPSC 145
                              SV    + IGSRE AFTHA++ AGVV A++R+C++G L +C
Sbjct: 97  ADNA---------------SVFGRVMQIGSRETAFTHAVSAAGVVNAISRACREGELSTC 141

Query: 146 GCSRTARPKDLKREWLWGGCGDNLEYGYKGGKKERRKQRRRKRKRKRKKEEE 197
           GCSRTARPKDL R+WLWGGCGDN+EYGY+   KE    R R++   +  EE+
Sbjct: 142 GCSRTARPKDLPRDWLWGGCGDNVEYGYRFA-KEFVDAREREKNFAKGSEEQ 192

Ligand for members of the frizzled family of seven transmembrane receptors. Probable developmental protein. May be a signaling molecule which affects the development of discrete regions of tissues. Is likely to signal over only few cell diameters.
Homo sapiens (taxid: 9606)

>sp|Q5NVK2|WNT5B_PONAB Protein Wnt-5b OS=Pongo abelii GN=WNT5B PE=2 SV=1

 Score =  172 bits (435), Expect = 3e-42,   Method: Compositional matrix adjust.
 Identities = 83/172 (48%), Positives = 110/172 (63%), Gaps = 16/172 (9%)

Query: 26  PPISLEDSARVCSRVPGLSFGQVRQCSLFADHMASVGRGAAESIAECQHQFRHHRWNCSS 85
           P + +  +  VCS++PGLS GQ + C L+ +HMA +G GA   I ECQHQFR  RWNCS+
Sbjct: 37  PEMFIIGAQPVCSQLPGLSPGQRKLCQLYQEHMAYIGEGAKTGIKECQHQFRQRRWNCST 96

Query: 86  GGPGAGGGGGGKSESTTAPSVLPPTLHIGSREAAFTHAIATAGVVYAVARSCKDGSLPSC 145
                              SV    + IGSRE AFT+A++ AGVV A++R+C++G L +C
Sbjct: 97  ---------------VDNASVFGRVMQIGSRETAFTYAVSAAGVVNAISRACREGELSTC 141

Query: 146 GCSRTARPKDLKREWLWGGCGDNLEYGYKGGKKERRKQRRRKRKRKRKKEEE 197
           GCSRTARPKDL R+WLWGGCGDN+EYGY+   KE    R R++   +  EE+
Sbjct: 142 GCSRTARPKDLPRDWLWGGCGDNVEYGYRFA-KEFVDAREREKNFAKGSEEQ 192

Ligand for members of the frizzled family of seven transmembrane receptors. Probable developmental protein. May be a signaling molecule which affects the development of discrete regions of tissues. Is likely to signal over only few cell diameters.

Pongo abelii (taxid: 9601)

>sp|P33945|WNT5B_XENLA Protein Wnt-5b OS=Xenopus laevis GN=wnt5b PE=2 SV=2

 Score =  170 bits (430), Expect = 1e-41,   Method: Compositional matrix adjust.
 Identities = 82/174 (47%), Positives = 111/174 (63%), Gaps = 16/174 (9%)

Query: 26  PPISLEDSARVCSRVPGLSFGQVRQCSLFADHMASVGRGAAESIAECQHQFRHHRWNCSS 85
           P + +  +  +CS++ GLS GQ + C L+ DHM  +G GA   I ECQHQF+H RWNCS+
Sbjct: 38  PEMFIIGAQPLCSQLTGLSPGQRKLCQLYQDHMVHIGEGAKTGIKECQHQFKHRRWNCST 97

Query: 86  GGPGAGGGGGGKSESTTAPSVLPPTLHIGSREAAFTHAIATAGVVYAVARSCKDGSLPSC 145
                              SV    + IGSREAAFT+AI++AGVV A++R+C++G L +C
Sbjct: 98  ---------------VDNNSVFGRVMQIGSREAAFTYAISSAGVVNAISRACREGELSTC 142

Query: 146 GCSRTARPKDLKREWLWGGCGDNLEYGYKGGKKERRKQRRRKRKRKRKKEEEEK 199
           GCSRT RPKDL R+WLWGGCGDN+EYGY+   KE    R R++   +  EE+ +
Sbjct: 143 GCSRTPRPKDLPRDWLWGGCGDNVEYGYRFA-KEFVDAREREKNFPKGSEEQAR 195

Ligand for members of the frizzled family of seven transmembrane receptors. Probable developmental protein. May be a signaling molecule which affects the development of discrete regions of tissues. Is likely to signal over only few cell diameters.

Xenopus laevis (taxid: 8355)

>sp|Q06442|WNT5A_AMBME Protein Wnt-5a OS=Ambystoma mexicanum GN=WNT-5A PE=2 SV=1

 Score =  169 bits (429), Expect = 2e-41,   Method: Compositional matrix adjust.
 Identities = 81/160 (50%), Positives = 103/160 (64%), Gaps = 15/160 (9%)

Query: 36  VCSRVPGLSFGQVRQCSLFADHMASVGRGAAESIAECQHQFRHHRWNCSSGGPGAGGGGG 95
           +CS++PGLS GQ + C L+ DHM  +G GA   I ECQ+QFRH RWNCS+          
Sbjct: 47  LCSQLPGLSPGQKKLCQLYQDHMPYIGEGAKTGIKECQYQFRHRRWNCST---------- 96

Query: 96  GKSESTTAPSVLPPTLHIGSREAAFTHAIATAGVVYAVARSCKDGSLPSCGCSRTARPKD 155
                    SV    + IGSRE AFT++I+ AGVV AV+R+C++G L +CGCSR ARPKD
Sbjct: 97  -----VDNASVFGRVMQIGSRETAFTYSISAAGVVNAVSRACREGELSTCGCSRAARPKD 151

Query: 156 LKREWLWGGCGDNLEYGYKGGKKERRKQRRRKRKRKRKKE 195
           L+R+WLWGGCGDNLEYGY+  K+    + R K   K   E
Sbjct: 152 LQRDWLWGGCGDNLEYGYRFAKEFVDAREREKIHTKGSYE 191

Ligand for members of the frizzled family of seven transmembrane receptors. Probable developmental protein. May be a signaling molecule which affects the development of discrete regions of tissues. Is likely to signal over only few cell diameters.

Ambystoma mexicanum (taxid: 8296)

>sp|P31286|WNT5A_XENLA Protein Wnt-5a OS=Xenopus laevis GN=wnt5a PE=2 SV=2

 Score =  168 bits (425), Expect = 4e-41,   Method: Compositional matrix adjust.
 Identities = 81/170 (47%), Positives = 106/170 (62%), Gaps = 15/170 (8%)

Query: 26  PPISLEDSARVCSRVPGLSFGQVRQCSLFADHMASVGRGAAESIAECQHQFRHHRWNCSS 85
           P + +  +  +CS++ GLS GQ + C L+ DHM  +G GA   I ECQ+QFRH RWNCS+
Sbjct: 58  PEVYIIGAQPLCSQLSGLSQGQKKLCQLYQDHMQFIGDGAKTGIKECQYQFRHRRWNCST 117

Query: 86  GGPGAGGGGGGKSESTTAPSVLPPTLHIGSREAAFTHAIATAGVVYAVARSCKDGSLPSC 145
                              SV    + IGSRE AFT+AI+ AGVV AV+R+C++G L +C
Sbjct: 118 ---------------VDNTSVFGRVMQIGSRETAFTYAISAAGVVNAVSRACREGELSTC 162

Query: 146 GCSRTARPKDLKREWLWGGCGDNLEYGYKGGKKERRKQRRRKRKRKRKKE 195
           GCSR ARPKDL R+WLWGGCGDNL+YGY+  K+    + R K  +K   E
Sbjct: 163 GCSRAARPKDLPRDWLWGGCGDNLDYGYRFAKEFVDAREREKIHQKGSYE 212

Ligand for members of the frizzled family of seven transmembrane receptors. Probable developmental protein. May be a signaling molecule which affects the development of discrete regions of tissues. Is likely to signal over only few cell diameters. Affects morphogenetic movement.

Xenopus laevis (taxid: 8355)

>sp|P22726|WNT5B_MOUSE Protein Wnt-5b OS=Mus musculus GN=Wnt5b PE=1 SV=2

 Score =  167 bits (424), Expect = 6e-41,   Method: Compositional matrix adjust.
 Identities = 81/172 (47%), Positives = 109/172 (63%), Gaps = 16/172 (9%)

Query: 26  PPISLEDSARVCSRVPGLSFGQVRQCSLFADHMASVGRGAAESIAECQHQFRHHRWNCSS 85
           P + +  +  VCS++PGLS GQ + C L+ +HM+ +G GA   I ECQHQFR  RWNCS+
Sbjct: 37  PEMFIIGAQPVCSQLPGLSPGQRKLCQLYQEHMSYIGEGAKTGIRECQHQFRQRRWNCST 96

Query: 86  GGPGAGGGGGGKSESTTAPSVLPPTLHIGSREAAFTHAIATAGVVYAVARSCKDGSLPSC 145
                              SV    + IGSRE AFT+A++ AGVV A++R+C++G L +C
Sbjct: 97  ---------------VDNTSVFGRVMQIGSRETAFTYAVSAAGVVNAISRACREGELSTC 141

Query: 146 GCSRTARPKDLKREWLWGGCGDNLEYGYKGGKKERRKQRRRKRKRKRKKEEE 197
           GCSR ARPKDL R+WLWGGCGDN+EYGY+   KE    R R++   +  EE+
Sbjct: 142 GCSRAARPKDLPRDWLWGGCGDNVEYGYRFA-KEFVDAREREKNFAKGSEEQ 192

Ligand for members of the frizzled family of seven transmembrane receptors. Probable developmental protein. May be a signaling molecule which affects the development of discrete regions of tissues. Is likely to signal over only few cell diameters.

Mus musculus (taxid: 10090)

>sp|Q27Q52|WNT5A_RABIT Protein Wnt-5a OS=Oryctolagus cuniculus GN=WNT5A PE=2 SV=1

 Score =  164 bits (415), Expect = 7e-40,   Method: Compositional matrix adjust.
 Identities = 80/183 (43%), Positives = 109/183 (59%), Gaps = 21/183 (11%)

Query: 22  VGFAPPISLEDSARV-----CSRVPGLSFGQVRQCSLFADHMASVGRGAAESIAECQHQF 76
           +G   P+ + +   +     CS++ GLS GQ + C L+ DHM  +G GA   I ECQ+QF
Sbjct: 49  LGMNNPVQMSEVYIIGAQPLCSQLAGLSQGQKKLCHLYQDHMQYIGEGAKTGIKECQYQF 108

Query: 77  RHHRWNCSSGGPGAGGGGGGKSESTTAPSVLPPTLHIGSREAAFTHAIATAGVVYAVARS 136
           RH RWNCS+                   SV    + IGSRE AFT+A++ AGVV A++R+
Sbjct: 109 RHRRWNCST---------------VDNTSVFGRVMQIGSRETAFTYAVSAAGVVNAMSRA 153

Query: 137 CKDGSLPSCGCSRTARPKDLKREWLWGGCGDNLEYGYKGGKKERRKQRRRKRKRKRKKEE 196
           C++G L +CGCSR ARPKDL R+WLWGGCGDN++YGY+   KE    R R+R   +   E
Sbjct: 154 CREGELSTCGCSRAARPKDLPRDWLWGGCGDNIDYGYRFA-KEFVDARERERIHAKGSYE 212

Query: 197 EEK 199
             +
Sbjct: 213 SAR 215

Ligand for members of the frizzled family of seven transmembrane receptors. Can activate or inhibit canonical Wnt signaling, depending on receptor context. In the presence of FZD4, activates beta-catenin signaling. In the presence of ROR2, inhibits the canonical Wnt pathway by promoting beta-catenin degradation through a GSK3-independent pathway which involves down-regulation of beta-catenin-induced reporter gene expression. Suppression of the canonical pathway allows chondrogenesis to occur and inhibits tumor formation. Stimulates cell migration. Decreases proliferation, migration, invasiveness and clonogenicity of carcinoma cells and may act as a tumor suppressor. Mediates motility of melanoma cells. Required during embryogenesis for extension of the primary anterior-posterior axis and for outgrowth of limbs and the genital tubercle (By similarity). Inhibits type II collagen expression in chondrocytes.

Oryctolagus cuniculus (taxid: 9986)

>sp|P41221|WNT5A_HUMAN Protein Wnt-5a OS=Homo sapiens GN=WNT5A PE=1 SV=2

 Score =  164 bits (415), Expect = 7e-40,   Method: Compositional matrix adjust.
 Identities = 80/183 (43%), Positives = 109/183 (59%), Gaps = 21/183 (11%)

Query: 22  VGFAPPISLEDSARV-----CSRVPGLSFGQVRQCSLFADHMASVGRGAAESIAECQHQF 76
           +G   P+ + +   +     CS++ GLS GQ + C L+ DHM  +G GA   I ECQ+QF
Sbjct: 49  LGMNNPVQMSEVYIIGAQPLCSQLAGLSQGQKKLCHLYQDHMQYIGEGAKTGIKECQYQF 108

Query: 77  RHHRWNCSSGGPGAGGGGGGKSESTTAPSVLPPTLHIGSREAAFTHAIATAGVVYAVARS 136
           RH RWNCS+                   SV    + IGSRE AFT+A++ AGVV A++R+
Sbjct: 109 RHRRWNCST---------------VDNTSVFGRVMQIGSRETAFTYAVSAAGVVNAMSRA 153

Query: 137 CKDGSLPSCGCSRTARPKDLKREWLWGGCGDNLEYGYKGGKKERRKQRRRKRKRKRKKEE 196
           C++G L +CGCSR ARPKDL R+WLWGGCGDN++YGY+   KE    R R+R   +   E
Sbjct: 154 CREGELSTCGCSRAARPKDLPRDWLWGGCGDNIDYGYRFA-KEFVDARERERIHAKGSYE 212

Query: 197 EEK 199
             +
Sbjct: 213 SAR 215

Ligand for members of the frizzled family of seven transmembrane receptors. Can activate or inhibit canonical Wnt signaling, depending on receptor context. In the presence of FZD4, activates beta-catenin signaling. In the presence of ROR2, inhibits the canonical Wnt pathway by promoting beta-catenin degradation through a GSK3-independent pathway which involves down-regulation of beta-catenin-induced reporter gene expression. Suppression of the canonical pathway allows chondrogenesis to occur and inhibits tumor formation. Stimulates cell migration. Decreases proliferation, migration, invasiveness and clonogenicity of carcinoma cells and may act as a tumor suppressor. Mediates motility of melanoma cells. Required during embryogenesis for extension of the primary anterior-posterior axis and for outgrowth of limbs and the genital tubercle. Inhibits type II collagen expression in chondrocytes.

Homo sapiens (taxid: 9606)

>sp|P22725|WNT5A_MOUSE Protein Wnt-5a OS=Mus musculus GN=Wnt5a PE=1 SV=2

 Score =  164 bits (414), Expect = 8e-40,   Method: Compositional matrix adjust.
 Identities = 80/183 (43%), Positives = 109/183 (59%), Gaps = 21/183 (11%)

Query: 22  VGFAPPISLEDSARV-----CSRVPGLSFGQVRQCSLFADHMASVGRGAAESIAECQHQF 76
           +G   P+ + +   +     CS++ GLS GQ + C L+ DHM  +G GA   I ECQ+QF
Sbjct: 49  LGMNNPVQMSEVYIIGAQPLCSQLAGLSQGQKKLCHLYQDHMQYIGEGAKTGIKECQYQF 108

Query: 77  RHHRWNCSSGGPGAGGGGGGKSESTTAPSVLPPTLHIGSREAAFTHAIATAGVVYAVARS 136
           RH RWNCS+                   SV    + IGSRE AFT+A++ AGVV A++R+
Sbjct: 109 RHRRWNCST---------------VDNTSVFGRVMQIGSRETAFTYAVSAAGVVNAMSRA 153

Query: 137 CKDGSLPSCGCSRTARPKDLKREWLWGGCGDNLEYGYKGGKKERRKQRRRKRKRKRKKEE 196
           C++G L +CGCSR ARPKDL R+WLWGGCGDN++YGY+   KE    R R+R   +   E
Sbjct: 154 CREGELSTCGCSRAARPKDLPRDWLWGGCGDNIDYGYRFA-KEFVDARERERIHAKGSYE 212

Query: 197 EEK 199
             +
Sbjct: 213 SAR 215

Ligand for members of the frizzled family of seven transmembrane receptors. Can activate or inhibit canonical Wnt signaling, depending on receptor context. In the presence of FZD4, activates beta-catenin signaling. In the presence of ROR2, inhibits the canonical Wnt pathway by promoting beta-catenin degradation through a GSK3-independent pathway which involves down-regulation of beta-catenin-induced reporter gene expression. Suppression of the canonical pathway allows chondrogenesis to occur and inhibits tumor formation. Stimulates cell migration. Decreases proliferation, migration, invasiveness and clonogenicity of carcinoma cells and may act as a tumor suppressor. Mediates motility of melanoma cells. Required during embryogenesis for extension of the primary anterior-posterior axis and for outgrowth of limbs and the genital tubercle. Inhibits type II collagen expression in chondrocytes.

Mus musculus (taxid: 10090)

>sp|Q9QXQ7|WNT5A_RAT Protein Wnt-5a OS=Rattus norvegicus GN=Wnt5a PE=2 SV=2

 Score =  163 bits (412), Expect = 1e-39,   Method: Compositional matrix adjust.
 Identities = 80/183 (43%), Positives = 109/183 (59%), Gaps = 21/183 (11%)

Query: 22  VGFAPPISLEDSARV-----CSRVPGLSFGQVRQCSLFADHMASVGRGAAESIAECQHQF 76
           +G   P+ + +   +     CS++ GLS GQ + C L+ DHM  +G GA   I ECQ+QF
Sbjct: 49  LGMNNPVQMSEVHIIGAQPLCSQLAGLSQGQKKLCHLYQDHMQYIGEGAKTGIKECQYQF 108

Query: 77  RHHRWNCSSGGPGAGGGGGGKSESTTAPSVLPPTLHIGSREAAFTHAIATAGVVYAVARS 136
           RH RWNCS+                   SV    + IGSRE AFT+A++ AGVV A++R+
Sbjct: 109 RHRRWNCST---------------VDNTSVFGRVMQIGSRETAFTYAVSAAGVVNAMSRA 153

Query: 137 CKDGSLPSCGCSRTARPKDLKREWLWGGCGDNLEYGYKGGKKERRKQRRRKRKRKRKKEE 196
           C++G L +CGCSR ARPKDL R+WLWGGCGDN++YGY+   KE    R R+R   +   E
Sbjct: 154 CREGELSTCGCSRAARPKDLPRDWLWGGCGDNIDYGYRFA-KEFVDARERERIHAKGSYE 212

Query: 197 EEK 199
             +
Sbjct: 213 SAR 215

Ligand for members of the frizzled family of seven transmembrane receptors. Can activate or inhibit canonical Wnt signaling, depending on receptor context. In the presence of FZD4, activates beta-catenin signaling. In the presence of ROR2, inhibits the canonical Wnt pathway by promoting beta-catenin degradation through a GSK3-independent pathway which involves down-regulation of beta-catenin-induced reporter gene expression. Suppression of the canonical pathway allows chondrogenesis to occur and inhibits tumor formation. Stimulates cell migration. Decreases proliferation, migration, invasiveness and clonogenicity of carcinoma cells and may act as a tumor suppressor. Mediates motility of melanoma cells. Required during embryogenesis for extension of the primary anterior-posterior axis and for outgrowth of limbs and the genital tubercle. Inhibits type II collagen expression in chondrocytes.

Rattus norvegicus (taxid: 10116)

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	275
156543977	389	PREDICTED: protein Wnt-5b-like [Nasonia	0.730	0.516	0.434	5e-42
405952368	321	Protein Wnt-5a [Crassostrea gigas]	0.530	0.454	0.506	1e-41
14249180	359	protein Wnt-5b precursor [Homo sapiens]	0.567	0.434	0.488	6e-41
62088036	284	wingless-type MMTV integration site fami	0.567	0.549	0.488	9e-41
119609332	411	wingless-type MMTV integration site fami	0.567	0.379	0.488	1e-40
91085809	373	PREDICTED: similar to wnt5 protein [Trib	0.607	0.447	0.448	1e-40
432091430	234	Protein Wnt-5b [Myotis davidii]	0.567	0.666	0.482	2e-40
197100357	359	protein Wnt-5b precursor [Pongo abelii]	0.567	0.434	0.482	2e-40
355563881	330	Protein Wnt-5b, partial [Macaca mulatta]	0.567	0.472	0.476	2e-40
332838277	359	PREDICTED: protein Wnt-5b isoform 2 [Pan	0.567	0.434	0.482	2e-40

>gi|156543977|ref|XP_001605266.1| PREDICTED: protein Wnt-5b-like [Nasonia vitripennis]

 Score =  177 bits (449), Expect = 5e-42,   Method: Compositional matrix adjust.
 Identities = 97/223 (43%), Positives = 123/223 (55%), Gaps = 22/223 (9%)

Query: 1   MSSDLSSQPISEP-SSPPINAGVGFAPPISLEDSARVCSRVPGLSFGQVRQCSLFADHMA 59
           + S L    + EP +S   N+ +     +   +++ +CS + GLS GQ + C L  DHM 
Sbjct: 41  IYSGLRGISLLEPATSSSGNSDLPGIVDVRTMEASSLCSSLKGLSQGQEKLCQLSHDHMP 100

Query: 60  SVGRGAAESIAECQHQFRHHRWNCSSGGPGAGGGGGGKSESTTAPSVLPPTLHIGSREAA 119
            V RGA   I ECQHQFRH RWNCS+               +   SV  P L +GSRE A
Sbjct: 101 CVARGAKAGIHECQHQFRHRRWNCST---------------SNDESVFGPVLDLGSRETA 145

Query: 120 FTHAIATAGVVYAVARSCKDGSLPSCGCSRTARPKDLKREWLWGGCGDNLEYGYKGGK-- 177
           F HAI  AGVVY++ R+C+DG L SCGCSR+ RPKDL REW+WGGCGDNLEYGYK  +  
Sbjct: 146 FVHAITAAGVVYSLGRACRDGQLSSCGCSRSGRPKDLNREWIWGGCGDNLEYGYKFAQSF 205

Query: 178 ---KER-RKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKK 216
              +ER R  +RR R+  R        E  +    K  K   K
Sbjct: 206 VDVRERERSYKRRSRQHGRSLMNLHNNEAGRRAVIKSSKVTCK 248

Source: Nasonia vitripennis

Species: Nasonia vitripennis

Genus: Nasonia

Family: Pteromalidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|405952368|gb|EKC20188.1| Protein Wnt-5a [Crassostrea gigas]

 Score =  176 bits (446), Expect = 1e-41,   Method: Compositional matrix adjust.
 Identities = 81/160 (50%), Positives = 107/160 (66%), Gaps = 14/160 (8%)

Query: 36  VCSRVPGLSFGQVRQCSLFADHMASVGRGAAESIAECQHQFRHHRWNCSSGGPGAGGGGG 95
           +C+++ GLS GQVR C LF DHM SVGRGA   I ECQHQF + RWNCS+          
Sbjct: 7   MCTQLKGLSQGQVRLCQLFTDHMPSVGRGAQLGILECQHQFANRRWNCST---------- 56

Query: 96  GKSESTTAPSVLPPTLHIGSREAAFTHAIATAGVVYAVARSCKDGSLPSCGCSRTARPKD 155
                    SV  P L+I SREAAFTHA+++AGV+++V+RSC++G L  CGCS+ +RPKD
Sbjct: 57  ----IEGDSSVFGPVLNIASREAAFTHAVSSAGVIHSVSRSCREGELSKCGCSKASRPKD 112

Query: 156 LKREWLWGGCGDNLEYGYKGGKKERRKQRRRKRKRKRKKE 195
           + R+W+WGGCGDN+EYGY+  K     + R K  R+  +E
Sbjct: 113 MARDWIWGGCGDNIEYGYRFAKYFVDTRERDKNHRRGSRE 152

Source: Crassostrea gigas

Species: Crassostrea gigas

Genus: Crassostrea

Family: Ostreidae

Order: Ostreoida

Class: Bivalvia

Phylum: Mollusca

Superkingdom: Eukaryota

>gi|14249180|ref|NP_116031.1| protein Wnt-5b precursor [Homo sapiens] gi|17402919|ref|NP_110402.2| protein Wnt-5b precursor [Homo sapiens] gi|20532427|sp|Q9H1J7.2|WNT5B_HUMAN RecName: Full=Protein Wnt-5b; Flags: Precursor gi|12804649|gb|AAH01749.1| Wingless-type MMTV integration site family, member 5B [Homo sapiens] gi|14715478|dbj|BAB62039.1| WNT5B [Homo sapiens] gi|119609331|gb|EAW88925.1| wingless-type MMTV integration site family, member 5B, isoform CRA_a [Homo sapiens] gi|119609333|gb|EAW88927.1| wingless-type MMTV integration site family, member 5B, isoform CRA_a [Homo sapiens] gi|123981906|gb|ABM82782.1| wingless-type MMTV integration site family, member 5B [synthetic construct] gi|123996739|gb|ABM85971.1| wingless-type MMTV integration site family, member 5B [synthetic construct] gi|158261883|dbj|BAF83119.1| unnamed protein product [Homo sapiens] gi|307684504|dbj|BAJ20292.1| wingless-type MMTV integration site family, member 5B [synthetic construct]

 Score =  173 bits (439), Expect = 6e-41,   Method: Compositional matrix adjust.
 Identities = 84/172 (48%), Positives = 110/172 (63%), Gaps = 16/172 (9%)

Query: 26  PPISLEDSARVCSRVPGLSFGQVRQCSLFADHMASVGRGAAESIAECQHQFRHHRWNCSS 85
           P + +  +  VCS++PGLS GQ + C L+ +HMA +G GA   I ECQHQFR  RWNCS+
Sbjct: 37  PEMFIIGAQPVCSQLPGLSPGQRKLCQLYQEHMAYIGEGAKTGIKECQHQFRQRRWNCST 96

Query: 86  GGPGAGGGGGGKSESTTAPSVLPPTLHIGSREAAFTHAIATAGVVYAVARSCKDGSLPSC 145
                              SV    + IGSRE AFTHA++ AGVV A++R+C++G L +C
Sbjct: 97  ADNA---------------SVFGRVMQIGSRETAFTHAVSAAGVVNAISRACREGELSTC 141

Query: 146 GCSRTARPKDLKREWLWGGCGDNLEYGYKGGKKERRKQRRRKRKRKRKKEEE 197
           GCSRTARPKDL R+WLWGGCGDN+EYGY+   KE    R R++   +  EE+
Sbjct: 142 GCSRTARPKDLPRDWLWGGCGDNVEYGYRFA-KEFVDAREREKNFAKGSEEQ 192

Source: Homo sapiens

Species: Homo sapiens

Genus: Homo

Family: Hominidae

Order: Primates

Class: Mammalia

Phylum: Chordata

Superkingdom: Eukaryota

>gi|62088036|dbj|BAD92465.1| wingless-type MMTV integration site family, member 5B precursor variant [Homo sapiens]

 Score =  173 bits (438), Expect = 9e-41,   Method: Compositional matrix adjust.
 Identities = 84/172 (48%), Positives = 110/172 (63%), Gaps = 16/172 (9%)

Query: 26  PPISLEDSARVCSRVPGLSFGQVRQCSLFADHMASVGRGAAESIAECQHQFRHHRWNCSS 85
           P + +  +  VCS++PGLS GQ + C L+ +HMA +G GA   I ECQHQFR  RWNCS+
Sbjct: 68  PEMFIIGAQPVCSQLPGLSPGQRKLCQLYQEHMAYIGEGAKTGIKECQHQFRQRRWNCST 127

Query: 86  GGPGAGGGGGGKSESTTAPSVLPPTLHIGSREAAFTHAIATAGVVYAVARSCKDGSLPSC 145
                              SV    + IGSRE AFTHA++ AGVV A++R+C++G L +C
Sbjct: 128 ADNA---------------SVFGRVMQIGSRETAFTHAVSAAGVVNAISRACREGELSTC 172

Query: 146 GCSRTARPKDLKREWLWGGCGDNLEYGYKGGKKERRKQRRRKRKRKRKKEEE 197
           GCSRTARPKDL R+WLWGGCGDN+EYGY+   KE    R R++   +  EE+
Sbjct: 173 GCSRTARPKDLPRDWLWGGCGDNVEYGYRFA-KEFVDAREREKNFAKGSEEQ 223

Source: Homo sapiens

Species: Homo sapiens

Genus: Homo

Family: Hominidae

Order: Primates

Class: Mammalia

Phylum: Chordata

Superkingdom: Eukaryota

>gi|119609332|gb|EAW88926.1| wingless-type MMTV integration site family, member 5B, isoform CRA_b [Homo sapiens]

 Score =  172 bits (437), Expect = 1e-40,   Method: Compositional matrix adjust.
 Identities = 84/172 (48%), Positives = 110/172 (63%), Gaps = 16/172 (9%)

Query: 26  PPISLEDSARVCSRVPGLSFGQVRQCSLFADHMASVGRGAAESIAECQHQFRHHRWNCSS 85
           P + +  +  VCS++PGLS GQ + C L+ +HMA +G GA   I ECQHQFR  RWNCS+
Sbjct: 89  PEMFIIGAQPVCSQLPGLSPGQRKLCQLYQEHMAYIGEGAKTGIKECQHQFRQRRWNCST 148

Query: 86  GGPGAGGGGGGKSESTTAPSVLPPTLHIGSREAAFTHAIATAGVVYAVARSCKDGSLPSC 145
                              SV    + IGSRE AFTHA++ AGVV A++R+C++G L +C
Sbjct: 149 ADNA---------------SVFGRVMQIGSRETAFTHAVSAAGVVNAISRACREGELSTC 193

Query: 146 GCSRTARPKDLKREWLWGGCGDNLEYGYKGGKKERRKQRRRKRKRKRKKEEE 197
           GCSRTARPKDL R+WLWGGCGDN+EYGY+   KE    R R++   +  EE+
Sbjct: 194 GCSRTARPKDLPRDWLWGGCGDNVEYGYRFA-KEFVDAREREKNFAKGSEEQ 244

Source: Homo sapiens

Species: Homo sapiens

Genus: Homo

Family: Hominidae

Order: Primates

Class: Mammalia

Phylum: Chordata

Superkingdom: Eukaryota

>gi|91085809|ref|XP_974684.1| PREDICTED: similar to wnt5 protein [Tribolium castaneum] gi|270011028|gb|EFA07476.1| hypothetical protein TcasGA2_TC009318 [Tribolium castaneum]

 Score =  172 bits (436), Expect = 1e-40,   Method: Compositional matrix adjust.
 Identities = 82/183 (44%), Positives = 113/183 (61%), Gaps = 16/183 (8%)

Query: 37  CSRVPGLSFGQVRQCSLFADHMASVGRGAAESIAECQHQFRHHRWNCSSGGPGAGGGGGG 96
           C  +PGLS GQ+R C L+ DHM +V  GA ++++EC+HQF + RWNCS            
Sbjct: 62  CHTLPGLSPGQIRLCQLYMDHMNAVALGARQALSECKHQFENRRWNCSL----------- 110

Query: 97  KSESTTAPSVLPPTLHIGSREAAFTHAIATAGVVYAVARSCKDGSLPSCGCSRTARPKDL 156
                   +V  P + I SRE+AF HA+A+AGV YAV+R+C+DG L SCGCSR  RPKDL
Sbjct: 111 ----LNDVNVFGPVITIASRESAFAHALASAGVSYAVSRACRDGQLASCGCSRMGRPKDL 166

Query: 157 KREWLWGGCGDNLEYGYKGGKKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKK 216
           +++W+WGGCGDNLEYGYK   +     R ++RK KR  +E+ +        +  ++   K
Sbjct: 167 RKDWVWGGCGDNLEYGYK-FTQNFVDVREKERKFKRGSKEQGRNLMNLHNNEAGRRAVIK 225

Query: 217 KEK 219
           K K
Sbjct: 226 KSK 228

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|432091430|gb|ELK24512.1| Protein Wnt-5b [Myotis davidii]

 Score =  172 bits (435), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 83/172 (48%), Positives = 110/172 (63%), Gaps = 16/172 (9%)

Query: 26  PPISLEDSARVCSRVPGLSFGQVRQCSLFADHMASVGRGAAESIAECQHQFRHHRWNCSS 85
           P + +  +  VCS++PGLS GQ + C L+ +HMA +G GA   I ECQHQFR  RWNCS+
Sbjct: 36  PEMFIIGAQPVCSQLPGLSPGQRKLCQLYQEHMAYIGEGAKMGIKECQHQFRQRRWNCST 95

Query: 86  GGPGAGGGGGGKSESTTAPSVLPPTLHIGSREAAFTHAIATAGVVYAVARSCKDGSLPSC 145
                              SV    + IGSRE AFT+A++ AGVV A++R+C++G L +C
Sbjct: 96  ---------------VDDASVFGRVMQIGSRETAFTYAVSAAGVVNAISRACREGELSTC 140

Query: 146 GCSRTARPKDLKREWLWGGCGDNLEYGYKGGKKERRKQRRRKRKRKRKKEEE 197
           GCSRTARPKDL R+WLWGGCGDN+EYGY+   KE    R R++   +  EE+
Sbjct: 141 GCSRTARPKDLPRDWLWGGCGDNVEYGYRFA-KEFVDAREREKNFAKGSEEQ 191

Source: Myotis davidii

Species: Myotis davidii

Genus: Myotis

Family: Vespertilionidae

Order: Chiroptera

Class: Mammalia

Phylum: Chordata

Superkingdom: Eukaryota

>gi|197100357|ref|NP_001127098.1| protein Wnt-5b precursor [Pongo abelii] gi|75061496|sp|Q5NVK2.1|WNT5B_PONAB RecName: Full=Protein Wnt-5b; Flags: Precursor gi|56403742|emb|CAI29661.1| hypothetical protein [Pongo abelii]

 Score =  172 bits (435), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 83/172 (48%), Positives = 110/172 (63%), Gaps = 16/172 (9%)

Query: 26  PPISLEDSARVCSRVPGLSFGQVRQCSLFADHMASVGRGAAESIAECQHQFRHHRWNCSS 85
           P + +  +  VCS++PGLS GQ + C L+ +HMA +G GA   I ECQHQFR  RWNCS+
Sbjct: 37  PEMFIIGAQPVCSQLPGLSPGQRKLCQLYQEHMAYIGEGAKTGIKECQHQFRQRRWNCST 96

Query: 86  GGPGAGGGGGGKSESTTAPSVLPPTLHIGSREAAFTHAIATAGVVYAVARSCKDGSLPSC 145
                              SV    + IGSRE AFT+A++ AGVV A++R+C++G L +C
Sbjct: 97  ---------------VDNASVFGRVMQIGSRETAFTYAVSAAGVVNAISRACREGELSTC 141

Query: 146 GCSRTARPKDLKREWLWGGCGDNLEYGYKGGKKERRKQRRRKRKRKRKKEEE 197
           GCSRTARPKDL R+WLWGGCGDN+EYGY+   KE    R R++   +  EE+
Sbjct: 142 GCSRTARPKDLPRDWLWGGCGDNVEYGYRFA-KEFVDAREREKNFAKGSEEQ 192

Source: Pongo abelii

Species: Pongo abelii

Genus: Pongo

Family: Hominidae

Order: Primates

Class: Mammalia

Phylum: Chordata

Superkingdom: Eukaryota

>gi|355563881|gb|EHH20381.1| Protein Wnt-5b, partial [Macaca mulatta]

 Score =  172 bits (435), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 82/172 (47%), Positives = 110/172 (63%), Gaps = 16/172 (9%)

Query: 26  PPISLEDSARVCSRVPGLSFGQVRQCSLFADHMASVGRGAAESIAECQHQFRHHRWNCSS 85
           P + +  +  VCS++PGLS GQ + C L+ +HMA +G GA   I ECQHQFR  RWNCS+
Sbjct: 37  PEMFIIGAQPVCSQLPGLSPGQRKLCQLYQEHMAYIGEGAKTGIKECQHQFRQRRWNCST 96

Query: 86  GGPGAGGGGGGKSESTTAPSVLPPTLHIGSREAAFTHAIATAGVVYAVARSCKDGSLPSC 145
                              SV    + IGSRE AFT+A++ AGVV A++R+C++G L +C
Sbjct: 97  ---------------VDNVSVFGRVMQIGSRETAFTYAVSAAGVVNAISRACREGELSTC 141

Query: 146 GCSRTARPKDLKREWLWGGCGDNLEYGYKGGKKERRKQRRRKRKRKRKKEEE 197
           GCSRTARPKDL R+WLWGGCGDN++YGY+   KE    R R++   +  EE+
Sbjct: 142 GCSRTARPKDLPRDWLWGGCGDNVDYGYRFA-KEFVDAREREKNFAKGSEEQ 192

Source: Macaca mulatta

Species: Macaca mulatta

Genus: Macaca

Family: Cercopithecidae

Order: Primates

Class: Mammalia

Phylum: Chordata

Superkingdom: Eukaryota

>gi|332838277|ref|XP_522589.3| PREDICTED: protein Wnt-5b isoform 2 [Pan troglodytes] gi|332838279|ref|XP_003339271.1| PREDICTED: protein Wnt-5b [Pan troglodytes] gi|397499352|ref|XP_003820418.1| PREDICTED: protein Wnt-5b isoform 1 [Pan paniscus] gi|397499354|ref|XP_003820419.1| PREDICTED: protein Wnt-5b isoform 2 [Pan paniscus] gi|397499356|ref|XP_003820420.1| PREDICTED: protein Wnt-5b isoform 3 [Pan paniscus] gi|410046120|ref|XP_003952129.1| PREDICTED: protein Wnt-5b [Pan troglodytes] gi|410046122|ref|XP_003952130.1| PREDICTED: protein Wnt-5b [Pan troglodytes] gi|410332041|gb|JAA34967.1| wingless-type MMTV integration site family, member 5B [Pan troglodytes]

 Score =  171 bits (434), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 83/172 (48%), Positives = 110/172 (63%), Gaps = 16/172 (9%)

Query: 26  PPISLEDSARVCSRVPGLSFGQVRQCSLFADHMASVGRGAAESIAECQHQFRHHRWNCSS 85
           P + +  +  VCS++PGLS GQ + C L+ +HMA +G GA   I ECQHQFR  RWNCS+
Sbjct: 37  PEMFIIGAQPVCSQLPGLSPGQRKLCQLYQEHMAYIGEGAKTGIKECQHQFRQRRWNCST 96

Query: 86  GGPGAGGGGGGKSESTTAPSVLPPTLHIGSREAAFTHAIATAGVVYAVARSCKDGSLPSC 145
                              SV    + IGSRE AFT+A++ AGVV A++R+C++G L +C
Sbjct: 97  ADNA---------------SVFGRVMQIGSRETAFTYAVSAAGVVNAISRACREGELSTC 141

Query: 146 GCSRTARPKDLKREWLWGGCGDNLEYGYKGGKKERRKQRRRKRKRKRKKEEE 197
           GCSRTARPKDL R+WLWGGCGDN+EYGY+   KE    R R++   +  EE+
Sbjct: 142 GCSRTARPKDLPRDWLWGGCGDNVEYGYRFA-KEFVDAREREKNFAKGSEEQ 192

Source: Pan troglodytes

Species: Pan troglodytes

Genus: Pan

Family: Hominidae

Order: Primates

Class: Mammalia

Phylum: Chordata

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	275
ZFIN|ZDB-GENE-060328-3	374	wnt5a "wingless-type MMTV inte	0.487	0.358	0.523	2.3e-39
UNIPROTKB|F5H7Q6	254	WNT5B "Protein Wnt" [Homo sapi	0.487	0.527	0.523	2.9e-39
UNIPROTKB|Q9H1J7	359	WNT5B "Protein Wnt-5b" [Homo s	0.487	0.373	0.523	2.9e-39
UNIPROTKB|Q5NVK2	359	WNT5B "Protein Wnt-5b" [Pongo	0.487	0.373	0.516	1.6e-38
UNIPROTKB|F1Q0S4	358	WNT5B "Protein Wnt" [Canis lup	0.487	0.374	0.516	2.6e-38
UNIPROTKB|F1NMK4	332	WNT5B "Protein Wnt" [Gallus ga	0.487	0.403	0.516	3.4e-38
UNIPROTKB|F1NMK6	358	WNT5B "Protein Wnt" [Gallus ga	0.487	0.374	0.516	3.4e-38
UNIPROTKB|F1MP15	363	WNT5B "Protein Wnt" [Bos tauru	0.487	0.369	0.510	4.3e-38
MGI|MGI:98959	359	Wnt5b "wingless-related MMTV i	0.487	0.373	0.510	5.5e-38
UNIPROTKB|Q6DII0	360	wnt5b "Protein Wnt" [Xenopus (	0.487	0.372	0.510	8.9e-38

ZFIN|ZDB-GENE-060328-3 wnt5a "wingless-type MMTV integration site family, member 5a" [Danio rerio (taxid:7955)]

 Score = 420 (152.9 bits), Expect = 2.3e-39, P = 2.3e-39
 Identities = 78/149 (52%), Positives = 103/149 (69%)

Query:    26 PPISLEDSARVCSRVPGLSFGQVRQCSLFADHMASVGRGAAESIAECQHQFRHHRWNCSS 85
             P + +     +CS++ GLS GQ + C L+ DHM  +G GA   I ECQHQFRHHRWNCS+
Sbjct:    52 PEVYVIGGQPLCSQLSGLSKGQKKLCQLYQDHMQYIGEGAKTGIRECQHQFRHHRWNCST 111

Query:    86 XXXXXXXXXXXKSESTTAPSVLPPTLHIGSREAAFTHAIATAGVVYAVARSCKDGSLPSC 145
                          +++T   VL   +HIGSRE+AF  AI+ AGV++AV+R+C++G+L SC
Sbjct:   112 V------------DNST---VLGRVMHIGSRESAFAFAISAAGVLHAVSRACREGALSSC 156

Query:   146 GCSRTARPKDLKREWLWGGCGDNLEYGYK 174
             GCSR +RPKDL R+WLWGGCGDNL YGY+
Sbjct:   157 GCSRASRPKDLPRDWLWGGCGDNLNYGYR 185

GO:0005102 "receptor binding" evidence=IEA

GO:0005576 "extracellular region" evidence=IEA

GO:0016055 "Wnt receptor signaling pathway" evidence=IEA

GO:0007275 "multicellular organismal development" evidence=IEA

GO:0090009 "primitive streak formation" evidence=IBA

GO:0001756 "somitogenesis" evidence=IBA

GO:0060599 "lateral sprouting involved in mammary gland duct morphogenesis" evidence=IBA

GO:0060029 "convergent extension involved in organogenesis" evidence=IBA

GO:0003323 "type B pancreatic cell development" evidence=IBA

GO:0090103 "cochlea morphogenesis" evidence=IBA

GO:0060157 "urinary bladder development" evidence=IBA

GO:0050679 "positive regulation of epithelial cell proliferation" evidence=IBA

GO:0003344 "pericardium morphogenesis" evidence=IBA

GO:0005886 "plasma membrane" evidence=IBA

GO:0043507 "positive regulation of JUN kinase activity" evidence=IBA

GO:0090090 "negative regulation of canonical Wnt receptor signaling pathway" evidence=IBA

GO:0060744 "mammary gland branching involved in thelarche" evidence=IBA

GO:0042733 "embryonic digit morphogenesis" evidence=IBA

GO:0060762 "regulation of branching involved in mammary gland duct morphogenesis" evidence=IBA

GO:0007223 "Wnt receptor signaling pathway, calcium modulating pathway" evidence=IBA

GO:0046330 "positive regulation of JNK cascade" evidence=IBA

GO:0001947 "heart looping" evidence=IBA

GO:0002053 "positive regulation of mesenchymal cell proliferation" evidence=IBA

GO:0071425 "hematopoietic stem cell proliferation" evidence=IBA

GO:0040037 "negative regulation of fibroblast growth factor receptor signaling pathway" evidence=IBA

GO:0005110 "frizzled-2 binding" evidence=IBA

GO:0030514 "negative regulation of BMP signaling pathway" evidence=IBA

GO:0005615 "extracellular space" evidence=IBA

GO:0061036 "positive regulation of cartilage development" evidence=IBA

GO:0060071 "Wnt receptor signaling pathway, planar cell polarity pathway" evidence=IBA

GO:0060750 "epithelial cell proliferation involved in mammary gland duct elongation" evidence=IBA

GO:0009950 "dorsal/ventral axis specification" evidence=IBA

GO:0071542 "dopaminergic neuron differentiation" evidence=IBA

GO:0048546 "digestive tract morphogenesis" evidence=IBA

GO:0060541 "respiratory system development" evidence=IBA

GO:0001843 "neural tube closure" evidence=IBA

GO:0005578 "proteinaceous extracellular matrix" evidence=IEA

UNIPROTKB|F5H7Q6 WNT5B "Protein Wnt" [Homo sapiens (taxid:9606)]

 Score = 419 (152.6 bits), Expect = 2.9e-39, P = 2.9e-39
 Identities = 78/149 (52%), Positives = 100/149 (67%)

Query:    26 PPISLEDSARVCSRVPGLSFGQVRQCSLFADHMASVGRGAAESIAECQHQFRHHRWNCSS 85
             P + +  +  VCS++PGLS GQ + C L+ +HMA +G GA   I ECQHQFR  RWNCS+
Sbjct:    37 PEMFIIGAQPVCSQLPGLSPGQRKLCQLYQEHMAYIGEGAKTGIKECQHQFRQRRWNCST 96

Query:    86 XXXXXXXXXXXKSESTTAPSVLPPTLHIGSREAAFTHAIATAGVVYAVARSCKDGSLPSC 145
                                SV    + IGSRE AFTHA++ AGVV A++R+C++G L +C
Sbjct:    97 ADNA---------------SVFGRVMQIGSRETAFTHAVSAAGVVNAISRACREGELSTC 141

Query:   146 GCSRTARPKDLKREWLWGGCGDNLEYGYK 174
             GCSRTARPKDL R+WLWGGCGDN+EYGY+
Sbjct:   142 GCSRTARPKDLPRDWLWGGCGDNVEYGYR 170

GO:0005102 "receptor binding" evidence=IEA

GO:0007275 "multicellular organismal development" evidence=IEA

GO:0016055 "Wnt receptor signaling pathway" evidence=IEA

GO:0009986 "cell surface" evidence=IEA

GO:0045600 "positive regulation of fat cell differentiation" evidence=IEA

GO:0090090 "negative regulation of canonical Wnt receptor signaling pathway" evidence=IEA

GO:0005578 "proteinaceous extracellular matrix" evidence=IEA

UNIPROTKB|Q9H1J7 WNT5B "Protein Wnt-5b" [Homo sapiens (taxid:9606)]

 Score = 419 (152.6 bits), Expect = 2.9e-39, P = 2.9e-39
 Identities = 78/149 (52%), Positives = 100/149 (67%)

Query:    26 PPISLEDSARVCSRVPGLSFGQVRQCSLFADHMASVGRGAAESIAECQHQFRHHRWNCSS 85
             P + +  +  VCS++PGLS GQ + C L+ +HMA +G GA   I ECQHQFR  RWNCS+
Sbjct:    37 PEMFIIGAQPVCSQLPGLSPGQRKLCQLYQEHMAYIGEGAKTGIKECQHQFRQRRWNCST 96

Query:    86 XXXXXXXXXXXKSESTTAPSVLPPTLHIGSREAAFTHAIATAGVVYAVARSCKDGSLPSC 145
                                SV    + IGSRE AFTHA++ AGVV A++R+C++G L +C
Sbjct:    97 ADNA---------------SVFGRVMQIGSRETAFTHAVSAAGVVNAISRACREGELSTC 141

Query:   146 GCSRTARPKDLKREWLWGGCGDNLEYGYK 174
             GCSRTARPKDL R+WLWGGCGDN+EYGY+
Sbjct:   142 GCSRTARPKDLPRDWLWGGCGDNVEYGYR 170

GO:0009986 "cell surface" evidence=IEA

GO:0005578 "proteinaceous extracellular matrix" evidence=IEA

GO:0001525 "angiogenesis" evidence=IBA

GO:0005110 "frizzled-2 binding" evidence=IBA

GO:0005615 "extracellular space" evidence=NAS;IBA

GO:0005886 "plasma membrane" evidence=IBA

GO:0007223 "Wnt receptor signaling pathway, calcium modulating pathway" evidence=IBA

GO:0009950 "dorsal/ventral axis specification" evidence=IBA

GO:0009952 "anterior/posterior pattern specification" evidence=IBA

GO:0031018 "endocrine pancreas development" evidence=IBA

GO:0042074 "cell migration involved in gastrulation" evidence=IBA

GO:0045600 "positive regulation of fat cell differentiation" evidence=IBA

GO:0060027 "convergent extension involved in gastrulation" evidence=IBA

GO:0060028 "convergent extension involved in axis elongation" evidence=IBA

GO:0060541 "respiratory system development" evidence=IBA

GO:0090090 "negative regulation of canonical Wnt receptor signaling pathway" evidence=IBA

GO:0045444 "fat cell differentiation" evidence=NAS

GO:0005102 "receptor binding" evidence=IPI

GO:0030335 "positive regulation of cell migration" evidence=IDA

GO:0016055 "Wnt receptor signaling pathway" evidence=IDA;IMP

GO:0002062 "chondrocyte differentiation" evidence=IEP

GO:0030182 "neuron differentiation" evidence=ISS

GO:0071300 "cellular response to retinoic acid" evidence=ISS

GO:0070307 "lens fiber cell development" evidence=ISS

UNIPROTKB|Q5NVK2 WNT5B "Protein Wnt-5b" [Pongo abelii (taxid:9601)]

 Score = 412 (150.1 bits), Expect = 1.6e-38, P = 1.6e-38
 Identities = 77/149 (51%), Positives = 100/149 (67%)

Query:    26 PPISLEDSARVCSRVPGLSFGQVRQCSLFADHMASVGRGAAESIAECQHQFRHHRWNCSS 85
             P + +  +  VCS++PGLS GQ + C L+ +HMA +G GA   I ECQHQFR  RWNCS+
Sbjct:    37 PEMFIIGAQPVCSQLPGLSPGQRKLCQLYQEHMAYIGEGAKTGIKECQHQFRQRRWNCST 96

Query:    86 XXXXXXXXXXXKSESTTAPSVLPPTLHIGSREAAFTHAIATAGVVYAVARSCKDGSLPSC 145
                                SV    + IGSRE AFT+A++ AGVV A++R+C++G L +C
Sbjct:    97 VDNA---------------SVFGRVMQIGSRETAFTYAVSAAGVVNAISRACREGELSTC 141

Query:   146 GCSRTARPKDLKREWLWGGCGDNLEYGYK 174
             GCSRTARPKDL R+WLWGGCGDN+EYGY+
Sbjct:   142 GCSRTARPKDLPRDWLWGGCGDNVEYGYR 170

GO:0005102 "receptor binding" evidence=ISS

GO:0016055 "Wnt receptor signaling pathway" evidence=ISS

GO:0030335 "positive regulation of cell migration" evidence=ISS

UNIPROTKB|F1Q0S4 WNT5B "Protein Wnt" [Canis lupus familiaris (taxid:9615)]

 Score = 410 (149.4 bits), Expect = 2.6e-38, P = 2.6e-38
 Identities = 77/149 (51%), Positives = 104/149 (69%)

Query:    26 PPISLEDSARVCSRVPGLSFGQVRQCSLFADHMASVGRGAAESIAECQHQFRHHRWNCSS 85
             P + +  +  VCS++PGLS GQ + C L+ +HMA +G GA   I ECQ+QFR  RWNCS+
Sbjct:    36 PEMFIIGAQPVCSQLPGLSPGQRKLCQLYQEHMAYIGEGAKTGIKECQYQFRQRRWNCST 95

Query:    86 XXXXXXXXXXXKSESTTAPSVLPPTLHIGSREAAFTHAIATAGVVYAVARSCKDGSLPSC 145
                          ++T   SV    + IGSREAAFT+A++ AGVV+AV+R+C++G L +C
Sbjct:    96 V------------DNT---SVFGRVMQIGSREAAFTYAVSAAGVVHAVSRACREGELSTC 140

Query:   146 GCSRTARPKDLKREWLWGGCGDNLEYGYK 174
             GCSR ARP+DL R+WLWGGCGDN+EYGY+
Sbjct:   141 GCSRAARPRDLPRDWLWGGCGDNVEYGYR 169

GO:0005578 "proteinaceous extracellular matrix" evidence=IEA

GO:0090090 "negative regulation of canonical Wnt receptor signaling pathway" evidence=IEA

GO:0045600 "positive regulation of fat cell differentiation" evidence=IEA

GO:0030335 "positive regulation of cell migration" evidence=IEA

GO:0009986 "cell surface" evidence=IEA

GO:0002062 "chondrocyte differentiation" evidence=IEA

GO:0016055 "Wnt receptor signaling pathway" evidence=IEA

GO:0005102 "receptor binding" evidence=IEA

UNIPROTKB|F1NMK4 WNT5B "Protein Wnt" [Gallus gallus (taxid:9031)]

 Score = 409 (149.0 bits), Expect = 3.4e-38, P = 3.4e-38
 Identities = 77/149 (51%), Positives = 103/149 (69%)

Query:    26 PPISLEDSARVCSRVPGLSFGQVRQCSLFADHMASVGRGAAESIAECQHQFRHHRWNCSS 85
             P + +  +  VCS++PGLS GQ + C L+ +HM  +G GA  +I ECQ+QFR  RWNCS+
Sbjct:    10 PEMYIIGAQPVCSQLPGLSPGQRKLCQLYQEHMVFIGEGARSAIKECQYQFRQRRWNCST 69

Query:    86 XXXXXXXXXXXKSESTTAPSVLPPTLHIGSREAAFTHAIATAGVVYAVARSCKDGSLPSC 145
                          ++T   SV    + IGSRE AFT+A++ AGVV A++R+C++G L SC
Sbjct:    70 V------------DNT---SVFGRVMKIGSRETAFTYAVSAAGVVNAISRACREGELSSC 114

Query:   146 GCSRTARPKDLKREWLWGGCGDNLEYGYK 174
             GCSRTARPKDL R+WLWGGCGDN+EYGY+
Sbjct:   115 GCSRTARPKDLPRDWLWGGCGDNVEYGYR 143

GO:0005102 "receptor binding" evidence=IEA

GO:0016055 "Wnt receptor signaling pathway" evidence=IEA

GO:0005578 "proteinaceous extracellular matrix" evidence=IEA

GO:0002062 "chondrocyte differentiation" evidence=IEA

GO:0009986 "cell surface" evidence=IEA

GO:0030335 "positive regulation of cell migration" evidence=IEA

GO:0045600 "positive regulation of fat cell differentiation" evidence=IEA

GO:0090090 "negative regulation of canonical Wnt receptor signaling pathway" evidence=IEA

UNIPROTKB|F1NMK6 WNT5B "Protein Wnt" [Gallus gallus (taxid:9031)]

 Score = 409 (149.0 bits), Expect = 3.4e-38, P = 3.4e-38
 Identities = 77/149 (51%), Positives = 103/149 (69%)

Query:    26 PPISLEDSARVCSRVPGLSFGQVRQCSLFADHMASVGRGAAESIAECQHQFRHHRWNCSS 85
             P + +  +  VCS++PGLS GQ + C L+ +HM  +G GA  +I ECQ+QFR  RWNCS+
Sbjct:    36 PEMYIIGAQPVCSQLPGLSPGQRKLCQLYQEHMVFIGEGARSAIKECQYQFRQRRWNCST 95

Query:    86 XXXXXXXXXXXKSESTTAPSVLPPTLHIGSREAAFTHAIATAGVVYAVARSCKDGSLPSC 145
                          ++T   SV    + IGSRE AFT+A++ AGVV A++R+C++G L SC
Sbjct:    96 V------------DNT---SVFGRVMKIGSRETAFTYAVSAAGVVNAISRACREGELSSC 140

Query:   146 GCSRTARPKDLKREWLWGGCGDNLEYGYK 174
             GCSRTARPKDL R+WLWGGCGDN+EYGY+
Sbjct:   141 GCSRTARPKDLPRDWLWGGCGDNVEYGYR 169

GO:0005102 "receptor binding" evidence=IEA

GO:0016055 "Wnt receptor signaling pathway" evidence=IEA

GO:0005578 "proteinaceous extracellular matrix" evidence=IEA

GO:0002062 "chondrocyte differentiation" evidence=IEA

GO:0009986 "cell surface" evidence=IEA

GO:0030335 "positive regulation of cell migration" evidence=IEA

GO:0045600 "positive regulation of fat cell differentiation" evidence=IEA

GO:0090090 "negative regulation of canonical Wnt receptor signaling pathway" evidence=IEA

UNIPROTKB|F1MP15 WNT5B "Protein Wnt" [Bos taurus (taxid:9913)]

 Score = 408 (148.7 bits), Expect = 4.3e-38, P = 4.3e-38
 Identities = 76/149 (51%), Positives = 99/149 (66%)

Query:    26 PPISLEDSARVCSRVPGLSFGQVRQCSLFADHMASVGRGAAESIAECQHQFRHHRWNCSS 85
             P + +  +  VCS++PGLS GQ + C L+ +HMA +G GA   I ECQHQFR  RWNCS+
Sbjct:    41 PEMFIIGAQPVCSQLPGLSAGQRKLCQLYQEHMAYIGEGARTGIRECQHQFRQRRWNCST 100

Query:    86 XXXXXXXXXXXKSESTTAPSVLPPTLHIGSREAAFTHAIATAGVVYAVARSCKDGSLPSC 145
                                SV    L IGSRE AFT+A++ AGVV A++R+C++G L +C
Sbjct:   101 VDDA---------------SVFGRVLQIGSRETAFTYAVSAAGVVNAISRACREGELSTC 145

Query:   146 GCSRTARPKDLKREWLWGGCGDNLEYGYK 174
             GCSR ARPKDL R+WLWGGCGDN++YGY+
Sbjct:   146 GCSRAARPKDLPRDWLWGGCGDNVDYGYR 174

GO:0005578 "proteinaceous extracellular matrix" evidence=IEA

GO:0090090 "negative regulation of canonical Wnt receptor signaling pathway" evidence=IEA

GO:0045600 "positive regulation of fat cell differentiation" evidence=IEA

GO:0030335 "positive regulation of cell migration" evidence=IEA

GO:0009986 "cell surface" evidence=IEA

GO:0002062 "chondrocyte differentiation" evidence=IEA

GO:0016055 "Wnt receptor signaling pathway" evidence=IEA

GO:0005102 "receptor binding" evidence=IEA

MGI|MGI:98959 Wnt5b "wingless-related MMTV integration site 5B" [Mus musculus (taxid:10090)]

 Score = 407 (148.3 bits), Expect = 5.5e-38, P = 5.5e-38
 Identities = 76/149 (51%), Positives = 102/149 (68%)

Query:    26 PPISLEDSARVCSRVPGLSFGQVRQCSLFADHMASVGRGAAESIAECQHQFRHHRWNCSS 85
             P + +  +  VCS++PGLS GQ + C L+ +HM+ +G GA   I ECQHQFR  RWNCS+
Sbjct:    37 PEMFIIGAQPVCSQLPGLSPGQRKLCQLYQEHMSYIGEGAKTGIRECQHQFRQRRWNCST 96

Query:    86 XXXXXXXXXXXKSESTTAPSVLPPTLHIGSREAAFTHAIATAGVVYAVARSCKDGSLPSC 145
                          ++T   SV    + IGSRE AFT+A++ AGVV A++R+C++G L +C
Sbjct:    97 V------------DNT---SVFGRVMQIGSRETAFTYAVSAAGVVNAISRACREGELSTC 141

Query:   146 GCSRTARPKDLKREWLWGGCGDNLEYGYK 174
             GCSR ARPKDL R+WLWGGCGDN+EYGY+
Sbjct:   142 GCSRAARPKDLPRDWLWGGCGDNVEYGYR 170

GO:0000122 "negative regulation of transcription from RNA polymerase II promoter" evidence=IBA

GO:0001525 "angiogenesis" evidence=IBA

GO:0002062 "chondrocyte differentiation" evidence=IBA

GO:0005102 "receptor binding" evidence=ISO;TAS

GO:0005110 "frizzled-2 binding" evidence=IBA

GO:0005515 "protein binding" evidence=IPI

GO:0005576 "extracellular region" evidence=IEA

GO:0005578 "proteinaceous extracellular matrix" evidence=IEA

GO:0005615 "extracellular space" evidence=IBA

GO:0005886 "plasma membrane" evidence=IBA

GO:0007165 "signal transduction" evidence=TAS

GO:0007223 "Wnt receptor signaling pathway, calcium modulating pathway" evidence=IBA

GO:0007267 "cell-cell signaling" evidence=TAS

GO:0007275 "multicellular organismal development" evidence=IEA

GO:0009887 "organ morphogenesis" evidence=TAS

GO:0009950 "dorsal/ventral axis specification" evidence=IBA

GO:0009952 "anterior/posterior pattern specification" evidence=IBA

GO:0009986 "cell surface" evidence=IDA

GO:0016055 "Wnt receptor signaling pathway" evidence=ISO

GO:0030335 "positive regulation of cell migration" evidence=ISO

GO:0031012 "extracellular matrix" evidence=IDA

GO:0031018 "endocrine pancreas development" evidence=IBA

GO:0042074 "cell migration involved in gastrulation" evidence=IBA

GO:0045600 "positive regulation of fat cell differentiation" evidence=IGI

GO:0060027 "convergent extension involved in gastrulation" evidence=IBA

GO:0060028 "convergent extension involved in axis elongation" evidence=IBA

GO:0060541 "respiratory system development" evidence=IBA

GO:0090090 "negative regulation of canonical Wnt receptor signaling pathway" evidence=IGI

UNIPROTKB|Q6DII0 wnt5b "Protein Wnt" [Xenopus (Silurana) tropicalis (taxid:8364)]

 Score = 405 (147.6 bits), Expect = 8.9e-38, P = 8.9e-38
 Identities = 76/149 (51%), Positives = 99/149 (66%)

Query:    26 PPISLEDSARVCSRVPGLSFGQVRQCSLFADHMASVGRGAAESIAECQHQFRHHRWNCSS 85
             P + +  +  +CS++ GLS GQ + C L+ DHM  +G GA   I ECQHQF+H RWNCS+
Sbjct:    38 PEMYIIGAQPLCSQLTGLSPGQRKLCQLYQDHMVYIGEGAKTGIKECQHQFKHRRWNCST 97

Query:    86 XXXXXXXXXXXKSESTTAPSVLPPTLHIGSREAAFTHAIATAGVVYAVARSCKDGSLPSC 145
                                SV    + IGSREAAFT+AI+ AGVV A++R+C++G L +C
Sbjct:    98 VDNN---------------SVFGRVMQIGSREAAFTYAISAAGVVNAISRACREGELSTC 142

Query:   146 GCSRTARPKDLKREWLWGGCGDNLEYGYK 174
             GCSRT RPKDL R+WLWGGCGDN+EYGY+
Sbjct:   143 GCSRTPRPKDLPRDWLWGGCGDNVEYGYR 171

GO:0001525 "angiogenesis" evidence=ISS

GO:0002062 "chondrocyte differentiation" evidence=ISS

GO:0005110 "frizzled-2 binding" evidence=ISS

GO:0005615 "extracellular space" evidence=ISS

GO:0005886 "plasma membrane" evidence=ISS

GO:0007223 "Wnt receptor signaling pathway, calcium modulating pathway" evidence=ISS

GO:0009950 "dorsal/ventral axis specification" evidence=ISS

GO:0009952 "anterior/posterior pattern specification" evidence=ISS

GO:0031018 "endocrine pancreas development" evidence=ISS

GO:0042074 "cell migration involved in gastrulation" evidence=ISS

GO:0045600 "positive regulation of fat cell differentiation" evidence=ISS

GO:0060027 "convergent extension involved in gastrulation" evidence=ISS

GO:0060028 "convergent extension involved in axis elongation" evidence=ISS

GO:0060541 "respiratory system development" evidence=ISS

GO:0090090 "negative regulation of canonical Wnt receptor signaling pathway" evidence=ISS

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	275
pfam00110	308	pfam00110, wnt, wnt family	4e-50
smart00097	305	smart00097, WNT1, found in Wnt-1	4e-49
PRK04195	482	PRK04195, PRK04195, replication factor C large sub	2e-12
PRK04195	482	PRK04195, PRK04195, replication factor C large sub	3e-12
PRK04195	482	PRK04195, PRK04195, replication factor C large sub	1e-11
PRK04195	482	PRK04195, PRK04195, replication factor C large sub	3e-11
PRK04195	482	PRK04195, PRK04195, replication factor C large sub	4e-11
PRK04195	482	PRK04195, PRK04195, replication factor C large sub	6e-11
PRK04195	482	PRK04195, PRK04195, replication factor C large sub	1e-10
PRK04195	482	PRK04195, PRK04195, replication factor C large sub	2e-10
PRK04195	482	PRK04195, PRK04195, replication factor C large sub	2e-10
PRK04195	482	PRK04195, PRK04195, replication factor C large sub	3e-10
PRK04195	482	PRK04195, PRK04195, replication factor C large sub	3e-10
PTZ00372	413	PTZ00372, PTZ00372, endonuclease 4-like protein; P	4e-10
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	5e-10
PRK11192	434	PRK11192, PRK11192, ATP-dependent RNA helicase Srm	6e-10
PTZ00372	413	PTZ00372, PTZ00372, endonuclease 4-like protein; P	8e-10
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	8e-10
PRK04195	482	PRK04195, PRK04195, replication factor C large sub	9e-10
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	9e-10
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	9e-10
PRK11192	434	PRK11192, PRK11192, ATP-dependent RNA helicase Srm	9e-10
PRK11192	434	PRK11192, PRK11192, ATP-dependent RNA helicase Srm	1e-09
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	2e-09
PRK11192	434	PRK11192, PRK11192, ATP-dependent RNA helicase Srm	2e-09
PRK04195	482	PRK04195, PRK04195, replication factor C large sub	3e-09
PRK04195	482	PRK04195, PRK04195, replication factor C large sub	3e-09
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	4e-09
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	4e-09
PRK11192	434	PRK11192, PRK11192, ATP-dependent RNA helicase Srm	4e-09
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	5e-09
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	6e-09
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	7e-09
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	7e-09
TIGR02794	346	TIGR02794, tolA_full, TolA protein	7e-09
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	8e-09
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	8e-09
PTZ00372	413	PTZ00372, PTZ00372, endonuclease 4-like protein; P	1e-08
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	1e-08
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	1e-08
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	1e-08
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	1e-08
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	1e-08
PRK11192	434	PRK11192, PRK11192, ATP-dependent RNA helicase Srm	1e-08
pfam07946	322	pfam07946, DUF1682, Protein of unknown function (D	1e-08
pfam07946	322	pfam07946, DUF1682, Protein of unknown function (D	1e-08
pfam08432	182	pfam08432, DUF1742, Fungal protein of unknown func	1e-08
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	2e-08
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	2e-08
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	2e-08
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	2e-08
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	2e-08
pfam08432	182	pfam08432, DUF1742, Fungal protein of unknown func	2e-08
pfam08432	182	pfam08432, DUF1742, Fungal protein of unknown func	2e-08
pfam10243	506	pfam10243, MIP-T3, Microtubule-binding protein MIP	2e-08
PRK12704	520	PRK12704, PRK12704, phosphodiesterase; Provisional	4e-08
PLN02381	1066	PLN02381, PLN02381, valyl-tRNA synthetase	4e-08
pfam05087	887	pfam05087, Rota_VP2, Rotavirus VP2 protein	4e-08
PRK12704	520	PRK12704, PRK12704, phosphodiesterase; Provisional	5e-08
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	6e-08
PRK04195	482	PRK04195, PRK04195, replication factor C large sub	7e-08
COG4499	434	COG4499, COG4499, Predicted membrane protein [Func	7e-08
PRK04195	482	PRK04195, PRK04195, replication factor C large sub	8e-08
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	8e-08
pfam08432	182	pfam08432, DUF1742, Fungal protein of unknown func	8e-08
pfam08208	193	pfam08208, RNA_polI_A34, DNA-directed RNA polymera	9e-08
PTZ00372	413	PTZ00372, PTZ00372, endonuclease 4-like protein; P	1e-07
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	1e-07
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	1e-07
pfam10243	506	pfam10243, MIP-T3, Microtubule-binding protein MIP	1e-07
COG4499	434	COG4499, COG4499, Predicted membrane protein [Func	1e-07
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	1e-07
PTZ00372	413	PTZ00372, PTZ00372, endonuclease 4-like protein; P	2e-07
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	2e-07
TIGR02794	346	TIGR02794, tolA_full, TolA protein	2e-07
pfam08432	182	pfam08432, DUF1742, Fungal protein of unknown func	2e-07
pfam10243	506	pfam10243, MIP-T3, Microtubule-binding protein MIP	2e-07
COG4499	434	COG4499, COG4499, Predicted membrane protein [Func	2e-07
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	2e-07
PTZ00108	1388	PTZ00108, PTZ00108, DNA topoisomerase 2-like prote	2e-07
PRK05901	509	PRK05901, PRK05901, RNA polymerase sigma factor; P	2e-07
PRK05901	509	PRK05901, PRK05901, RNA polymerase sigma factor; P	2e-07
PRK04195	482	PRK04195, PRK04195, replication factor C large sub	3e-07
PRK04195	482	PRK04195, PRK04195, replication factor C large sub	3e-07
PTZ00372	413	PTZ00372, PTZ00372, endonuclease 4-like protein; P	3e-07
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	3e-07
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	3e-07
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	3e-07
pfam08208	193	pfam08208, RNA_polI_A34, DNA-directed RNA polymera	3e-07
pfam12569	516	pfam12569, NARP1, NMDA receptor-regulated protein	3e-07
pfam12569	516	pfam12569, NARP1, NMDA receptor-regulated protein	3e-07
COG0810	244	COG0810, TonB, Periplasmic protein TonB, links inn	3e-07
pfam09468	287	pfam09468, RNase_H2-Ydr279, Ydr279p protein family	3e-07
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	4e-07
TIGR02794	346	TIGR02794, tolA_full, TolA protein	4e-07
pfam08432	182	pfam08432, DUF1742, Fungal protein of unknown func	4e-07
PLN02381	1066	PLN02381, PLN02381, valyl-tRNA synthetase	4e-07
COG0810	244	COG0810, TonB, Periplasmic protein TonB, links inn	4e-07
pfam09468	287	pfam09468, RNase_H2-Ydr279, Ydr279p protein family	4e-07
pfam05262	489	pfam05262, Borrelia_P83, Borrelia P83/100 protein	4e-07
pfam07946	322	pfam07946, DUF1682, Protein of unknown function (D	5e-07
pfam12569	516	pfam12569, NARP1, NMDA receptor-regulated protein	5e-07
TIGR02794	346	TIGR02794, tolA_full, TolA protein	6e-07
pfam07946	322	pfam07946, DUF1682, Protein of unknown function (D	6e-07
pfam10243	506	pfam10243, MIP-T3, Microtubule-binding protein MIP	6e-07
pfam10243	506	pfam10243, MIP-T3, Microtubule-binding protein MIP	6e-07
COG4499	434	COG4499, COG4499, Predicted membrane protein [Func	6e-07
PRK05901	509	PRK05901, PRK05901, RNA polymerase sigma factor; P	7e-07
PRK00409	782	PRK00409, PRK00409, recombination and DNA strand e	7e-07
pfam07946	322	pfam07946, DUF1682, Protein of unknown function (D	9e-07
pfam10243	506	pfam10243, MIP-T3, Microtubule-binding protein MIP	9e-07
PRK00409	782	PRK00409, PRK00409, recombination and DNA strand e	9e-07
PLN02967	581	PLN02967, PLN02967, kinase	9e-07
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	1e-06
PLN02381	1066	PLN02381, PLN02381, valyl-tRNA synthetase	1e-06
COG4499	434	COG4499, COG4499, Predicted membrane protein [Func	1e-06
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	1e-06
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	1e-06
PTZ00108	1388	PTZ00108, PTZ00108, DNA topoisomerase 2-like prote	1e-06
PTZ00108	1388	PTZ00108, PTZ00108, DNA topoisomerase 2-like prote	1e-06
PRK05901	509	PRK05901, PRK05901, RNA polymerase sigma factor; P	1e-06
pfam12569	516	pfam12569, NARP1, NMDA receptor-regulated protein	1e-06
pfam12569	516	pfam12569, NARP1, NMDA receptor-regulated protein	1e-06
pfam09468	287	pfam09468, RNase_H2-Ydr279, Ydr279p protein family	1e-06
PRK05306	746	PRK05306, infB, translation initiation factor IF-2	1e-06
smart00435	391	smart00435, TOPEUc, DNA Topoisomerase I (eukaryota	1e-06
smart00435	391	smart00435, TOPEUc, DNA Topoisomerase I (eukaryota	1e-06
pfam13166	713	pfam13166, AAA_13, AAA domain	1e-06
pfam07946	322	pfam07946, DUF1682, Protein of unknown function (D	2e-06
pfam10243	506	pfam10243, MIP-T3, Microtubule-binding protein MIP	2e-06
pfam10243	506	pfam10243, MIP-T3, Microtubule-binding protein MIP	2e-06
PRK12704	520	PRK12704, PRK12704, phosphodiesterase; Provisional	2e-06
PTZ00108	1388	PTZ00108, PTZ00108, DNA topoisomerase 2-like prote	2e-06
PRK05901	509	PRK05901, PRK05901, RNA polymerase sigma factor; P	2e-06
PRK05901	509	PRK05901, PRK05901, RNA polymerase sigma factor; P	2e-06
smart00435	391	smart00435, TOPEUc, DNA Topoisomerase I (eukaryota	2e-06
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	2e-06
PRK14552	414	PRK14552, PRK14552, C/D box methylation guide ribo	2e-06
PRK14552	414	PRK14552, PRK14552, C/D box methylation guide ribo	2e-06
TIGR01554	384	TIGR01554, major_cap_HK97, phage major capsid prot	2e-06
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	3e-06
TIGR02794	346	TIGR02794, tolA_full, TolA protein	3e-06
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	3e-06
COG0810	244	COG0810, TonB, Periplasmic protein TonB, links inn	3e-06
PRK00409	782	PRK00409, PRK00409, recombination and DNA strand e	3e-06
smart00435	391	smart00435, TOPEUc, DNA Topoisomerase I (eukaryota	3e-06
PRK14552	414	PRK14552, PRK14552, C/D box methylation guide ribo	3e-06
PRK14552	414	PRK14552, PRK14552, C/D box methylation guide ribo	3e-06
PRK14552	414	PRK14552, PRK14552, C/D box methylation guide ribo	3e-06
PRK11642	813	PRK11642, PRK11642, exoribonuclease R; Provisional	3e-06
PRK11642	813	PRK11642, PRK11642, exoribonuclease R; Provisional	3e-06
pfam08597	242	pfam08597, eIF3_subunit, Translation initiation fa	3e-06
TIGR01069	771	TIGR01069, mutS2, MutS2 family protein	3e-06
TIGR02794	346	TIGR02794, tolA_full, TolA protein	4e-06
TIGR02794	346	TIGR02794, tolA_full, TolA protein	4e-06
pfam10243	506	pfam10243, MIP-T3, Microtubule-binding protein MIP	4e-06
COG4499	434	COG4499, COG4499, Predicted membrane protein [Func	4e-06
pfam08208	193	pfam08208, RNA_polI_A34, DNA-directed RNA polymera	4e-06
PRK14552	414	PRK14552, PRK14552, C/D box methylation guide ribo	4e-06
PRK14552	414	PRK14552, PRK14552, C/D box methylation guide ribo	4e-06
pfam08432	182	pfam08432, DUF1742, Fungal protein of unknown func	5e-06
pfam10243	506	pfam10243, MIP-T3, Microtubule-binding protein MIP	5e-06
pfam08208	193	pfam08208, RNA_polI_A34, DNA-directed RNA polymera	5e-06
pfam12569	516	pfam12569, NARP1, NMDA receptor-regulated protein	5e-06
CHL00204	1832	CHL00204, ycf1, Ycf1; Provisional	5e-06
PRK12903	925	PRK12903, secA, preprotein translocase subunit Sec	5e-06
PTZ00108	1388	PTZ00108, PTZ00108, DNA topoisomerase 2-like prote	6e-06
PRK05901	509	PRK05901, PRK05901, RNA polymerase sigma factor; P	6e-06
PRK14552	414	PRK14552, PRK14552, C/D box methylation guide ribo	6e-06
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	7e-06
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	7e-06
pfam10243	506	pfam10243, MIP-T3, Microtubule-binding protein MIP	7e-06
PRK12704	520	PRK12704, PRK12704, phosphodiesterase; Provisional	7e-06
PLN02381	1066	PLN02381, PLN02381, valyl-tRNA synthetase	7e-06
PRK05901	509	PRK05901, PRK05901, RNA polymerase sigma factor; P	7e-06
PRK11642	813	PRK11642, PRK11642, exoribonuclease R; Provisional	7e-06
pfam00183	529	pfam00183, HSP90, Hsp90 protein	7e-06
pfam10243	506	pfam10243, MIP-T3, Microtubule-binding protein MIP	8e-06
PRK13808	333	PRK13808, PRK13808, adenylate kinase; Provisional	8e-06
pfam03962	188	pfam03962, Mnd1, Mnd1 family	8e-06
PRK09510	387	PRK09510, tolA, cell envelope integrity inner memb	8e-06
PTZ00053	470	PTZ00053, PTZ00053, methionine aminopeptidase 2; P	8e-06
PTZ00372	413	PTZ00372, PTZ00372, endonuclease 4-like protein; P	9e-06
COG4499	434	COG4499, COG4499, Predicted membrane protein [Func	9e-06
PRK14552	414	PRK14552, PRK14552, C/D box methylation guide ribo	9e-06
PRK12903	925	PRK12903, secA, preprotein translocase subunit Sec	9e-06
PRK12280	158	PRK12280, rplW, 50S ribosomal protein L23; Reviewe	9e-06
PRK12280	158	PRK12280, rplW, 50S ribosomal protein L23; Reviewe	9e-06
PTZ00372	413	PTZ00372, PTZ00372, endonuclease 4-like protein; P	1e-05
PTZ00372	413	PTZ00372, PTZ00372, endonuclease 4-like protein; P	1e-05
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	1e-05
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	1e-05
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	1e-05
PRK11192	434	PRK11192, PRK11192, ATP-dependent RNA helicase Srm	1e-05
TIGR02794	346	TIGR02794, tolA_full, TolA protein	1e-05
PRK12704	520	PRK12704, PRK12704, phosphodiesterase; Provisional	1e-05
pfam08208	193	pfam08208, RNA_polI_A34, DNA-directed RNA polymera	1e-05
pfam08208	193	pfam08208, RNA_polI_A34, DNA-directed RNA polymera	1e-05
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	1e-05
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	1e-05
PTZ00108	1388	PTZ00108, PTZ00108, DNA topoisomerase 2-like prote	1e-05
pfam12569	516	pfam12569, NARP1, NMDA receptor-regulated protein	1e-05
pfam09468	287	pfam09468, RNase_H2-Ydr279, Ydr279p protein family	1e-05
PRK14552	414	PRK14552, PRK14552, C/D box methylation guide ribo	1e-05
PRK14552	414	PRK14552, PRK14552, C/D box methylation guide ribo	1e-05
PRK14552	414	PRK14552, PRK14552, C/D box methylation guide ribo	1e-05
pfam03962	188	pfam03962, Mnd1, Mnd1 family	1e-05
PRK12280	158	PRK12280, rplW, 50S ribosomal protein L23; Reviewe	1e-05
pfam14181	155	pfam14181, YqfQ, YqfQ-like protein	1e-05
pfam14181	155	pfam14181, YqfQ, YqfQ-like protein	1e-05
CHL00189	742	CHL00189, infB, translation initiation factor 2; P	1e-05
PTZ00399	651	PTZ00399, PTZ00399, cysteinyl-tRNA-synthetase; Pro	1e-05
pfam08496	154	pfam08496, Peptidase_S49_N, Peptidase family S49 N	1e-05
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	2e-05
PLN02381	1066	PLN02381, PLN02381, valyl-tRNA synthetase	2e-05
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	2e-05
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	2e-05
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	2e-05
PRK05901	509	PRK05901, PRK05901, RNA polymerase sigma factor; P	2e-05
pfam09468	287	pfam09468, RNase_H2-Ydr279, Ydr279p protein family	2e-05
pfam05262	489	pfam05262, Borrelia_P83, Borrelia P83/100 protein	2e-05
PRK00409	782	PRK00409, PRK00409, recombination and DNA strand e	2e-05
smart00435	391	smart00435, TOPEUc, DNA Topoisomerase I (eukaryota	2e-05
PRK14552	414	PRK14552, PRK14552, C/D box methylation guide ribo	2e-05
PRK14552	414	PRK14552, PRK14552, C/D box methylation guide ribo	2e-05
TIGR01554	384	TIGR01554, major_cap_HK97, phage major capsid prot	2e-05
CHL00204	1832	CHL00204, ycf1, Ycf1; Provisional	2e-05
PRK12903	925	PRK12903, secA, preprotein translocase subunit Sec	2e-05
pfam00183	529	pfam00183, HSP90, Hsp90 protein	2e-05
PTZ00053	470	PTZ00053, PTZ00053, methionine aminopeptidase 2; P	2e-05
PTZ00053	470	PTZ00053, PTZ00053, methionine aminopeptidase 2; P	2e-05
PRK12280	158	PRK12280, rplW, 50S ribosomal protein L23; Reviewe	2e-05
PRK12280	158	PRK12280, rplW, 50S ribosomal protein L23; Reviewe	2e-05
CHL00189	742	CHL00189, infB, translation initiation factor 2; P	2e-05
CHL00189	742	CHL00189, infB, translation initiation factor 2; P	2e-05
PTZ00399	651	PTZ00399, PTZ00399, cysteinyl-tRNA-synthetase; Pro	2e-05
PRK00247	429	PRK00247, PRK00247, putative inner membrane protei	2e-05
PRK04950	213	PRK04950, PRK04950, ProP expression regulator; Pro	2e-05
PRK04950	213	PRK04950, PRK04950, ProP expression regulator; Pro	2e-05
cd09270	211	cd09270, RNase_H2-B, Ribonuclease H2-B is a subuni	2e-05
pfam13904	261	pfam13904, DUF4207, Domain of unknown function (DU	2e-05
pfam09756	189	pfam09756, DDRGK, DDRGK domain	2e-05
pfam07423	214	pfam07423, DUF1510, Protein of unknown function (D	2e-05
COG5116	926	COG5116, RPN2, 26S proteasome regulatory complex c	2e-05
PTZ00372	413	PTZ00372, PTZ00372, endonuclease 4-like protein; P	3e-05
pfam10243	506	pfam10243, MIP-T3, Microtubule-binding protein MIP	3e-05
PTZ00108	1388	PTZ00108, PTZ00108, DNA topoisomerase 2-like prote	3e-05
PRK05901	509	PRK05901, PRK05901, RNA polymerase sigma factor; P	3e-05
PRK05901	509	PRK05901, PRK05901, RNA polymerase sigma factor; P	3e-05
PRK11642	813	PRK11642, PRK11642, exoribonuclease R; Provisional	3e-05
PRK13808	333	PRK13808, PRK13808, adenylate kinase; Provisional	3e-05
pfam14181	155	pfam14181, YqfQ, YqfQ-like protein	3e-05
PRK04950	213	PRK04950, PRK04950, ProP expression regulator; Pro	3e-05
pfam09756	189	pfam09756, DDRGK, DDRGK domain	3e-05
pfam09756	189	pfam09756, DDRGK, DDRGK domain	3e-05
pfam07423	214	pfam07423, DUF1510, Protein of unknown function (D	3e-05
COG5116	926	COG5116, RPN2, 26S proteasome regulatory complex c	3e-05
TIGR03927	150	TIGR03927, T7SS_EssA_Firm, type VII secretion prot	3e-05
pfam03839	217	pfam03839, Sec62, Translocation protein Sec62	3e-05
pfam03839	217	pfam03839, Sec62, Translocation protein Sec62	3e-05
TIGR03319	514	TIGR03319, RNase_Y, ribonuclease Y	3e-05
pfam04615	728	pfam04615, Utp14, Utp14 protein	3e-05
PRK11192	434	PRK11192, PRK11192, ATP-dependent RNA helicase Srm	4e-05
COG4499	434	COG4499, COG4499, Predicted membrane protein [Func	4e-05
PTZ00108	1388	PTZ00108, PTZ00108, DNA topoisomerase 2-like prote	4e-05
smart00435	391	smart00435, TOPEUc, DNA Topoisomerase I (eukaryota	4e-05
pfam13166	713	pfam13166, AAA_13, AAA domain	4e-05
PRK14552	414	PRK14552, PRK14552, C/D box methylation guide ribo	4e-05
TIGR01069	771	TIGR01069, mutS2, MutS2 family protein	4e-05
pfam09756	189	pfam09756, DDRGK, DDRGK domain	4e-05
pfam04615	728	pfam04615, Utp14, Utp14 protein	4e-05
pfam07767	387	pfam07767, Nop53, Nop53 (60S ribosomal biogenesis)	4e-05
pfam04641	254	pfam04641, Rtf2, Replication termination factor 2	4e-05
PLN02381	1066	PLN02381, PLN02381, valyl-tRNA synthetase	5e-05
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	5e-05
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	5e-05
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	5e-05
pfam13166	713	pfam13166, AAA_13, AAA domain	5e-05
pfam13166	713	pfam13166, AAA_13, AAA domain	5e-05
CHL00204	1832	CHL00204, ycf1, Ycf1; Provisional	5e-05
pfam07423	214	pfam07423, DUF1510, Protein of unknown function (D	5e-05
COG5116	926	COG5116, RPN2, 26S proteasome regulatory complex c	5e-05
COG5116	926	COG5116, RPN2, 26S proteasome regulatory complex c	5e-05
PRK00448	1437	PRK00448, polC, DNA polymerase III PolC; Validated	5e-05
pfam12720	169	pfam12720, DUF3807, Protein of unknown function (D	5e-05
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	6e-05
PTZ00108	1388	PTZ00108, PTZ00108, DNA topoisomerase 2-like prote	6e-05
pfam00183	529	pfam00183, HSP90, Hsp90 protein	6e-05
PRK09510	387	PRK09510, tolA, cell envelope integrity inner memb	6e-05
PTZ00053	470	PTZ00053, PTZ00053, methionine aminopeptidase 2; P	6e-05
PTZ00053	470	PTZ00053, PTZ00053, methionine aminopeptidase 2; P	6e-05
pfam11861	154	pfam11861, DUF3381, Domain of unknown function (DU	6e-05
pfam05764	238	pfam05764, YL1, YL1 nuclear protein	6e-05
pfam10243	506	pfam10243, MIP-T3, Microtubule-binding protein MIP	7e-05
pfam05087	887	pfam05087, Rota_VP2, Rotavirus VP2 protein	7e-05
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	7e-05
pfam09468	287	pfam09468, RNase_H2-Ydr279, Ydr279p protein family	7e-05
PRK14552	414	PRK14552, PRK14552, C/D box methylation guide ribo	7e-05
PRK14552	414	PRK14552, PRK14552, C/D box methylation guide ribo	7e-05
PRK04950	213	PRK04950, PRK04950, ProP expression regulator; Pro	7e-05
TIGR02794	346	TIGR02794, tolA_full, TolA protein	8e-05
pfam09468	287	pfam09468, RNase_H2-Ydr279, Ydr279p protein family	8e-05
CHL00204	1832	CHL00204, ycf1, Ycf1; Provisional	8e-05
pfam00183	529	pfam00183, HSP90, Hsp90 protein	8e-05
CHL00189	742	CHL00189, infB, translation initiation factor 2; P	8e-05
TIGR03927	150	TIGR03927, T7SS_EssA_Firm, type VII secretion prot	8e-05
PRK00448	1437	PRK00448, polC, DNA polymerase III PolC; Validated	8e-05
pfam00183	529	pfam00183, HSP90, Hsp90 protein	9e-05
PRK04950	213	PRK04950, PRK04950, ProP expression regulator; Pro	9e-05
pfam10278	178	pfam10278, Med19, Mediator of RNA pol II transcrip	9e-05
pfam13476	204	pfam13476, AAA_23, AAA domain	9e-05
TIGR02794	346	TIGR02794, tolA_full, TolA protein	1e-04
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	1e-04
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	1e-04
PTZ00108	1388	PTZ00108, PTZ00108, DNA topoisomerase 2-like prote	1e-04
PTZ00108	1388	PTZ00108, PTZ00108, DNA topoisomerase 2-like prote	1e-04
PRK05901	509	PRK05901, PRK05901, RNA polymerase sigma factor; P	1e-04
pfam12569	516	pfam12569, NARP1, NMDA receptor-regulated protein	1e-04
pfam12569	516	pfam12569, NARP1, NMDA receptor-regulated protein	1e-04
CHL00204	1832	CHL00204, ycf1, Ycf1; Provisional	1e-04
PRK09510	387	PRK09510, tolA, cell envelope integrity inner memb	1e-04
pfam14181	155	pfam14181, YqfQ, YqfQ-like protein	1e-04
PTZ00399	651	PTZ00399, PTZ00399, cysteinyl-tRNA-synthetase; Pro	1e-04
pfam08496	154	pfam08496, Peptidase_S49_N, Peptidase family S49 N	1e-04
pfam07423	214	pfam07423, DUF1510, Protein of unknown function (D	1e-04
pfam07423	214	pfam07423, DUF1510, Protein of unknown function (D	1e-04
pfam03839	217	pfam03839, Sec62, Translocation protein Sec62	1e-04
pfam07767	387	pfam07767, Nop53, Nop53 (60S ribosomal biogenesis)	1e-04
pfam05758	832	pfam05758, Ycf1, Ycf1	1e-04
pfam05758	832	pfam05758, Ycf1, Ycf1	1e-04
PRK07561	859	PRK07561, PRK07561, DNA topoisomerase I subunit om	1e-04
pfam14265	125	pfam14265, DUF4355, Domain of unknown function (DU	1e-04
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	2e-04
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	2e-04
pfam08208	193	pfam08208, RNA_polI_A34, DNA-directed RNA polymera	2e-04
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	2e-04
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	2e-04
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	2e-04
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	2e-04
pfam12569	516	pfam12569, NARP1, NMDA receptor-regulated protein	2e-04
COG0810	244	COG0810, TonB, Periplasmic protein TonB, links inn	2e-04
smart00435	391	smart00435, TOPEUc, DNA Topoisomerase I (eukaryota	2e-04
pfam13166	713	pfam13166, AAA_13, AAA domain	2e-04
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	2e-04
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	2e-04
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	2e-04
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	2e-04
PRK09510	387	PRK09510, tolA, cell envelope integrity inner memb	2e-04
PRK12280	158	PRK12280, rplW, 50S ribosomal protein L23; Reviewe	2e-04
pfam14181	155	pfam14181, YqfQ, YqfQ-like protein	2e-04
CHL00189	742	CHL00189, infB, translation initiation factor 2; P	2e-04
pfam08496	154	pfam08496, Peptidase_S49_N, Peptidase family S49 N	2e-04
pfam08496	154	pfam08496, Peptidase_S49_N, Peptidase family S49 N	2e-04
pfam07423	214	pfam07423, DUF1510, Protein of unknown function (D	2e-04
TIGR03319	514	TIGR03319, RNase_Y, ribonuclease Y	2e-04
TIGR03319	514	TIGR03319, RNase_Y, ribonuclease Y	2e-04
pfam04615	728	pfam04615, Utp14, Utp14 protein	2e-04
pfam10278	178	pfam10278, Med19, Mediator of RNA pol II transcrip	2e-04
pfam05758	832	pfam05758, Ycf1, Ycf1	2e-04
PRK07561	859	PRK07561, PRK07561, DNA topoisomerase I subunit om	2e-04
PRK07561	859	PRK07561, PRK07561, DNA topoisomerase I subunit om	2e-04
PRK07561	859	PRK07561, PRK07561, DNA topoisomerase I subunit om	2e-04
PRK11778	330	PRK11778, PRK11778, putative inner membrane peptid	2e-04
PRK11778	330	PRK11778, PRK11778, putative inner membrane peptid	2e-04
pfam09736	141	pfam09736, Bud13, Pre-mRNA-splicing factor of RES	2e-04
PRK07219	822	PRK07219, PRK07219, DNA topoisomerase I; Validated	2e-04
PRK07219	822	PRK07219, PRK07219, DNA topoisomerase I; Validated	2e-04
pfam13868	349	pfam13868, Trichoplein, Tumour suppressor, Mitosta	2e-04
COG1293	564	COG1293, COG1293, Predicted RNA-binding protein ho	2e-04
COG3611	417	COG3611, DnaB, Replication initiation/membrane att	2e-04
COG5192	1077	COG5192, BMS1, GTP-binding protein required for 40	2e-04
COG5163	591	COG5163, NOP7, Protein required for biogenesis of	2e-04
COG3064	387	COG3064, TolA, Membrane protein involved in colici	2e-04
COG5019	373	COG5019, CDC3, Septin family protein [Cell divisio	2e-04
pfam04147	809	pfam04147, Nop14, Nop14-like family	2e-04
PRK14907	295	PRK14907, rplD, 50S ribosomal protein L4; Provisio	2e-04
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	3e-04
pfam10243	506	pfam10243, MIP-T3, Microtubule-binding protein MIP	3e-04
PRK12704	520	PRK12704, PRK12704, phosphodiesterase; Provisional	3e-04
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	3e-04
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	3e-04
PLN02967	581	PLN02967, PLN02967, kinase	3e-04
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	3e-04
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	3e-04
TIGR01069	771	TIGR01069, mutS2, MutS2 family protein	3e-04
PRK09510	387	PRK09510, tolA, cell envelope integrity inner memb	3e-04
PRK09510	387	PRK09510, tolA, cell envelope integrity inner memb	3e-04
PRK07561	859	PRK07561, PRK07561, DNA topoisomerase I subunit om	3e-04
PRK07561	859	PRK07561, PRK07561, DNA topoisomerase I subunit om	3e-04
PRK07219	822	PRK07219, PRK07219, DNA topoisomerase I; Validated	3e-04
COG5163	591	COG5163, NOP7, Protein required for biogenesis of	3e-04
COG3064	387	COG3064, TolA, Membrane protein involved in colici	3e-04
COG3064	387	COG3064, TolA, Membrane protein involved in colici	3e-04
PRK03918	880	PRK03918, PRK03918, chromosome segregation protein	3e-04
PRK03918	880	PRK03918, PRK03918, chromosome segregation protein	3e-04
COG2604	594	COG2604, COG2604, Uncharacterized protein conserve	3e-04
pfam06658	142	pfam06658, DUF1168, Protein of unknown function (D	3e-04
COG1498	395	COG1498, SIK1, Protein implicated in ribosomal bio	3e-04
PLN02381	1066	PLN02381, PLN02381, valyl-tRNA synthetase	4e-04
TIGR01554	384	TIGR01554, major_cap_HK97, phage major capsid prot	4e-04
PRK11642	813	PRK11642, PRK11642, exoribonuclease R; Provisional	4e-04
PRK13808	333	PRK13808, PRK13808, adenylate kinase; Provisional	4e-04
PTZ00053	470	PTZ00053, PTZ00053, methionine aminopeptidase 2; P	4e-04
PRK04950	213	PRK04950, PRK04950, ProP expression regulator; Pro	4e-04
pfam07423	214	pfam07423, DUF1510, Protein of unknown function (D	4e-04
PRK00448	1437	PRK00448, polC, DNA polymerase III PolC; Validated	4e-04
pfam10278	178	pfam10278, Med19, Mediator of RNA pol II transcrip	4e-04
COG5192	1077	COG5192, BMS1, GTP-binding protein required for 40	4e-04
pfam06375	561	pfam06375, BLVR, Bovine leukaemia virus receptor (	4e-04
pfam10310	436	pfam10310, DUF2413, Protein of unknown function (D	4e-04
COG0419	908	COG0419, SbcC, ATPase involved in DNA repair [DNA	4e-04
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	5e-04
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	5e-04
PRK13808	333	PRK13808, PRK13808, adenylate kinase; Provisional	5e-04
PRK09510	387	PRK09510, tolA, cell envelope integrity inner memb	5e-04
cd09270	211	cd09270, RNase_H2-B, Ribonuclease H2-B is a subuni	5e-04
pfam04641	254	pfam04641, Rtf2, Replication termination factor 2	5e-04
COG5192	1077	COG5192, BMS1, GTP-binding protein required for 40	5e-04
PRK03918	880	PRK03918, PRK03918, chromosome segregation protein	5e-04
PRK03918	880	PRK03918, PRK03918, chromosome segregation protein	5e-04
pfam05424	276	pfam05424, Duffy_binding, Duffy binding domain	5e-04
pfam08229	196	pfam08229, SHR3_chaperone, ER membrane protein SH3	5e-04
TIGR02168	1179	TIGR02168, SMC_prok_B, chromosome segregation prot	5e-04
COG1193	753	COG1193, COG1193, Mismatch repair ATPase (MutS fam	5e-04
pfam13148	379	pfam13148, DUF3987, Protein of unknown function (D	5e-04
COG0525	877	COG0525, ValS, Valyl-tRNA synthetase [Translation,	5e-04
pfam10243	506	pfam10243, MIP-T3, Microtubule-binding protein MIP	6e-04
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	6e-04
pfam12569	516	pfam12569, NARP1, NMDA receptor-regulated protein	6e-04
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	6e-04
PRK14552	414	PRK14552, PRK14552, C/D box methylation guide ribo	6e-04
PTZ00399	651	PTZ00399, PTZ00399, cysteinyl-tRNA-synthetase; Pro	6e-04
PRK00247	429	PRK00247, PRK00247, putative inner membrane protei	6e-04
pfam03839	217	pfam03839, Sec62, Translocation protein Sec62	6e-04
pfam04641	254	pfam04641, Rtf2, Replication termination factor 2	6e-04
COG5019	373	COG5019, CDC3, Septin family protein [Cell divisio	6e-04
COG1498	395	COG1498, SIK1, Protein implicated in ribosomal bio	6e-04
COG0610	962	COG0610, COG0610, Type I site-specific restriction	6e-04
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	7e-04
pfam05087	887	pfam05087, Rota_VP2, Rotavirus VP2 protein	7e-04
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	7e-04
PRK05901	509	PRK05901, PRK05901, RNA polymerase sigma factor; P	7e-04
pfam05262	489	pfam05262, Borrelia_P83, Borrelia P83/100 protein	7e-04
PRK00247	429	PRK00247, PRK00247, putative inner membrane protei	7e-04
PRK00448	1437	PRK00448, polC, DNA polymerase III PolC; Validated	7e-04
pfam13476	204	pfam13476, AAA_23, AAA domain	7e-04
pfam05758	832	pfam05758, Ycf1, Ycf1	7e-04
COG3064	387	COG3064, TolA, Membrane protein involved in colici	7e-04
COG3064	387	COG3064, TolA, Membrane protein involved in colici	7e-04
PRK03918	880	PRK03918, PRK03918, chromosome segregation protein	7e-04
COG0419	908	COG0419, SbcC, ATPase involved in DNA repair [DNA	7e-04
pfam10211	189	pfam10211, Ax_dynein_light, Axonemal dynein light	7e-04
COG4499	434	COG4499, COG4499, Predicted membrane protein [Func	8e-04
TIGR01069	771	TIGR01069, mutS2, MutS2 family protein	8e-04
PRK12280	158	PRK12280, rplW, 50S ribosomal protein L23; Reviewe	8e-04
pfam08496	154	pfam08496, Peptidase_S49_N, Peptidase family S49 N	8e-04
pfam10278	178	pfam10278, Med19, Mediator of RNA pol II transcrip	8e-04
COG1498	395	COG1498, SIK1, Protein implicated in ribosomal bio	8e-04
COG0711	161	COG0711, AtpF, F0F1-type ATP synthase, subunit b [	8e-04
pfam09507	427	pfam09507, CDC27, DNA polymerase subunit Cdc27	8e-04
smart00435	391	smart00435, TOPEUc, DNA Topoisomerase I (eukaryota	9e-04
PRK09510	387	PRK09510, tolA, cell envelope integrity inner memb	9e-04
cd09270	211	cd09270, RNase_H2-B, Ribonuclease H2-B is a subuni	9e-04
TIGR03927	150	TIGR03927, T7SS_EssA_Firm, type VII secretion prot	9e-04
COG1498	395	COG1498, SIK1, Protein implicated in ribosomal bio	9e-04
pfam09428	130	pfam09428, DUF2011, Fungal protein of unknown func	9e-04
PRK05658	619	PRK05658, PRK05658, RNA polymerase sigma factor Rp	9e-04
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	0.001
pfam07946	322	pfam07946, DUF1682, Protein of unknown function (D	0.001
pfam07946	322	pfam07946, DUF1682, Protein of unknown function (D	0.001
PLN02381	1066	PLN02381, PLN02381, valyl-tRNA synthetase	0.001
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	0.001
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	0.001
PRK05901	509	PRK05901, PRK05901, RNA polymerase sigma factor; P	0.001
COG0810	244	COG0810, TonB, Periplasmic protein TonB, links inn	0.001
pfam05262	489	pfam05262, Borrelia_P83, Borrelia P83/100 protein	0.001
pfam05262	489	pfam05262, Borrelia_P83, Borrelia P83/100 protein	0.001
pfam05262	489	pfam05262, Borrelia_P83, Borrelia P83/100 protein	0.001
PRK05306	746	PRK05306, infB, translation initiation factor IF-2	0.001
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	0.001
PRK13808	333	PRK13808, PRK13808, adenylate kinase; Provisional	0.001
PRK09510	387	PRK09510, tolA, cell envelope integrity inner memb	0.001
PTZ00053	470	PTZ00053, PTZ00053, methionine aminopeptidase 2; P	0.001
PTZ00053	470	PTZ00053, PTZ00053, methionine aminopeptidase 2; P	0.001
PRK12280	158	PRK12280, rplW, 50S ribosomal protein L23; Reviewe	0.001
COG5116	926	COG5116, RPN2, 26S proteasome regulatory complex c	0.001
pfam03839	217	pfam03839, Sec62, Translocation protein Sec62	0.001
TIGR03319	514	TIGR03319, RNase_Y, ribonuclease Y	0.001
PRK07561	859	PRK07561, PRK07561, DNA topoisomerase I subunit om	0.001
PRK07219	822	PRK07219, PRK07219, DNA topoisomerase I; Validated	0.001
PRK07219	822	PRK07219, PRK07219, DNA topoisomerase I; Validated	0.001
pfam13868	349	pfam13868, Trichoplein, Tumour suppressor, Mitosta	0.001
COG5192	1077	COG5192, BMS1, GTP-binding protein required for 40	0.001
COG5019	373	COG5019, CDC3, Septin family protein [Cell divisio	0.001
PRK14907	295	PRK14907, rplD, 50S ribosomal protein L4; Provisio	0.001
PRK03918	880	PRK03918, PRK03918, chromosome segregation protein	0.001
PRK03918	880	PRK03918, PRK03918, chromosome segregation protein	0.001
COG1498	395	COG1498, SIK1, Protein implicated in ribosomal bio	0.001
COG0419	908	COG0419, SbcC, ATPase involved in DNA repair [DNA	0.001
pfam13148	379	pfam13148, DUF3987, Protein of unknown function (D	0.001
pfam10211	189	pfam10211, Ax_dynein_light, Axonemal dynein light	0.001
pfam09428	130	pfam09428, DUF2011, Fungal protein of unknown func	0.001
pfam09428	130	pfam09428, DUF2011, Fungal protein of unknown func	0.001
PRK14900	1052	PRK14900, valS, valyl-tRNA synthetase; Provisional	0.001
smart00786	196	smart00786, SHR3_chaperone, ER membrane protein SH	0.001
COG0016	335	COG0016, PheS, Phenylalanyl-tRNA synthetase alpha	0.001
PRK05035	695	PRK05035, PRK05035, electron transport complex pro	0.001
TIGR02169	1164	TIGR02169, SMC_prok_A, chromosome segregation prot	0.001
COG4487	438	COG4487, COG4487, Uncharacterized protein conserve	0.001
COG0488	530	COG0488, Uup, ATPase components of ABC transporter	0.001
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	0.002
PLN02381	1066	PLN02381, PLN02381, valyl-tRNA synthetase	0.002
pfam08208	193	pfam08208, RNA_polI_A34, DNA-directed RNA polymera	0.002
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	0.002
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	0.002
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	0.002
PRK05901	509	PRK05901, PRK05901, RNA polymerase sigma factor; P	0.002
COG0810	244	COG0810, TonB, Periplasmic protein TonB, links inn	0.002
PRK00409	782	PRK00409, PRK00409, recombination and DNA strand e	0.002
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	0.002
PRK14552	414	PRK14552, PRK14552, C/D box methylation guide ribo	0.002
pfam00183	529	pfam00183, HSP90, Hsp90 protein	0.002
PRK09510	387	PRK09510, tolA, cell envelope integrity inner memb	0.002
PRK09510	387	PRK09510, tolA, cell envelope integrity inner memb	0.002
PRK00247	429	PRK00247, PRK00247, putative inner membrane protei	0.002
PRK00247	429	PRK00247, PRK00247, putative inner membrane protei	0.002
PRK04950	213	PRK04950, PRK04950, ProP expression regulator; Pro	0.002
pfam09756	189	pfam09756, DDRGK, DDRGK domain	0.002
pfam09756	189	pfam09756, DDRGK, DDRGK domain	0.002
pfam07423	214	pfam07423, DUF1510, Protein of unknown function (D	0.002
pfam04615	728	pfam04615, Utp14, Utp14 protein	0.002
pfam04615	728	pfam04615, Utp14, Utp14 protein	0.002
pfam04615	728	pfam04615, Utp14, Utp14 protein	0.002
pfam12720	169	pfam12720, DUF3807, Protein of unknown function (D	0.002
pfam11861	154	pfam11861, DUF3381, Domain of unknown function (DU	0.002
pfam05764	238	pfam05764, YL1, YL1 nuclear protein	0.002
pfam05764	238	pfam05764, YL1, YL1 nuclear protein	0.002
PRK07561	859	PRK07561, PRK07561, DNA topoisomerase I subunit om	0.002
PRK07561	859	PRK07561, PRK07561, DNA topoisomerase I subunit om	0.002
PRK07561	859	PRK07561, PRK07561, DNA topoisomerase I subunit om	0.002
pfam14265	125	pfam14265, DUF4355, Domain of unknown function (DU	0.002
pfam13868	349	pfam13868, Trichoplein, Tumour suppressor, Mitosta	0.002
pfam13868	349	pfam13868, Trichoplein, Tumour suppressor, Mitosta	0.002
COG3064	387	COG3064, TolA, Membrane protein involved in colici	0.002
PRK03918	880	PRK03918, PRK03918, chromosome segregation protein	0.002
PRK03918	880	PRK03918, PRK03918, chromosome segregation protein	0.002
pfam06658	142	pfam06658, DUF1168, Protein of unknown function (D	0.002
COG1498	395	COG1498, SIK1, Protein implicated in ribosomal bio	0.002
COG1498	395	COG1498, SIK1, Protein implicated in ribosomal bio	0.002
COG0419	908	COG0419, SbcC, ATPase involved in DNA repair [DNA	0.002
COG0419	908	COG0419, SbcC, ATPase involved in DNA repair [DNA	0.002
COG0419	908	COG0419, SbcC, ATPase involved in DNA repair [DNA	0.002
COG0419	908	COG0419, SbcC, ATPase involved in DNA repair [DNA	0.002
pfam08229	196	pfam08229, SHR3_chaperone, ER membrane protein SH3	0.002
COG0610	962	COG0610, COG0610, Type I site-specific restriction	0.002
smart00786	196	smart00786, SHR3_chaperone, ER membrane protein SH	0.002
smart00786	196	smart00786, SHR3_chaperone, ER membrane protein SH	0.002
PRK05035	695	PRK05035, PRK05035, electron transport complex pro	0.002
pfam06102	168	pfam06102, DUF947, Domain of unknown function (DUF	0.002
pfam09731	493	pfam09731, Mitofilin, Mitochondrial inner membrane	0.002
pfam14153	185	pfam14153, Spore_coat_CotO, Spore coat protein Cot	0.002
pfam11208	132	pfam11208, DUF2992, Protein of unknown function (D	0.002
pfam11208	132	pfam11208, DUF2992, Protein of unknown function (D	0.002
PRK14953	486	PRK14953, PRK14953, DNA polymerase III subunits ga	0.002
PRK13735	942	PRK13735, PRK13735, conjugal transfer mating pair	0.002
COG5421	480	COG5421, COG5421, Transposase [DNA replication, re	0.002
pfam11262	296	pfam11262, Tho2, Transcription factor/nuclear expo	0.002
PRK09535	366	PRK09535, btuC, corrinoid ABC transporter permease	0.002
PTZ00342	746	PTZ00342, PTZ00342, acyl-CoA synthetase; Provision	0.002
COG2433	652	COG2433, COG2433, Uncharacterized conserved protei	0.002
pfam09831	177	pfam09831, DUF2058, Uncharacterized protein conser	0.002
pfam05917	417	pfam05917, DUF874, Helicobacter pylori protein of	0.002
pfam07133	164	pfam07133, Merozoite_SPAM, Merozoite surface prote	0.002
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	0.003
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	0.003
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	0.003
pfam09468	287	pfam09468, RNase_H2-Ydr279, Ydr279p protein family	0.003
pfam05262	489	pfam05262, Borrelia_P83, Borrelia P83/100 protein	0.003
PRK05306	746	PRK05306, infB, translation initiation factor IF-2	0.003
pfam13166	713	pfam13166, AAA_13, AAA domain	0.003
pfam13166	713	pfam13166, AAA_13, AAA domain	0.003
pfam13166	713	pfam13166, AAA_13, AAA domain	0.003
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	0.003
PRK09510	387	PRK09510, tolA, cell envelope integrity inner memb	0.003
PTZ00399	651	PTZ00399, PTZ00399, cysteinyl-tRNA-synthetase; Pro	0.003
pfam09756	189	pfam09756, DDRGK, DDRGK domain	0.003
TIGR03927	150	TIGR03927, T7SS_EssA_Firm, type VII secretion prot	0.003
pfam07767	387	pfam07767, Nop53, Nop53 (60S ribosomal biogenesis)	0.003
pfam13476	204	pfam13476, AAA_23, AAA domain	0.003
pfam14265	125	pfam14265, DUF4355, Domain of unknown function (DU	0.003
pfam14265	125	pfam14265, DUF4355, Domain of unknown function (DU	0.003
pfam13868	349	pfam13868, Trichoplein, Tumour suppressor, Mitosta	0.003
COG3064	387	COG3064, TolA, Membrane protein involved in colici	0.003
COG3064	387	COG3064, TolA, Membrane protein involved in colici	0.003
COG1498	395	COG1498, SIK1, Protein implicated in ribosomal bio	0.003
COG0419	908	COG0419, SbcC, ATPase involved in DNA repair [DNA	0.003
COG0419	908	COG0419, SbcC, ATPase involved in DNA repair [DNA	0.003
COG0419	908	COG0419, SbcC, ATPase involved in DNA repair [DNA	0.003
pfam08229	196	pfam08229, SHR3_chaperone, ER membrane protein SH3	0.003
pfam08229	196	pfam08229, SHR3_chaperone, ER membrane protein SH3	0.003
PRK05658	619	PRK05658, PRK05658, RNA polymerase sigma factor Rp	0.003
pfam06102	168	pfam06102, DUF947, Domain of unknown function (DUF	0.003
pfam11262	296	pfam11262, Tho2, Transcription factor/nuclear expo	0.003
pfam07133	164	pfam07133, Merozoite_SPAM, Merozoite surface prote	0.003
PLN03237	1465	PLN03237, PLN03237, DNA topoisomerase 2; Provision	0.003
COG0172	429	COG0172, SerS, Seryl-tRNA synthetase [Translation,	0.003
PTZ00069	300	PTZ00069, PTZ00069, 60S ribosomal protein L5; Prov	0.003
PRK04098	158	PRK04098, PRK04098, sec-independent translocase; P	0.003
pfam06098	288	pfam06098, Radial_spoke_3, Radial spoke protein 3	0.003
pfam03998	239	pfam03998, Utp11, Utp11 protein	0.003
COG5269	379	COG5269, ZUO1, Ribosome-associated chaperone zuoti	0.003
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	0.004
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	0.004
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	0.004
PRK05901	509	PRK05901, PRK05901, RNA polymerase sigma factor; P	0.004
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	0.004
pfam00183	529	pfam00183, HSP90, Hsp90 protein	0.004
pfam09756	189	pfam09756, DDRGK, DDRGK domain	0.004
pfam04615	728	pfam04615, Utp14, Utp14 protein	0.004
pfam04615	728	pfam04615, Utp14, Utp14 protein	0.004
PRK00448	1437	PRK00448, polC, DNA polymerase III PolC; Validated	0.004
pfam12720	169	pfam12720, DUF3807, Protein of unknown function (D	0.004
pfam14265	125	pfam14265, DUF4355, Domain of unknown function (DU	0.004
PRK11778	330	PRK11778, PRK11778, putative inner membrane peptid	0.004
pfam09736	141	pfam09736, Bud13, Pre-mRNA-splicing factor of RES	0.004
pfam13868	349	pfam13868, Trichoplein, Tumour suppressor, Mitosta	0.004
COG5019	373	COG5019, CDC3, Septin family protein [Cell divisio	0.004
PRK14907	295	PRK14907, rplD, 50S ribosomal protein L4; Provisio	0.004
PRK14907	295	PRK14907, rplD, 50S ribosomal protein L4; Provisio	0.004
PRK03918	880	PRK03918, PRK03918, chromosome segregation protein	0.004
COG0419	908	COG0419, SbcC, ATPase involved in DNA repair [DNA	0.004
pfam08229	196	pfam08229, SHR3_chaperone, ER membrane protein SH3	0.004
pfam09428	130	pfam09428, DUF2011, Fungal protein of unknown func	0.004
pfam09428	130	pfam09428, DUF2011, Fungal protein of unknown func	0.004
PRK05035	695	PRK05035, PRK05035, electron transport complex pro	0.004
TIGR02169	1164	TIGR02169, SMC_prok_A, chromosome segregation prot	0.004
COG0172	429	COG0172, SerS, Seryl-tRNA synthetase [Translation,	0.004
pfam06644	250	pfam06644, ATP11, ATP11 protein	0.004
pfam11719	397	pfam11719, Drc1-Sld2, DNA replication and checkpoi	0.004
PHA00727	278	PHA00727, PHA00727, hypothetical protein	0.004

>gnl|CDD|215724 pfam00110, wnt, wnt family

 Score =  166 bits (423), Expect = 4e-50
 Identities = 67/157 (42%), Positives = 90/157 (57%), Gaps = 20/157 (12%)

Query: 36  VCSRVPGLSFGQVRQCSLFADHMASVGRGAAESIAECQHQFRHHRWNCSSGGPGAGGGGG 95
           +CS++PGLS  Q R C    D MASVG GA   I ECQHQFR+ RWNCS+          
Sbjct: 1   ICSKLPGLSRKQRRLCRRNPDVMASVGEGARLGIEECQHQFRNRRWNCST---------- 50

Query: 96  GKSESTTAPSVLPPTLHIGSREAAFTHAIATAGVVYAVARSCKDGSLPSCGCSRTARPKD 155
                  + SV    L  G+RE AF +AI++AGVV+AV R+C +G+L SCGC R+ R + 
Sbjct: 51  -----LDSSSVFGKILKRGTRETAFVYAISSAGVVHAVTRACSEGNLESCGCDRSRRGRS 105

Query: 156 LKREWLWGGCGDNLEYGYKGGKK-----ERRKQRRRK 187
               W WGGC DN+++G +  ++     ER +  R  
Sbjct: 106 GPGGWEWGGCSDNIKFGIRFSREFLDARERGRDARAL 142

Wnt genes have been identified in vertebrates and invertebrates but not in plants, unicellular eukaryotes or prokaryotes. In humans, 19 WNT proteins are known. Because of their insolubility little is known about Wnt protein structure, but all have 23 or 24 Cys residues whose spacing is highly conserved. Signal transduction by Wnt proteins (including the Wnt/beta-catenin, the Wnt/Ca++, and the Wnt/polarity pathway) is mediated by receptors of the Frizzled and LDL-receptor-related protein (LRP) families. Length = 308

>gnl|CDD|128408 smart00097, WNT1, found in Wnt-1

 Score =  164 bits (417), Expect = 4e-49
 Identities = 64/153 (41%), Positives = 80/153 (52%), Gaps = 20/153 (13%)

Query: 40  VPGLSFGQVRQCSLFADHMASVGRGAAESIAECQHQFRHHRWNCSSGGPGAGGGGGGKSE 99
           +PGLS  Q R C    D M SV  GA E I ECQHQFR  RWNCS+              
Sbjct: 2   LPGLSRRQRRLCRANPDVMISVAEGAQEGIEECQHQFRFRRWNCSTLDN----------- 50

Query: 100 STTAPSVLPPTLHIGSREAAFTHAIATAGVVYAVARSCKDGSLPSCGCSRTARPKDLKRE 159
                SV    L  G+RE AF +AI++AGV +AV R+C +G L SCGC    R +   R 
Sbjct: 51  ----ASVFGKVLRQGTRETAFVYAISSAGVAHAVTRACSEGELDSCGCDYRKRGRAGGRG 106

Query: 160 WLWGGCGDNLEYGYKGGKK-----ERRKQRRRK 187
           W WGGC DN+++G +  ++     ER K  R  
Sbjct: 107 WKWGGCSDNIDFGIRFSREFVDARERGKDARAL 139

Length = 305

>gnl|CDD|235250 PRK04195, PRK04195, replication factor C large subunit; Provisional

 Score = 66.5 bits (163), Expect = 2e-12
 Identities = 30/80 (37%), Positives = 61/80 (76%)

Query: 194 KEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKK 253
           +EE E     K+  KK KK  +K EKK++E+KKEKKKK    K+K+++++E+K+KKEE+K
Sbjct: 396 EEEIEFLTGSKKATKKIKKIVEKAEKKREEEKKEKKKKAFAGKKKEEEEEEEKEKKEEEK 455

Query: 254 KEKKKKKKKKEKKKKKDEGR 273
           +E++++ +++++++++ + +
Sbjct: 456 EEEEEEAEEEKEEEEEKKKK 475

Length = 482

>gnl|CDD|235250 PRK04195, PRK04195, replication factor C large subunit; Provisional

 Score = 65.7 bits (161), Expect = 3e-12
 Identities = 28/73 (38%), Positives = 59/73 (80%)

Query: 188 RKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKK 247
              K+  ++ +K  EK E+K++E+KKEKKK+    +KK+E+++++K+KKE++K+++E++ 
Sbjct: 403 TGSKKATKKIKKIVEKAEKKREEEKKEKKKKAFAGKKKEEEEEEEKEKKEEEKEEEEEEA 462

Query: 248 KKEEKKKEKKKKK 260
           ++E++++E+KKKK
Sbjct: 463 EEEKEEEEEKKKK 475

Length = 482

>gnl|CDD|235250 PRK04195, PRK04195, replication factor C large subunit; Provisional

 Score = 63.8 bits (156), Expect = 1e-11
 Identities = 27/71 (38%), Positives = 59/71 (83%)

Query: 191 KRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKE 250
            +K  ++ K+  +K EKK+E++K++KK+K    KKKE++++++K+K++++K++E+++ +E
Sbjct: 405 SKKATKKIKKIVEKAEKKREEEKKEKKKKAFAGKKKEEEEEEEKEKKEEEKEEEEEEAEE 464

Query: 251 EKKKEKKKKKK 261
           EK++E++KKKK
Sbjct: 465 EKEEEEEKKKK 475

Length = 482

>gnl|CDD|235250 PRK04195, PRK04195, replication factor C large subunit; Provisional

 Score = 63.0 bits (154), Expect = 3e-11
 Identities = 25/73 (34%), Positives = 60/73 (82%)

Query: 193 KKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEK 252
            K+  +K ++  E+ +K++++EKK++KKK    K+K+++++++KEKK+++KE+++++ E+
Sbjct: 405 SKKATKKIKKIVEKAEKKREEEKKEKKKKAFAGKKKEEEEEEEKEKKEEEKEEEEEEAEE 464

Query: 253 KKEKKKKKKKKEK 265
           +KE++++KKKK+ 
Sbjct: 465 EKEEEEEKKKKQA 477

Length = 482

>gnl|CDD|235250 PRK04195, PRK04195, replication factor C large subunit; Provisional

 Score = 62.2 bits (152), Expect = 4e-11
 Identities = 32/73 (43%), Positives = 59/73 (80%)

Query: 184 RRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKK 243
              K+  K+ K+  EK E+K+EE+KKEKKK+    KKK+E+++E+K+KK+++KE+++++ 
Sbjct: 403 TGSKKATKKIKKIVEKAEKKREEEKKEKKKKAFAGKKKEEEEEEEKEKKEEEKEEEEEEA 462

Query: 244 EKKKKKEEKKKEK 256
           E++K++EE+KK+K
Sbjct: 463 EEEKEEEEEKKKK 475

Length = 482

>gnl|CDD|235250 PRK04195, PRK04195, replication factor C large subunit; Provisional

 Score = 61.9 bits (151), Expect = 6e-11
 Identities = 29/76 (38%), Positives = 59/76 (77%), Gaps = 3/76 (3%)

Query: 192 RKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEE 251
              ++  K+ +K  EK ++K++E+KKEKK   KK    KKK++++E++K+KKE++K++EE
Sbjct: 403 TGSKKATKKIKKIVEKAEKKREEEKKEKK---KKAFAGKKKEEEEEEEKEKKEEEKEEEE 459

Query: 252 KKKEKKKKKKKKEKKK 267
           ++ E++K++++++KKK
Sbjct: 460 EEAEEEKEEEEEKKKK 475

Length = 482

>gnl|CDD|235250 PRK04195, PRK04195, replication factor C large subunit; Provisional

 Score = 61.1 bits (149), Expect = 1e-10
 Identities = 24/73 (32%), Positives = 58/73 (79%)

Query: 186 RKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEK 245
              K+  KK ++  E+ +K+ ++++K+K+KK    KK++++E+++K+KK++EK+++++E 
Sbjct: 403 TGSKKATKKIKKIVEKAEKKREEEKKEKKKKAFAGKKKEEEEEEEKEKKEEEKEEEEEEA 462

Query: 246 KKKKEEKKKEKKK 258
           +++KEE++++KKK
Sbjct: 463 EEEKEEEEEKKKK 475

Length = 482

>gnl|CDD|235250 PRK04195, PRK04195, replication factor C large subunit; Provisional

 Score = 60.3 bits (147), Expect = 2e-10
 Identities = 22/73 (30%), Positives = 58/73 (79%)

Query: 190 RKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKK 249
              KK  ++ ++  ++ +KK ++++K+K+KK    KK++++++++K++K+++K+E++++ 
Sbjct: 403 TGSKKATKKIKKIVEKAEKKREEEKKEKKKKAFAGKKKEEEEEEEKEKKEEEKEEEEEEA 462

Query: 250 EEKKKEKKKKKKK 262
           EE+K+E+++KKKK
Sbjct: 463 EEEKEEEEEKKKK 475

Length = 482

>gnl|CDD|235250 PRK04195, PRK04195, replication factor C large subunit; Provisional

 Score = 60.3 bits (147), Expect = 2e-10
 Identities = 24/73 (32%), Positives = 58/73 (79%)

Query: 185 RRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKE 244
              +K  +K ++  ++ EKK E++K++KK+K    KKKE+++E++K+KK++++++++++ 
Sbjct: 403 TGSKKATKKIKKIVEKAEKKREEEKKEKKKKAFAGKKKEEEEEEEKEKKEEEKEEEEEEA 462

Query: 245 KKKKKEEKKKEKK 257
           +++K+EE++K+KK
Sbjct: 463 EEEKEEEEEKKKK 475

Length = 482

>gnl|CDD|235250 PRK04195, PRK04195, replication factor C large subunit; Provisional

 Score = 59.9 bits (146), Expect = 3e-10
 Identities = 23/72 (31%), Positives = 58/72 (80%)

Query: 176 GKKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKK 235
           G K+  K+ ++  ++  KK EEEK+E+KK+    +KK+E+++E+K+K+++++++++++ +
Sbjct: 404 GSKKATKKIKKIVEKAEKKREEEKKEKKKKAFAGKKKEEEEEEEKEKKEEEKEEEEEEAE 463

Query: 236 KEKKKKKKEKKK 247
           +EK++++++KKK
Sbjct: 464 EEKEEEEEKKKK 475

Length = 482

>gnl|CDD|235250 PRK04195, PRK04195, replication factor C large subunit; Provisional

 Score = 59.9 bits (146), Expect = 3e-10
 Identities = 24/72 (33%), Positives = 57/72 (79%)

Query: 177 KKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKK 236
             ++  ++ +K   K +K+ EE+++EKK++    KKKE+++E++K++K++EK++++++ +
Sbjct: 404 GSKKATKKIKKIVEKAEKKREEEKKEKKKKAFAGKKKEEEEEEEKEKKEEEKEEEEEEAE 463

Query: 237 EKKKKKKEKKKK 248
           E+K++++EKKKK
Sbjct: 464 EEKEEEEEKKKK 475

Length = 482

>gnl|CDD|240388 PTZ00372, PTZ00372, endonuclease 4-like protein; Provisional

 Score = 59.3 bits (144), Expect = 4e-10
 Identities = 34/82 (41%), Positives = 44/82 (53%)

Query: 193 KKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEK 252
            KE      E++ +      K+ KKE K  E KK+ +KKKKKKKEKK+ K E + K   K
Sbjct: 35  SKEILSTFSEEENKVATTSTKKDKKEDKNNESKKKSEKKKKKKKEKKEPKSEGETKLGFK 94

Query: 253 KKEKKKKKKKKEKKKKKDEGRR 274
             +K KK KKK  K K +E   
Sbjct: 95  TPKKSKKTKKKPPKPKPNEDVD 116

Length = 413

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 59.8 bits (144), Expect = 5e-10
 Identities = 34/99 (34%), Positives = 57/99 (57%)

Query: 177  KKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKK 236
            KK+    +++  + K+  E  + E E   ++ +  +++ +  +KKKE+ K+K    KKK 
Sbjct: 1328 KKKADAAKKKAEEAKKAAEAAKAEAEAAADEAEAAEEKAEAAEKKKEEAKKKADAAKKKA 1387

Query: 237  EKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDEGRRR 275
            E+KKK  E KKK EE KK+  + KK    KKK DE +++
Sbjct: 1388 EEKKKADEAKKKAEEDKKKADELKKAAAAKKKADEAKKK 1426

Length = 2084

>gnl|CDD|236877 PRK11192, PRK11192, ATP-dependent RNA helicase SrmB; Provisional

 Score = 58.8 bits (143), Expect = 6e-10
 Identities = 17/59 (28%), Positives = 31/59 (52%)

Query: 197 EEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKKKE 255
           +E   + K   +K+  K  KK   K+ +KKEK+K+K K K++ +  K   K+++     
Sbjct: 374 DELRPKTKAPSEKKTGKPSKKVLAKRAEKKEKEKEKPKVKKRHRDTKNIGKRRKPSGTS 432

Length = 434

>gnl|CDD|240388 PTZ00372, PTZ00372, endonuclease 4-like protein; Provisional

 Score = 58.6 bits (142), Expect = 8e-10
 Identities = 29/80 (36%), Positives = 46/80 (57%)

Query: 192 RKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEE 251
            K+      EE+ +      KK+KK++K  + KKK +KKKKKKK++K+ K + + K   +
Sbjct: 35  SKEILSTFSEEENKVATTSTKKDKKEDKNNESKKKSEKKKKKKKEKKEPKSEGETKLGFK 94

Query: 252 KKKEKKKKKKKKEKKKKKDE 271
             K+ KK KKK  K K  ++
Sbjct: 95  TPKKSKKTKKKPPKPKPNED 114

Length = 413

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 59.0 bits (142), Expect = 8e-10
 Identities = 38/98 (38%), Positives = 57/98 (58%)

Query: 177  KKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKK 236
            KK+  + ++     K + E    E E  EEK +  +K+K++ KKK +  K+K ++KKK  
Sbjct: 1335 KKKAEEAKKAAEAAKAEAEAAADEAEAAEEKAEAAEKKKEEAKKKADAAKKKAEEKKKAD 1394

Query: 237  EKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDEGRR 274
            E KKK +E KKK +E KK    KKK  E KKK +E ++
Sbjct: 1395 EAKKKAEEDKKKADELKKAAAAKKKADEAKKKAEEKKK 1432

Length = 2084

>gnl|CDD|235250 PRK04195, PRK04195, replication factor C large subunit; Provisional

 Score = 58.4 bits (142), Expect = 9e-10
 Identities = 20/73 (27%), Positives = 58/73 (79%)

Query: 181 RKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKK 240
              ++  +K K+  E+ EK+ E+++++KK+K    KK+++++E++KEKK+++K+++E++ 
Sbjct: 403 TGSKKATKKIKKIVEKAEKKREEEKKEKKKKAFAGKKKEEEEEEEKEKKEEEKEEEEEEA 462

Query: 241 KKKEKKKKKEEKK 253
           +++++++++++KK
Sbjct: 463 EEEKEEEEEKKKK 475

Length = 482

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 59.0 bits (142), Expect = 9e-10
 Identities = 35/99 (35%), Positives = 59/99 (59%)

Query: 177  KKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKK 236
             K+  +  + + +    + E  +E+ +  EKKKE+ K+K    KKK ++K+K  + KKK 
Sbjct: 1341 AKKAAEAAKAEAEAAADEAEAAEEKAEAAEKKKEEAKKKADAAKKKAEEKKKADEAKKKA 1400

Query: 237  EKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDEGRRR 275
            E+ KKK ++ KK    KK+  + KKK E+KKK DE +++
Sbjct: 1401 EEDKKKADELKKAAAAKKKADEAKKKAEEKKKADEAKKK 1439

Length = 2084

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 59.0 bits (142), Expect = 9e-10
 Identities = 32/99 (32%), Positives = 56/99 (56%)

Query: 177  KKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKK 236
            KK    +++ +  +K+    ++K EE K+  +  K + +    + +  +++ +  +KKK+
Sbjct: 1315 KKADEAKKKAEEAKKKADAAKKKAEEAKKAAEAAKAEAEAAADEAEAAEEKAEAAEKKKE 1374

Query: 237  EKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDEGRRR 275
            E KKK    KKK EEKKK  + KKK +E KKK DE ++ 
Sbjct: 1375 EAKKKADAAKKKAEEKKKADEAKKKAEEDKKKADELKKA 1413

Length = 2084

>gnl|CDD|236877 PRK11192, PRK11192, ATP-dependent RNA helicase SrmB; Provisional

 Score = 58.4 bits (142), Expect = 9e-10
 Identities = 20/67 (29%), Positives = 35/67 (52%)

Query: 205 EEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKKKEKKKKKKKKE 264
           EE  K +  ++ + K K   +K+  K  KK   K+ +KKEK+K+K + KK  +  K   +
Sbjct: 365 EEPLKARVIDELRPKTKAPSEKKTGKPSKKVLAKRAEKKEKEKEKPKVKKRHRDTKNIGK 424

Query: 265 KKKKKDE 271
           ++K    
Sbjct: 425 RRKPSGT 431

Length = 434

>gnl|CDD|236877 PRK11192, PRK11192, ATP-dependent RNA helicase SrmB; Provisional

 Score = 58.0 bits (141), Expect = 1e-09
 Identities = 19/56 (33%), Positives = 30/56 (53%)

Query: 215 KKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKD 270
           K K   +K+  K  KK   K+ EKK+K+KEK K K+  +  K   K++K     ++
Sbjct: 379 KTKAPSEKKTGKPSKKVLAKRAEKKEKEKEKPKVKKRHRDTKNIGKRRKPSGTSEE 434

Length = 434

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 58.2 bits (140), Expect = 2e-09
 Identities = 39/103 (37%), Positives = 67/103 (65%)

Query: 173  YKGGKKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKK 232
            Y+  KK + ++ ++  + K K EE +K EE+K++ ++ KKKE +++KK +E KK +++ K
Sbjct: 1601 YEEEKKMKAEEAKKAEEAKIKAEELKKAEEEKKKVEQLKKKEAEEKKKAEELKKAEEENK 1660

Query: 233  KKKKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDEGRRR 275
             K  E+ KK +E KKK EE KK ++ +KK  E  KK+ E  ++
Sbjct: 1661 IKAAEEAKKAEEDKKKAEEAKKAEEDEKKAAEALKKEAEEAKK 1703

Length = 2084

>gnl|CDD|236877 PRK11192, PRK11192, ATP-dependent RNA helicase SrmB; Provisional

 Score = 57.3 bits (139), Expect = 2e-09
 Identities = 21/48 (43%), Positives = 29/48 (60%)

Query: 228 KKKKKKKKKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDEGRRR 275
           K K   +KK  K  KK   K+ E+K+KEK+K K KK  +  K+ G+RR
Sbjct: 379 KTKAPSEKKTGKPSKKVLAKRAEKKEKEKEKPKVKKRHRDTKNIGKRR 426

Length = 434

>gnl|CDD|235250 PRK04195, PRK04195, replication factor C large subunit; Provisional

 Score = 56.9 bits (138), Expect = 3e-09
 Identities = 24/71 (33%), Positives = 56/71 (78%)

Query: 174 KGGKKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKK 233
                ++ K+   K ++KR++E++EK+++    KKKE+++E++KEKK++EK++E+++ ++
Sbjct: 405 SKKATKKIKKIVEKAEKKREEEKKEKKKKAFAGKKKEEEEEEEKEKKEEEKEEEEEEAEE 464

Query: 234 KKKEKKKKKKE 244
           +K+E+++KKK+
Sbjct: 465 EKEEEEEKKKK 475

Length = 482

>gnl|CDD|235250 PRK04195, PRK04195, replication factor C large subunit; Provisional

 Score = 56.9 bits (138), Expect = 3e-09
 Identities = 24/73 (32%), Positives = 58/73 (79%)

Query: 180 RRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKK 239
              ++  K+ +K  ++ E+K EE+K+EKKK+    KKKE++++E+K++K+++K++++E+ 
Sbjct: 403 TGSKKATKKIKKIVEKAEKKREEEKKEKKKKAFAGKKKEEEEEEEKEKKEEEKEEEEEEA 462

Query: 240 KKKKEKKKKKEEK 252
           +++KE++++K++K
Sbjct: 463 EEEKEEEEEKKKK 475

Length = 482

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 57.1 bits (137), Expect = 4e-09
 Identities = 34/101 (33%), Positives = 59/101 (58%), Gaps = 3/101 (2%)

Query: 178  KERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKE---KKKEKKKKKKK 234
            +E++K    K+K +  K+ +E +++ +E KKK    +KK E+ KK     K E +    +
Sbjct: 1299 EEKKKADEAKKKAEEAKKADEAKKKAEEAKKKADAAKKKAEEAKKAAEAAKAEAEAAADE 1358

Query: 235  KKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDEGRRR 275
             +  ++K +  +KKKEE KK+    KKK E+KKK DE +++
Sbjct: 1359 AEAAEEKAEAAEKKKEEAKKKADAAKKKAEEKKKADEAKKK 1399

Length = 2084

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 56.7 bits (136), Expect = 4e-09
 Identities = 35/101 (34%), Positives = 63/101 (62%)

Query: 174  KGGKKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKK 233
            +    E + +   K+K + KK+ +  +++ +E+KK ++ K+K +E KKK  + +K    K
Sbjct: 1358 EAEAAEEKAEAAEKKKEEAKKKADAAKKKAEEKKKADEAKKKAEEDKKKADELKKAAAAK 1417

Query: 234  KKKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDEGRR 274
            KK ++ KKK E+KKK +E KK+ ++ KK  E KKK +E ++
Sbjct: 1418 KKADEAKKKAEEKKKADEAKKKAEEAKKADEAKKKAEEAKK 1458

Length = 2084

>gnl|CDD|236877 PRK11192, PRK11192, ATP-dependent RNA helicase SrmB; Provisional

 Score = 56.5 bits (137), Expect = 4e-09
 Identities = 22/76 (28%), Positives = 38/76 (50%)

Query: 189 KRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKK 248
           K +R  EE  K     E + K K   +KK  K  +K   K+ +KK+K+++K K K++ + 
Sbjct: 359 KIERYIEEPLKARVIDELRPKTKAPSEKKTGKPSKKVLAKRAEKKEKEKEKPKVKKRHRD 418

Query: 249 KEEKKKEKKKKKKKKE 264
            +   K +K     +E
Sbjct: 419 TKNIGKRRKPSGTSEE 434

Length = 434

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 56.7 bits (136), Expect = 5e-09
 Identities = 40/102 (39%), Positives = 61/102 (59%)

Query: 174  KGGKKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKK 233
            K    E +K    K+K    K++ E++++  E KKK ++ +K  E KKK ++ +K ++ K
Sbjct: 1404 KKKADELKKAAAAKKKADEAKKKAEEKKKADEAKKKAEEAKKADEAKKKAEEAKKAEEAK 1463

Query: 234  KKKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDEGRRR 275
            KK E+ KK  E KKK EE KK  + KKK +E KKK DE ++ 
Sbjct: 1464 KKAEEAKKADEAKKKAEEAKKADEAKKKAEEAKKKADEAKKA 1505

Length = 2084

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 56.3 bits (135), Expect = 6e-09
 Identities = 38/105 (36%), Positives = 59/105 (56%), Gaps = 3/105 (2%)

Query: 174  KGGKKERRKQRRRKRKRKRKKEEEEKEEEKK---EEKKKEKKKEKKKEKKKKEKKKEKKK 230
               + E         + K +  E++KEE KK     KKK ++K+K  E KKK ++ +KK 
Sbjct: 1348 AKAEAEAAADEAEAAEEKAEAAEKKKEEAKKKADAAKKKAEEKKKADEAKKKAEEDKKKA 1407

Query: 231  KKKKKKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDEGRRR 275
             + KK    KKK ++ KKK E+KK+  + KKK E+ KK DE +++
Sbjct: 1408 DELKKAAAAKKKADEAKKKAEEKKKADEAKKKAEEAKKADEAKKK 1452

Length = 2084

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 56.3 bits (135), Expect = 7e-09
 Identities = 36/101 (35%), Positives = 63/101 (62%)

Query: 174  KGGKKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKK 233
            K   +E++K    K+K +  K++ ++ ++    KKK  + +KK E+KKK  + +KK ++ 
Sbjct: 1384 KKKAEEKKKADEAKKKAEEDKKKADELKKAAAAKKKADEAKKKAEEKKKADEAKKKAEEA 1443

Query: 234  KKKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDEGRR 274
            KK ++ KKK E+ KK EE KK+ ++ KK  E KKK +E ++
Sbjct: 1444 KKADEAKKKAEEAKKAEEAKKKAEEAKKADEAKKKAEEAKK 1484

Length = 2084

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 56.3 bits (135), Expect = 7e-09
 Identities = 39/107 (36%), Positives = 62/107 (57%), Gaps = 2/107 (1%)

Query: 170  EYGYKGGKKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKK--EKKKKEKKKE 227
            E   K  +  + +      + +  +E+ E  E+KKEE KK+    KKK  EKKK ++ K+
Sbjct: 1339 EEAKKAAEAAKAEAEAAADEAEAAEEKAEAAEKKKEEAKKKADAAKKKAEEKKKADEAKK 1398

Query: 228  KKKKKKKKKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDEGRR 274
            K ++ KKK ++ KK    KKK +E KK+ ++KKK  E KKK +E ++
Sbjct: 1399 KAEEDKKKADELKKAAAAKKKADEAKKKAEEKKKADEAKKKAEEAKK 1445

Length = 2084

>gnl|CDD|234017 TIGR02794, tolA_full, TolA protein

 Score = 55.6 bits (134), Expect = 7e-09
 Identities = 34/91 (37%), Positives = 52/91 (57%), Gaps = 2/91 (2%)

Query: 183 QRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKK 242
           Q  ++ + K+K+ EE K ++  E K K + + +KK K++ +K+ E++ K K   E KKK 
Sbjct: 109 QAAKQAEEKQKQAEEAKAKQAAEAKAKAEAEAEKKAKEEAKKQAEEEAKAKAAAEAKKKA 168

Query: 243 KEKKKKKEEKKKEKK--KKKKKKEKKKKKDE 271
            E KKK E + K K   K K K E+ K K E
Sbjct: 169 AEAKKKAEAEAKAKAEAKAKAKAEEAKAKAE 199

TolA couples the inner membrane complex of itself with TolQ and TolR to the outer membrane complex of TolB and OprL (also called Pal). Most of the length of the protein consists of low-complexity sequence that may differ in both length and composition from one species to another, complicating efforts to discriminate TolA (the most divergent gene in the tol-pal system) from paralogs such as TonB. Selection of members of the seed alignment and criteria for setting scoring cutoffs are based largely conserved operon struction. //The Tol-Pal complex is required for maintaining outer membrane integrity. Also involved in transport (uptake) of colicins and filamentous DNA, and implicated in pathogenesis. Transport is energized by the proton motive force. TolA is an inner membrane protein that interacts with periplasmic TolB and with outer membrane porins ompC, phoE and lamB [Transport and binding proteins, Other, Cellular processes, Pathogenesis]. Length = 346

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 55.9 bits (134), Expect = 8e-09
 Identities = 32/100 (32%), Positives = 60/100 (60%), Gaps = 2/100 (2%)

Query: 178  KERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKE 237
            +E++K    K+  ++KK +E K++ ++ +K  E KK+ ++ KKK +  K+K ++ KK  E
Sbjct: 1287 EEKKKADEAKKAEEKKKADEAKKKAEEAKKADEAKKKAEEAKKKADAAKKKAEEAKKAAE 1346

Query: 238  KKKKKKEKKKKKEEKKKEKKK--KKKKKEKKKKKDEGRRR 275
              K + E    + E  +EK +  +KKK+E KKK D  +++
Sbjct: 1347 AAKAEAEAAADEAEAAEEKAEAAEKKKEEAKKKADAAKKK 1386

Length = 2084

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 55.9 bits (134), Expect = 8e-09
 Identities = 30/104 (28%), Positives = 60/104 (57%), Gaps = 2/104 (1%)

Query: 174  KGGKKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKK 233
            K  + +++ +  +K    +KK EE K++    +KK E+ K+  +  K + +    + +  
Sbjct: 1303 KADEAKKKAEEAKKADEAKKKAEEAKKKADAAKKKAEEAKKAAEAAKAEAEAAADEAEAA 1362

Query: 234  KKKEK--KKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDEGRRR 275
            ++K +  +KKK+E KKK +  KK+ ++KKK  E KKK +E +++
Sbjct: 1363 EEKAEAAEKKKEEAKKKADAAKKKAEEKKKADEAKKKAEEDKKK 1406

Length = 2084

>gnl|CDD|240388 PTZ00372, PTZ00372, endonuclease 4-like protein; Provisional

 Score = 55.1 bits (133), Expect = 1e-08
 Identities = 32/81 (39%), Positives = 43/81 (53%)

Query: 187 KRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKK 246
              +K KKE++  E +KK EKKK+KKKEKK+ K + E K   K  KK KK KKK  K K 
Sbjct: 52  TSTKKDKKEDKNNESKKKSEKKKKKKKEKKEPKSEGETKLGFKTPKKSKKTKKKPPKPKP 111

Query: 247 KKKEEKKKEKKKKKKKKEKKK 267
            +  +    K  +  +K    
Sbjct: 112 NEDVDNAFNKIAELAEKSNVY 132

Length = 413

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 55.5 bits (133), Expect = 1e-08
 Identities = 35/98 (35%), Positives = 65/98 (66%)

Query: 177  KKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKK 236
            ++ ++K    K+K + KK+ +E +++ +E+KKK  + +K    KKK  + +KK ++KKK 
Sbjct: 1374 EEAKKKADAAKKKAEEKKKADEAKKKAEEDKKKADELKKAAAAKKKADEAKKKAEEKKKA 1433

Query: 237  EKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDEGRR 274
            ++ KKK E+ KK +E KK+ ++ KK +E KKK +E ++
Sbjct: 1434 DEAKKKAEEAKKADEAKKKAEEAKKAEEAKKKAEEAKK 1471

Length = 2084

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 55.5 bits (133), Expect = 1e-08
 Identities = 39/105 (37%), Positives = 65/105 (61%), Gaps = 4/105 (3%)

Query: 174  KGGKKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKK 233
            K   +E +K    K+K +  K+ EE +++ +E KK ++ K+K +E KK ++ K+K ++ K
Sbjct: 1437 KKKAEEAKKADEAKKKAEEAKKAEEAKKKAEEAKKADEAKKKAEEAKKADEAKKKAEEAK 1496

Query: 234  KKKEKKKKKKEKKKKKEEKKKEKKKKK----KKKEKKKKKDEGRR 274
            KK ++ KK  E KKK +E KK ++ KK    KK E+ KK DE ++
Sbjct: 1497 KKADEAKKAAEAKKKADEAKKAEEAKKADEAKKAEEAKKADEAKK 1541

Length = 2084

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 55.5 bits (133), Expect = 1e-08
 Identities = 36/98 (36%), Positives = 66/98 (67%)

Query: 177  KKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKK 236
            KK+  + ++++ + K+K EE +K EE+ + K  E+ K+ +++KKK E+ K+ ++ +KK  
Sbjct: 1632 KKKVEQLKKKEAEEKKKAEELKKAEEENKIKAAEEAKKAEEDKKKAEEAKKAEEDEKKAA 1691

Query: 237  EKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDEGRR 274
            E  KK+ E+ KK EE KK++ ++KKK E+ KK +E  +
Sbjct: 1692 EALKKEAEEAKKAEELKKKEAEEKKKAEELKKAEEENK 1729

Length = 2084

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 55.1 bits (132), Expect = 1e-08
 Identities = 40/109 (36%), Positives = 64/109 (58%), Gaps = 4/109 (3%)

Query: 170  EYGYKGGKKERRKQRRRKRKRKRKKEEEEKEEEKK----EEKKKEKKKEKKKEKKKKEKK 225
            E       K++  + ++K + K+K +E +K+ E+     E KKK ++ +K +E KKK ++
Sbjct: 1409 ELKKAAAAKKKADEAKKKAEEKKKADEAKKKAEEAKKADEAKKKAEEAKKAEEAKKKAEE 1468

Query: 226  KEKKKKKKKKKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDEGRR 274
             +K  + KKK E+ KK  E KKK EE KK+  + KK  E KKK DE ++
Sbjct: 1469 AKKADEAKKKAEEAKKADEAKKKAEEAKKKADEAKKAAEAKKKADEAKK 1517

Length = 2084

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 55.1 bits (132), Expect = 1e-08
 Identities = 36/98 (36%), Positives = 64/98 (65%)

Query: 178  KERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKE 237
            K +  +  +K +  +KK EE K+ E+ E+K  E  K++ +E KK E+ K+K+ ++KKK E
Sbjct: 1660 KIKAAEEAKKAEEDKKKAEEAKKAEEDEKKAAEALKKEAEEAKKAEELKKKEAEEKKKAE 1719

Query: 238  KKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDEGRRR 275
            + KK +E+ K K E+ K++ ++ KKK ++ KKDE  ++
Sbjct: 1720 ELKKAEEENKIKAEEAKKEAEEDKKKAEEAKKDEEEKK 1757

Length = 2084

>gnl|CDD|236877 PRK11192, PRK11192, ATP-dependent RNA helicase SrmB; Provisional

 Score = 54.9 bits (133), Expect = 1e-08
 Identities = 19/67 (28%), Positives = 34/67 (50%)

Query: 178 KERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKE 237
           +E  K R     R + K   EK+  K  +K   K+ EKK+++K+K K K++ +  K   +
Sbjct: 365 EEPLKARVIDELRPKTKAPSEKKTGKPSKKVLAKRAEKKEKEKEKPKVKKRHRDTKNIGK 424

Query: 238 KKKKKKE 244
           ++K    
Sbjct: 425 RRKPSGT 431

Length = 434

>gnl|CDD|219655 pfam07946, DUF1682, Protein of unknown function (DUF1682)

 Score = 55.0 bits (133), Expect = 1e-08
 Identities = 22/68 (32%), Positives = 46/68 (67%), Gaps = 3/68 (4%)

Query: 196 EEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKK---EKKKKKEEK 252
            E   +  K  +++E+K  K  E++++E+ +EKK++KKK++ + K  K   E+++K EEK
Sbjct: 255 PEVLRKVDKTREEEEEKILKAAEEERQEEAQEKKEEKKKEEREAKLAKLSPEEQRKLEEK 314

Query: 253 KKEKKKKK 260
           +++K+ +K
Sbjct: 315 ERKKQARK 322

The members of this family are all hypothetical eukaryotic proteins of unknown function. One member is described as being an adipocyte-specific protein, but no evidence of this was found. Length = 322

>gnl|CDD|219655 pfam07946, DUF1682, Protein of unknown function (DUF1682)

 Score = 54.6 bits (132), Expect = 1e-08
 Identities = 26/73 (35%), Positives = 48/73 (65%), Gaps = 4/73 (5%)

Query: 181 RKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKK 240
             +  RK  + R++EEE+  +  +EE++ E+ +EKK+EKKK+E    + K  K   E+++
Sbjct: 254 SPEVLRKVDKTREEEEEKILKAAEEERQ-EEAQEKKEEKKKEE---REAKLAKLSPEEQR 309

Query: 241 KKKEKKKKKEEKK 253
           K +EK++KK+ +K
Sbjct: 310 KLEEKERKKQARK 322

The members of this family are all hypothetical eukaryotic proteins of unknown function. One member is described as being an adipocyte-specific protein, but no evidence of this was found. Length = 322

>gnl|CDD|219838 pfam08432, DUF1742, Fungal protein of unknown function (DUF1742)

 Score = 53.2 bits (128), Expect = 1e-08
 Identities = 34/83 (40%), Positives = 51/83 (61%), Gaps = 1/83 (1%)

Query: 189 KRKRKKEEEEKEEEKKE-EKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKK 247
           K+K+K+  EE E+ KKE E+K++ K +KKK KKKK+K K+KK  KK  K +KK +KE + 
Sbjct: 61  KKKKKELAEEIEKVKKEYEEKQKWKWKKKKSKKKKDKDKDKKDDKKDDKSEKKDEKEAED 120

Query: 248 KKEEKKKEKKKKKKKKEKKKKKD 270
           K E+  K   +      + K + 
Sbjct: 121 KLEDLTKSYSETLSTLSELKPRK 143

This is a family of fungal proteins of unknown function. Length = 182

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 55.1 bits (132), Expect = 2e-08
 Identities = 37/102 (36%), Positives = 64/102 (62%)

Query: 174  KGGKKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKK 233
            K   +E +K+    +K    K++ ++ ++K EEKKK  + +KK E+ KK  + +KK ++ 
Sbjct: 1397 KKKAEEDKKKADELKKAAAAKKKADEAKKKAEEKKKADEAKKKAEEAKKADEAKKKAEEA 1456

Query: 234  KKKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDEGRRR 275
            KK E+ KKK E+ KK +E KK+ ++ KK  E KKK +E +++
Sbjct: 1457 KKAEEAKKKAEEAKKADEAKKKAEEAKKADEAKKKAEEAKKK 1498

Length = 2084

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 55.1 bits (132), Expect = 2e-08
 Identities = 37/99 (37%), Positives = 64/99 (64%)

Query: 177  KKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKK 236
            KK+  + ++ + + K K  EE K+ E+ ++K +E KK ++ EKK  E  K++ ++ KK +
Sbjct: 1646 KKKAEELKKAEEENKIKAAEEAKKAEEDKKKAEEAKKAEEDEKKAAEALKKEAEEAKKAE 1705

Query: 237  EKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDEGRRR 275
            E KKK+ E+KKK EE KK +++ K K E+ KK+ E  ++
Sbjct: 1706 ELKKKEAEEKKKAEELKKAEEENKIKAEEAKKEAEEDKK 1744

Length = 2084

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 55.1 bits (132), Expect = 2e-08
 Identities = 34/95 (35%), Positives = 53/95 (55%), Gaps = 2/95 (2%)

Query: 177  KKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKK 236
            ++ R+    +K + K+K +E +K EEKK  K  E KK+ ++ KK  E KK+ ++ KKK  
Sbjct: 1275 EEARKADELKKAEEKKKADEAKKAEEKK--KADEAKKKAEEAKKADEAKKKAEEAKKKAD 1332

Query: 237  EKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDE 271
              KKK +E KK  E  K E +    + E  ++K E
Sbjct: 1333 AAKKKAEEAKKAAEAAKAEAEAAADEAEAAEEKAE 1367

Length = 2084

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 55.1 bits (132), Expect = 2e-08
 Identities = 40/106 (37%), Positives = 65/106 (61%), Gaps = 5/106 (4%)

Query: 174  KGGKKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKK 233
            K   +E++K    K+K +  K+ +E +++ +E KK E+ K+K +E KK ++ K+K ++ K
Sbjct: 1424 KKKAEEKKKADEAKKKAEEAKKADEAKKKAEEAKKAEEAKKKAEEAKKADEAKKKAEEAK 1483

Query: 234  KKKEKKKKKKEKKKKKEEKKKEKKKKKK-----KKEKKKKKDEGRR 274
            K  E KKK +E KKK +E KK  + KKK     K E+ KK DE ++
Sbjct: 1484 KADEAKKKAEEAKKKADEAKKAAEAKKKADEAKKAEEAKKADEAKK 1529

Length = 2084

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 54.4 bits (130), Expect = 2e-08
 Identities = 38/97 (39%), Positives = 57/97 (58%)

Query: 174  KGGKKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKK 233
            K     ++K   +K+  + KK+ EE +++  E KK    K+K  E KKK ++K+K  + K
Sbjct: 1378 KKADAAKKKAEEKKKADEAKKKAEEDKKKADELKKAAAAKKKADEAKKKAEEKKKADEAK 1437

Query: 234  KKKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKD 270
            KK E+ KK  E KKK EE KK ++ KKK +E KK  +
Sbjct: 1438 KKAEEAKKADEAKKKAEEAKKAEEAKKKAEEAKKADE 1474

Length = 2084

>gnl|CDD|219838 pfam08432, DUF1742, Fungal protein of unknown function (DUF1742)

 Score = 52.8 bits (127), Expect = 2e-08
 Identities = 31/77 (40%), Positives = 48/77 (62%)

Query: 194 KEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKK 253
            E ++K++E  EE +K KK+ ++K+K K +KKK KKKK K K +K  KK +K +KK+EK+
Sbjct: 58  TEAKKKKKELAEEIEKVKKEYEEKQKWKWKKKKSKKKKDKDKDKKDDKKDDKSEKKDEKE 117

Query: 254 KEKKKKKKKKEKKKKKD 270
            E K +   K   +   
Sbjct: 118 AEDKLEDLTKSYSETLS 134

This is a family of fungal proteins of unknown function. Length = 182

>gnl|CDD|219838 pfam08432, DUF1742, Fungal protein of unknown function (DUF1742)

 Score = 52.8 bits (127), Expect = 2e-08
 Identities = 31/78 (39%), Positives = 49/78 (62%)

Query: 195 EEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKKK 254
            E  + ++KK+E  +E +K KK+ ++K++ K +KKK KKKK + K KK +KK  K EKK 
Sbjct: 55  AEYTEAKKKKKELAEEIEKVKKEYEEKQKWKWKKKKSKKKKDKDKDKKDDKKDDKSEKKD 114

Query: 255 EKKKKKKKKEKKKKKDEG 272
           EK+ + K ++  K   E 
Sbjct: 115 EKEAEDKLEDLTKSYSET 132

This is a family of fungal proteins of unknown function. Length = 182

>gnl|CDD|220648 pfam10243, MIP-T3, Microtubule-binding protein MIP-T3

 Score = 54.5 bits (131), Expect = 2e-08
 Identities = 30/101 (29%), Positives = 68/101 (67%)

Query: 174 KGGKKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKK 233
              +++ ++Q + ++K+K++K +EE ++ K +E+ KEK+  K+KEK+K++K +E + +++
Sbjct: 103 GKEEEKEKEQVKEEKKKKKEKPKEEPKDRKPKEEAKEKRPPKEKEKEKEKKVEEPRDREE 162

Query: 234 KKKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDEGRR 274
           +KK ++ + K + KK  +KK   KKK+  +E+K+++     
Sbjct: 163 EKKRERVRAKSRPKKPPKKKPPNKKKEPPEEEKQRQAAREA 203

This protein, which interacts with both microtubules and TRAF3 (tumour necrosis factor receptor-associated factor 3), is conserved from worms to humans. The N-terminal region is the microtubule binding domain and is well-conserved; the C-terminal 100 residues, also well-conserved, constitute the coiled-coil region which binds to TRAF3. The central region of the protein is rich in lysine and glutamic acid and carries KKE motifs which may also be necessary for tubulin-binding, but this region is the least well-conserved. Length = 506

>gnl|CDD|237177 PRK12704, PRK12704, phosphodiesterase; Provisional

 Score = 53.6 bits (130), Expect = 4e-08
 Identities = 34/106 (32%), Positives = 61/106 (57%), Gaps = 11/106 (10%)

Query: 177 KKERRKQRRRKRKRKRKKEEEEKE-EEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKK 235
           K    K +  + + KR  EE +KE E  K+E   E K+E  K + + EK+  +++ + +K
Sbjct: 27  KIAEAKIKEAEEEAKRILEEAKKEAEAIKKEALLEAKEEIHKLRNEFEKELRERRNELQK 86

Query: 236 KEKK--------KKKKEKKKKKEEK--KKEKKKKKKKKEKKKKKDE 271
            EK+         +K E  +K+EE+  KKEK+ ++K++E +KK++E
Sbjct: 87  LEKRLLQKEENLDRKLELLEKREEELEKKEKELEQKQQELEKKEEE 132

Length = 520

>gnl|CDD|215214 PLN02381, PLN02381, valyl-tRNA synthetase

 Score = 53.7 bits (129), Expect = 4e-08
 Identities = 26/70 (37%), Positives = 43/70 (61%)

Query: 202 EKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKKKEKKKKKK 261
           E + EKK   ++E +++KKK+EK KEK+ KK K  +K+ K K + ++  +     KK +K
Sbjct: 5   ESEAEKKILTEEELERKKKKEEKAKEKELKKLKAAQKEAKAKLQAQQASDGTNVPKKSEK 64

Query: 262 KKEKKKKKDE 271
           K  K+  +DE
Sbjct: 65  KSRKRDVEDE 74

Length = 1066

>gnl|CDD|191187 pfam05087, Rota_VP2, Rotavirus VP2 protein

 Score = 53.8 bits (129), Expect = 4e-08
 Identities = 24/89 (26%), Positives = 47/89 (52%), Gaps = 3/89 (3%)

Query: 183 QRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKK---KEKKKEKKKKKKKKKEKK 239
           + RR+         +EK++EK+++K + + KEK  +KK+    +      K++  ++  K
Sbjct: 4   RNRREANINNNDRMQEKDDEKQDQKNRMELKEKVLDKKEEVVTDNVDSPVKEQSSQENLK 63

Query: 240 KKKKEKKKKKEEKKKEKKKKKKKKEKKKK 268
              + KK  KEE K+  +  K K+E +K+
Sbjct: 64  IADEVKKSTKEESKQLLEVLKTKEEHQKE 92

Rotavirus particles consist of three concentric proteinaceous capsid layers. The innermost capsid (core) is made of VP2. The genomic RNA and the two minor proteins VP1 and VP3 are encapsidated within this layer. The N-terminus of rotavirus VP2 is necessary for the encapsidation of VP1 and VP3. Length = 887

>gnl|CDD|237177 PRK12704, PRK12704, phosphodiesterase; Provisional

 Score = 53.2 bits (129), Expect = 5e-08
 Identities = 26/91 (28%), Positives = 59/91 (64%), Gaps = 2/91 (2%)

Query: 177 KKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKK 236
           KKE   + + +  + R + E+E  E + E +K EK+  +K+E    ++K E  +K++++ 
Sbjct: 55  KKEALLEAKEEIHKLRNEFEKELRERRNELQKLEKRLLQKEE--NLDRKLELLEKREEEL 112

Query: 237 EKKKKKKEKKKKKEEKKKEKKKKKKKKEKKK 267
           EKK+K+ E+K+++ EKK+E+ ++  +++ ++
Sbjct: 113 EKKEKELEQKQQELEKKEEELEELIEEQLQE 143

Length = 520

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 53.2 bits (127), Expect = 6e-08
 Identities = 38/100 (38%), Positives = 56/100 (56%), Gaps = 2/100 (2%)

Query: 178  KERRKQRRRKRKRKRKKEEEEKEEE--KKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKK 235
            +E R     +R+   K EE  K +E  K EEKKK  + +K +EKKK ++ K+K ++ KK 
Sbjct: 1258 EEARMAHFARRQAAIKAEEARKADELKKAEEKKKADEAKKAEEKKKADEAKKKAEEAKKA 1317

Query: 236  KEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDEGRRR 275
             E KKK +E KKK +  KK+ ++ KK  E  K + E    
Sbjct: 1318 DEAKKKAEEAKKKADAAKKKAEEAKKAAEAAKAEAEAAAD 1357

Length = 2084

>gnl|CDD|235250 PRK04195, PRK04195, replication factor C large subunit; Provisional

 Score = 52.6 bits (127), Expect = 7e-08
 Identities = 22/57 (38%), Positives = 40/57 (70%)

Query: 219 KKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDEGRRR 275
             KK  KK KK  +K +K+++++KKEKKKK    KK++++++++KEKK+++ E    
Sbjct: 404 GSKKATKKIKKIVEKAEKKREEEKKEKKKKAFAGKKKEEEEEEEKEKKEEEKEEEEE 460

Length = 482

>gnl|CDD|226894 COG4499, COG4499, Predicted membrane protein [Function unknown]

 Score = 52.5 bits (126), Expect = 7e-08
 Identities = 25/71 (35%), Positives = 45/71 (63%), Gaps = 1/71 (1%)

Query: 197 EEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKKKEK 256
           ++++E  KE  KK +   KK  + K E    ++ + K K+EK K++ E +KK++E+  E 
Sbjct: 365 DKRQELLKEYNKKLQDYTKKLGEVKDETDASEEAEAKAKEEKLKQE-ENEKKQKEQADED 423

Query: 257 KKKKKKKEKKK 267
           K+K++K E+KK
Sbjct: 424 KEKRQKDERKK 434

Length = 434

>gnl|CDD|235250 PRK04195, PRK04195, replication factor C large subunit; Provisional

 Score = 52.6 bits (127), Expect = 8e-08
 Identities = 21/62 (33%), Positives = 50/62 (80%)

Query: 177 KKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKK 236
            ++  K+R  ++K K+KK    K++E++EE++KEKK+E+K+E++++ +++++++++KKKK
Sbjct: 416 VEKAEKKREEEKKEKKKKAFAGKKKEEEEEEEKEKKEEEKEEEEEEAEEEKEEEEEKKKK 475

Query: 237 EK 238
           + 
Sbjct: 476 QA 477

Length = 482

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 52.8 bits (126), Expect = 8e-08
 Identities = 34/98 (34%), Positives = 64/98 (65%)

Query: 177  KKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKK 236
            K E   + +   + K+ +E+++K EE K+ ++ EKK  +  +K+ +E KK ++ KKK+ +
Sbjct: 1654 KAEEENKIKAAEEAKKAEEDKKKAEEAKKAEEDEKKAAEALKKEAEEAKKAEELKKKEAE 1713

Query: 237  EKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDEGRR 274
            EKKK ++ KK ++E K K ++ KK+ +E KKK +E ++
Sbjct: 1714 EKKKAEELKKAEEENKIKAEEAKKEAEEDKKKAEEAKK 1751

Length = 2084

>gnl|CDD|219838 pfam08432, DUF1742, Fungal protein of unknown function (DUF1742)

 Score = 50.8 bits (122), Expect = 8e-08
 Identities = 28/83 (33%), Positives = 52/83 (62%)

Query: 192 RKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEE 251
           +KK++E  EE +K +K+ E+K++ K +KKK +KKK+K K KK  K+  K +K+ +K+ E+
Sbjct: 61  KKKKKELAEEIEKVKKEYEEKQKWKWKKKKSKKKKDKDKDKKDDKKDDKSEKKDEKEAED 120

Query: 252 KKKEKKKKKKKKEKKKKKDEGRR 274
           K ++  K   +      + + R+
Sbjct: 121 KLEDLTKSYSETLSTLSELKPRK 143

This is a family of fungal proteins of unknown function. Length = 182

>gnl|CDD|219746 pfam08208, RNA_polI_A34, DNA-directed RNA polymerase I subunit RPA34

 Score = 50.9 bits (122), Expect = 9e-08
 Identities = 35/74 (47%), Positives = 49/74 (66%)

Query: 195 EEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKKK 254
             +    E   E +  +K+   K +K+ E ++E+KK+KKKKKE KK+KKEKK KKE+  +
Sbjct: 120 APDGPPSELGSESETSEKETTAKVEKEAEVEEEEKKEKKKKKEVKKEKKEKKDKKEKMVE 179

Query: 255 EKKKKKKKKEKKKK 268
            K  KKKKK+KKKK
Sbjct: 180 PKGSKKKKKKKKKK 193

5. This is a family of proteins conserved from yeasts to human. Subunit A34.5 of RNA polymerase I is a non-essential subunit which is thought to help Pol I overcome topological constraints imposed on ribosomal DNA during the process of transcription. Length = 193

>gnl|CDD|240388 PTZ00372, PTZ00372, endonuclease 4-like protein; Provisional

 Score = 52.0 bits (125), Expect = 1e-07
 Identities = 29/79 (36%), Positives = 44/79 (55%), Gaps = 1/79 (1%)

Query: 193 KKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEK 252
               EE+ +      KK+KK++K  E KKK +KK KKKKK+KK+ K + + +   K  +K
Sbjct: 40  STFSEEENKVATTSTKKDKKEDKNNESKKKSEKK-KKKKKEKKEPKSEGETKLGFKTPKK 98

Query: 253 KKEKKKKKKKKEKKKKKDE 271
            K+ KKK  K +  +  D 
Sbjct: 99  SKKTKKKPPKPKPNEDVDN 117

Length = 413

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 52.5 bits (125), Expect = 1e-07
 Identities = 39/104 (37%), Positives = 63/104 (60%), Gaps = 3/104 (2%)

Query: 174  KGGKKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKK 233
            K   +E +K    K+K +  K+ +E +++ +E KK ++ K+K +E KKK  + +K  + K
Sbjct: 1450 KKKAEEAKKAEEAKKKAEEAKKADEAKKKAEEAKKADEAKKKAEEAKKKADEAKKAAEAK 1509

Query: 234  KKKEKKKKKKEKKKKKEEKKKEKKKKK---KKKEKKKKKDEGRR 274
            KK ++ KK +E KK  E KK E+ KK    KK E+KKK DE ++
Sbjct: 1510 KKADEAKKAEEAKKADEAKKAEEAKKADEAKKAEEKKKADELKK 1553

Length = 2084

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 52.5 bits (125), Expect = 1e-07
 Identities = 36/97 (37%), Positives = 56/97 (57%)

Query: 174  KGGKKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKK 233
            K   + ++K    K+K    K+    +++  E KKK ++K+K  E KKK ++ +K  + K
Sbjct: 1391 KKADEAKKKAEEDKKKADELKKAAAAKKKADEAKKKAEEKKKADEAKKKAEEAKKADEAK 1450

Query: 234  KKKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKD 270
            KK E+ KK +E KKK EE KK  + KKK +E KK  +
Sbjct: 1451 KKAEEAKKAEEAKKKAEEAKKADEAKKKAEEAKKADE 1487

Length = 2084

>gnl|CDD|220648 pfam10243, MIP-T3, Microtubule-binding protein MIP-T3

 Score = 52.2 bits (125), Expect = 1e-07
 Identities = 35/100 (35%), Positives = 64/100 (64%), Gaps = 2/100 (2%)

Query: 174 KGGKKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKK 233
               KE  K++ + ++ K+KK+E+ KEE K  + K+E K  +K+  K+KEK+KEKK ++ 
Sbjct: 100 NESGKEEEKEKEQVKEEKKKKKEKPKEEPKDRKPKEEAK--EKRPPKEKEKEKEKKVEEP 157

Query: 234 KKKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDEGR 273
           + +E++KK++  + K   KK  KKK   KK++  ++++ R
Sbjct: 158 RDREEEKKRERVRAKSRPKKPPKKKPPNKKKEPPEEEKQR 197

This protein, which interacts with both microtubules and TRAF3 (tumour necrosis factor receptor-associated factor 3), is conserved from worms to humans. The N-terminal region is the microtubule binding domain and is well-conserved; the C-terminal 100 residues, also well-conserved, constitute the coiled-coil region which binds to TRAF3. The central region of the protein is rich in lysine and glutamic acid and carries KKE motifs which may also be necessary for tubulin-binding, but this region is the least well-conserved. Length = 506

>gnl|CDD|226894 COG4499, COG4499, Predicted membrane protein [Function unknown]

 Score = 51.7 bits (124), Expect = 1e-07
 Identities = 22/81 (27%), Positives = 48/81 (59%)

Query: 191 KRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKE 250
           K  +E +   +   +++++  K+  KK +   +K  E K +    +E + K KE+K K+E
Sbjct: 351 KLYEEVKSNTDLSGDKRQELLKEYNKKLQDYTKKLGEVKDETDASEEAEAKAKEEKLKQE 410

Query: 251 EKKKEKKKKKKKKEKKKKKDE 271
           E +K++K++  + ++K++KDE
Sbjct: 411 ENEKKQKEQADEDKEKRQKDE 431

Length = 434

>gnl|CDD|217051 pfam02463, SMC_N, RecF/RecN/SMC N terminal domain

 Score = 52.3 bits (125), Expect = 1e-07
 Identities = 28/91 (30%), Positives = 60/91 (65%)

Query: 181 RKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKK 240
            ++     K++ +KEEE   +  KE K++EK+K+ ++E+ K   K+E++ K +  K +++
Sbjct: 250 EQEEIESSKQELEKEEEILAQVLKENKEEEKEKKLQEEELKLLAKEEEELKSELLKLERR 309

Query: 241 KKKEKKKKKEEKKKEKKKKKKKKEKKKKKDE 271
           K  +++K KE +K+ KK +K+ K++K++ +E
Sbjct: 310 KVDDEEKLKESEKELKKLEKELKKEKEEIEE 340

This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination. Length = 1162

>gnl|CDD|240388 PTZ00372, PTZ00372, endonuclease 4-like protein; Provisional

 Score = 50.9 bits (122), Expect = 2e-07
 Identities = 25/84 (29%), Positives = 40/84 (47%)

Query: 186 RKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEK 245
           + + +             KE      ++E K      +K K++ K  + KK+ +KKKK+K
Sbjct: 18  KSKLQPISYIYSNVLVLSKEILSTFSEEENKVATTSTKKDKKEDKNNESKKKSEKKKKKK 77

Query: 246 KKKKEEKKKEKKKKKKKKEKKKKK 269
           K+KKE K + + K   K  KK KK
Sbjct: 78  KEKKEPKSEGETKLGFKTPKKSKK 101

Length = 413

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 51.3 bits (122), Expect = 2e-07
 Identities = 34/98 (34%), Positives = 68/98 (69%)

Query: 177  KKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKK 236
            KK   ++++ ++ +K++ EE++K EE K+ +++ K K  ++ KK +E KK+ ++ KK ++
Sbjct: 1626 KKAEEEKKKVEQLKKKEAEEKKKAEELKKAEEENKIKAAEEAKKAEEDKKKAEEAKKAEE 1685

Query: 237  EKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDEGRR 274
            ++KK  +  KK+ EE KK ++ KKK+ E+KKK +E ++
Sbjct: 1686 DEKKAAEALKKEAEEAKKAEELKKKEAEEKKKAEELKK 1723

Length = 2084

>gnl|CDD|234017 TIGR02794, tolA_full, TolA protein

 Score = 51.0 bits (122), Expect = 2e-07
 Identities = 30/104 (28%), Positives = 60/104 (57%), Gaps = 5/104 (4%)

Query: 177 KKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKE-KKKEKKKKKKKK 235
             E+ +Q+  +++   +K  ++ E+  K+ ++K+K+ E+ K K+  E K K + + +KK 
Sbjct: 85  AAEQARQKELEQRAAAEKAAKQAEQAAKQAEEKQKQAEEAKAKQAAEAKAKAEAEAEKKA 144

Query: 236 KEKKKKKKEKKKKKEE----KKKEKKKKKKKKEKKKKKDEGRRR 275
           KE+ KK+ E++ K +     KKK  + KKK + + K K E + +
Sbjct: 145 KEEAKKQAEEEAKAKAAAEAKKKAAEAKKKAEAEAKAKAEAKAK 188

TolA couples the inner membrane complex of itself with TolQ and TolR to the outer membrane complex of TolB and OprL (also called Pal). Most of the length of the protein consists of low-complexity sequence that may differ in both length and composition from one species to another, complicating efforts to discriminate TolA (the most divergent gene in the tol-pal system) from paralogs such as TonB. Selection of members of the seed alignment and criteria for setting scoring cutoffs are based largely conserved operon struction. //The Tol-Pal complex is required for maintaining outer membrane integrity. Also involved in transport (uptake) of colicins and filamentous DNA, and implicated in pathogenesis. Transport is energized by the proton motive force. TolA is an inner membrane protein that interacts with periplasmic TolB and with outer membrane porins ompC, phoE and lamB [Transport and binding proteins, Other, Cellular processes, Pathogenesis]. Length = 346

>gnl|CDD|219838 pfam08432, DUF1742, Fungal protein of unknown function (DUF1742)

 Score = 49.3 bits (118), Expect = 2e-07
 Identities = 30/83 (36%), Positives = 48/83 (57%)

Query: 193 KKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEK 252
           KK+++E  EE ++ KK+ ++K+K K KKKK KKK+ K K KK  +K  K ++K +K+ E 
Sbjct: 61  KKKKKELAEEIEKVKKEYEEKQKWKWKKKKSKKKKDKDKDKKDDKKDDKSEKKDEKEAED 120

Query: 253 KKEKKKKKKKKEKKKKKDEGRRR 275
           K E   K   +      +   R+
Sbjct: 121 KLEDLTKSYSETLSTLSELKPRK 143

This is a family of fungal proteins of unknown function. Length = 182

>gnl|CDD|220648 pfam10243, MIP-T3, Microtubule-binding protein MIP-T3

 Score = 51.4 bits (123), Expect = 2e-07
 Identities = 38/96 (39%), Positives = 65/96 (67%), Gaps = 3/96 (3%)

Query: 182 KQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKK---KEKKKKEKKKEKKKKKKKKKEK 238
           K +  K  +    +EEEKE+E+ +E+KK+KK++ K   K++K KE+ KEK+  K+K+KEK
Sbjct: 91  KTKPAKEPKNESGKEEEKEKEQVKEEKKKKKEKPKEEPKDRKPKEEAKEKRPPKEKEKEK 150

Query: 239 KKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDEGRR 274
           +KK +E + ++EEKK+E+ + K + +K  KK    +
Sbjct: 151 EKKVEEPRDREEEKKRERVRAKSRPKKPPKKKPPNK 186

This protein, which interacts with both microtubules and TRAF3 (tumour necrosis factor receptor-associated factor 3), is conserved from worms to humans. The N-terminal region is the microtubule binding domain and is well-conserved; the C-terminal 100 residues, also well-conserved, constitute the coiled-coil region which binds to TRAF3. The central region of the protein is rich in lysine and glutamic acid and carries KKE motifs which may also be necessary for tubulin-binding, but this region is the least well-conserved. Length = 506

>gnl|CDD|226894 COG4499, COG4499, Predicted membrane protein [Function unknown]

 Score = 51.3 bits (123), Expect = 2e-07
 Identities = 24/69 (34%), Positives = 44/69 (63%), Gaps = 1/69 (1%)

Query: 193 KKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKK-KKKEKKKKKKEKKKKKEE 251
           K++E  KE  KK +   +K  E K E    E+ + K K++K K++E +KK+KE+  + +E
Sbjct: 366 KRQELLKEYNKKLQDYTKKLGEVKDETDASEEAEAKAKEEKLKQEENEKKQKEQADEDKE 425

Query: 252 KKKEKKKKK 260
           K+++ ++KK
Sbjct: 426 KRQKDERKK 434

Length = 434

>gnl|CDD|217051 pfam02463, SMC_N, RecF/RecN/SMC N terminal domain

 Score = 51.5 bits (123), Expect = 2e-07
 Identities = 32/95 (33%), Positives = 57/95 (60%)

Query: 177 KKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKK 236
              +   R  + + +  K+E EKEEE   +  KE K+E+K++K ++E+ K   K++++ K
Sbjct: 241 DLLQELLRDEQEEIESSKQELEKEEEILAQVLKENKEEEKEKKLQEEELKLLAKEEEELK 300

Query: 237 EKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDE 271
            +  K + +K   EEK KE +K+ KK EK+ KK++
Sbjct: 301 SELLKLERRKVDDEEKLKESEKELKKLEKELKKEK 335

This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination. Length = 1162

>gnl|CDD|240271 PTZ00108, PTZ00108, DNA topoisomerase 2-like protein; Provisional

 Score = 51.6 bits (124), Expect = 2e-07
 Identities = 25/83 (30%), Positives = 43/83 (51%)

Query: 190  RKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKK 249
             +  +E+EE EE++  ++++ K K K K  K ++ K +KK+KKKKK    K KK      
Sbjct: 1138 EEALEEQEEVEEKEIAKEQRLKSKTKGKASKLRKPKLKKKEKKKKKSSADKSKKASVVGN 1197

Query: 250  EEKKKEKKKKKKKKEKKKKKDEG 272
             ++    +K+K   +   KK   
Sbjct: 1198 SKRVDSDEKRKLDDKPDNKKSNS 1220

Length = 1388

>gnl|CDD|235640 PRK05901, PRK05901, RNA polymerase sigma factor; Provisional

 Score = 51.1 bits (123), Expect = 2e-07
 Identities = 21/94 (22%), Positives = 32/94 (34%), Gaps = 1/94 (1%)

Query: 178 KERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKE 237
           KE  K+    +K+  ++ ++         K  +   E    KKK +    K    K   +
Sbjct: 35  KEEIKEALESKKKTPEQIDQVLIFLSGMVKDTDDATESDIPKKKTKTAA-KAAAAKAPAK 93

Query: 238 KKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDE 271
           KK K +    KK EKK    K       K     
Sbjct: 94  KKLKDELDSSKKAEKKNALDKDDDLNYVKDIDVL 127

Length = 509

>gnl|CDD|235640 PRK05901, PRK05901, RNA polymerase sigma factor; Provisional

 Score = 51.1 bits (123), Expect = 2e-07
 Identities = 27/102 (26%), Positives = 39/102 (38%), Gaps = 7/102 (6%)

Query: 177 KKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEK-------KKEKKKKEKKKEKK 229
           KK ++   + K K    KEE ++  E K++  ++  +         K      E    KK
Sbjct: 18  KKLKKLAAKSKSKGFITKEEIKEALESKKKTPEQIDQVLIFLSGMVKDTDDATESDIPKK 77

Query: 230 KKKKKKKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDE 271
           K K   K    K   KKK K+E    KK +KK    K     
Sbjct: 78  KTKTAAKAAAAKAPAKKKLKDELDSSKKAEKKNALDKDDDLN 119

Length = 509

>gnl|CDD|235250 PRK04195, PRK04195, replication factor C large subunit; Provisional

 Score = 50.7 bits (122), Expect = 3e-07
 Identities = 20/67 (29%), Positives = 50/67 (74%)

Query: 167 DNLEYGYKGGKKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKK 226
                      +++R++ ++++K+K    ++++EEE++E++KKE++KE+++E+ ++EK++
Sbjct: 409 TKKIKKIVEKAEKKREEEKKEKKKKAFAGKKKEEEEEEEKEKKEEEKEEEEEEAEEEKEE 468

Query: 227 EKKKKKK 233
           E++KKKK
Sbjct: 469 EEEKKKK 475

Length = 482

>gnl|CDD|235250 PRK04195, PRK04195, replication factor C large subunit; Provisional

 Score = 50.7 bits (122), Expect = 3e-07
 Identities = 20/60 (33%), Positives = 40/60 (66%)

Query: 216 KKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDEGRRR 275
           ++E +     K+  KK KK  EK +KK+E++KK+++KK    KKK+++E+++K+ +   +
Sbjct: 396 EEEIEFLTGSKKATKKIKKIVEKAEKKREEEKKEKKKKAFAGKKKEEEEEEEKEKKEEEK 455

Length = 482

>gnl|CDD|240388 PTZ00372, PTZ00372, endonuclease 4-like protein; Provisional

 Score = 50.5 bits (121), Expect = 3e-07
 Identities = 27/104 (25%), Positives = 49/104 (47%)

Query: 166 GDNLEYGYKGGKKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKK 225
            + L    +       ++ +      +K ++E+K  E K++ +K+KKK+K+K++ K E +
Sbjct: 29  SNVLVLSKEILSTFSEEENKVATTSTKKDKKEDKNNESKKKSEKKKKKKKEKKEPKSEGE 88

Query: 226 KEKKKKKKKKKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKK 269
            +   K  KK +K KKK  K K  E+      K  +  EK    
Sbjct: 89  TKLGFKTPKKSKKTKKKPPKPKPNEDVDNAFNKIAELAEKSNVY 132

Length = 413

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 51.3 bits (122), Expect = 3e-07
 Identities = 32/98 (32%), Positives = 66/98 (67%)

Query: 178  KERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKE 237
            K+  +++++  + K+K+ EE+K+ E+ ++ ++E K +  +E KK E+ K+K ++ KK +E
Sbjct: 1626 KKAEEEKKKVEQLKKKEAEEKKKAEELKKAEEENKIKAAEEAKKAEEDKKKAEEAKKAEE 1685

Query: 238  KKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDEGRRR 275
             +KK  E  KK+ E+ K+ ++ KKK+ ++KKK E  ++
Sbjct: 1686 DEKKAAEALKKEAEEAKKAEELKKKEAEEKKKAEELKK 1723

Length = 2084

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 50.9 bits (121), Expect = 3e-07
 Identities = 30/98 (30%), Positives = 64/98 (65%)

Query: 178  KERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKE 237
            K + ++ ++  + K+K E+ +K+E ++++K +E KK +++ K K  ++ +K ++ KKK E
Sbjct: 1619 KIKAEELKKAEEEKKKVEQLKKKEAEEKKKAEELKKAEEENKIKAAEEAKKAEEDKKKAE 1678

Query: 238  KKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDEGRRR 275
            + KK +E +KK  E  K++ ++ KK E+ KKK+   ++
Sbjct: 1679 EAKKAEEDEKKAAEALKKEAEEAKKAEELKKKEAEEKK 1716

Length = 2084

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 50.9 bits (121), Expect = 3e-07
 Identities = 31/92 (33%), Positives = 64/92 (69%)

Query: 178  KERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKE 237
             ++ ++ ++K +  +K EE+EK+  +  +K+ E+ K+ ++ KKK+ ++K+K ++ KK +E
Sbjct: 1667 AKKAEEDKKKAEEAKKAEEDEKKAAEALKKEAEEAKKAEELKKKEAEEKKKAEELKKAEE 1726

Query: 238  KKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKK 269
            + K K E+ KK+ E+ K+K ++ KK E++KKK
Sbjct: 1727 ENKIKAEEAKKEAEEDKKKAEEAKKDEEEKKK 1758

Length = 2084

>gnl|CDD|219746 pfam08208, RNA_polI_A34, DNA-directed RNA polymerase I subunit RPA34

 Score = 49.3 bits (118), Expect = 3e-07
 Identities = 33/70 (47%), Positives = 47/70 (67%)

Query: 194 KEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKK 253
               E   E +  +K+   K +K+ + ++E+KKEKKKKK+ KKEKK+KK +K+K  E K 
Sbjct: 123 GPPSELGSESETSEKETTAKVEKEAEVEEEEKKEKKKKKEVKKEKKEKKDKKEKMVEPKG 182

Query: 254 KEKKKKKKKK 263
            +KKKKKKKK
Sbjct: 183 SKKKKKKKKK 192

5. This is a family of proteins conserved from yeasts to human. Subunit A34.5 of RNA polymerase I is a non-essential subunit which is thought to help Pol I overcome topological constraints imposed on ribosomal DNA during the process of transcription. Length = 193

>gnl|CDD|221641 pfam12569, NARP1, NMDA receptor-regulated protein 1

 Score = 50.7 bits (122), Expect = 3e-07
 Identities = 23/66 (34%), Positives = 35/66 (53%), Gaps = 2/66 (3%)

Query: 193 KKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEK 252
             E EE+E E       E+KK +KK  ++K +KK +K++ +K   KKK +   KK K   
Sbjct: 393 LAEGEEEEGENGNLSPAERKKLRKK--QRKAEKKAEKEEAEKAAAKKKAEAAAKKAKGPD 450

Query: 253 KKEKKK 258
            + KK 
Sbjct: 451 GETKKV 456

This domain family is found in eukaryotes, and is approximately 40 amino acids in length. The family is found in association with pfam07719, pfam00515. There is a single completely conserved residue L that may be functionally important. NARP1 is the mammalian homologue of a yeast N-terminal acetyltransferase that regulates entry into the G(0) phase of the cell cycle. Length = 516

>gnl|CDD|221641 pfam12569, NARP1, NMDA receptor-regulated protein 1

 Score = 50.7 bits (122), Expect = 3e-07
 Identities = 18/67 (26%), Positives = 36/67 (53%), Gaps = 1/67 (1%)

Query: 206 EKKKEKKKEKKKEK-KKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKKKEKKKKKKKKE 264
              + +++E +       E+KK +KK++K +K+ +K++ EK   K++ +   KK K    
Sbjct: 392 LLAEGEEEEGENGNLSPAERKKLRKKQRKAEKKAEKEEAEKAAAKKKAEAAAKKAKGPDG 451

Query: 265 KKKKKDE 271
           + KK D 
Sbjct: 452 ETKKVDP 458

This domain family is found in eukaryotes, and is approximately 40 amino acids in length. The family is found in association with pfam07719, pfam00515. There is a single completely conserved residue L that may be functionally important. NARP1 is the mammalian homologue of a yeast N-terminal acetyltransferase that regulates entry into the G(0) phase of the cell cycle. Length = 516

>gnl|CDD|223880 COG0810, TonB, Periplasmic protein TonB, links inner and outer membranes [Cell envelope biogenesis, outer membrane]

 Score = 49.8 bits (119), Expect = 3e-07
 Identities = 23/74 (31%), Positives = 34/74 (45%)

Query: 193 KKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEK 252
            + E E  EE+ +   + +   +    K KEK K +KK KK K + K K K K K K + 
Sbjct: 56  PQPEPEPPEEQPKPPTEPETPPEPTPPKPKEKPKPEKKPKKPKPKPKPKPKPKPKVKPQP 115

Query: 253 KKEKKKKKKKKEKK 266
           K +K   K   +  
Sbjct: 116 KPKKPPSKTAAKAP 129

Length = 244

>gnl|CDD|220252 pfam09468, RNase_H2-Ydr279, Ydr279p protein family (RNase H2 complex component)

 Score = 50.0 bits (120), Expect = 3e-07
 Identities = 22/74 (29%), Positives = 41/74 (55%)

Query: 195 EEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKKK 254
           +E  K     E K  +K  ++ K+KK++ ++  +  + + +K++K K++ KKKK +E K 
Sbjct: 209 KELLKSLLIPEFKPLDKYLKESKKKKRETEEDVEAAESRAEKKRKSKEEIKKKKPKESKG 268

Query: 255 EKKKKKKKKEKKKK 268
            K  KK   +  KK
Sbjct: 269 VKALKKVVAKGMKK 282

RNases H are enzymes that specifically hydrolyse RNA when annealed to a complementary DNA and are present in all living organisms. In yeast RNase H2 is composed of a complex of three proteins (Rnh2Ap, Ydr279p and Ylr154p), this family represents the homologues of Ydr279p. It is not known whether non yeast proteins in this family fulfil the same function. Length = 287

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 50.9 bits (121), Expect = 4e-07
 Identities = 34/102 (33%), Positives = 59/102 (57%)

Query: 174  KGGKKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKK 233
            +  ++ R+ +  R     R++   + EE +K ++ K+ +++KK ++ KK ++K+K  + K
Sbjct: 1249 RNNEEIRKFEEARMAHFARRQAAIKAEEARKADELKKAEEKKKADEAKKAEEKKKADEAK 1308

Query: 234  KKKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDEGRRR 275
            KK E+ KK  E KKK EE KK+    KKK E+ KK  E  + 
Sbjct: 1309 KKAEEAKKADEAKKKAEEAKKKADAAKKKAEEAKKAAEAAKA 1350

Length = 2084

>gnl|CDD|234017 TIGR02794, tolA_full, TolA protein

 Score = 50.2 bits (120), Expect = 4e-07
 Identities = 24/93 (25%), Positives = 54/93 (58%)

Query: 177 KKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKK 236
            +++R   + ++K   ++   EK  ++ E+  K+ ++++K+ ++ K K+  + K K + +
Sbjct: 80  AEKQRAAEQARQKELEQRAAAEKAAKQAEQAAKQAEEKQKQAEEAKAKQAAEAKAKAEAE 139

Query: 237 EKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKK 269
            +KK K+E KK+ EE+ K K   + KK+  + K
Sbjct: 140 AEKKAKEEAKKQAEEEAKAKAAAEAKKKAAEAK 172

TolA couples the inner membrane complex of itself with TolQ and TolR to the outer membrane complex of TolB and OprL (also called Pal). Most of the length of the protein consists of low-complexity sequence that may differ in both length and composition from one species to another, complicating efforts to discriminate TolA (the most divergent gene in the tol-pal system) from paralogs such as TonB. Selection of members of the seed alignment and criteria for setting scoring cutoffs are based largely conserved operon struction. //The Tol-Pal complex is required for maintaining outer membrane integrity. Also involved in transport (uptake) of colicins and filamentous DNA, and implicated in pathogenesis. Transport is energized by the proton motive force. TolA is an inner membrane protein that interacts with periplasmic TolB and with outer membrane porins ompC, phoE and lamB [Transport and binding proteins, Other, Cellular processes, Pathogenesis]. Length = 346

>gnl|CDD|219838 pfam08432, DUF1742, Fungal protein of unknown function (DUF1742)

 Score = 48.9 bits (117), Expect = 4e-07
 Identities = 25/83 (30%), Positives = 51/83 (61%)

Query: 184 RRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKK 243
           +++K++   + E+ +KE E+K++ K +KKK KKK+ K K+KK +KK  K +KK++K+ + 
Sbjct: 61  KKKKKELAEEIEKVKKEYEEKQKWKWKKKKSKKKKDKDKDKKDDKKDDKSEKKDEKEAED 120

Query: 244 EKKKKKEEKKKEKKKKKKKKEKK 266
           + +   +   +      + K +K
Sbjct: 121 KLEDLTKSYSETLSTLSELKPRK 143

This is a family of fungal proteins of unknown function. Length = 182

>gnl|CDD|215214 PLN02381, PLN02381, valyl-tRNA synthetase

 Score = 50.7 bits (121), Expect = 4e-07
 Identities = 30/76 (39%), Positives = 44/76 (57%), Gaps = 5/76 (6%)

Query: 198 EKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKK---KEEKKK 254
           E E EKK   ++E +++KKKE+K KE  KE KK K  +KE K K + ++        KK 
Sbjct: 5   ESEAEKKILTEEELERKKKKEEKAKE--KELKKLKAAQKEAKAKLQAQQASDGTNVPKKS 62

Query: 255 EKKKKKKKKEKKKKKD 270
           EKK +K+  E +  +D
Sbjct: 63  EKKSRKRDVEDENPED 78

Length = 1066

>gnl|CDD|223880 COG0810, TonB, Periplasmic protein TonB, links inner and outer membranes [Cell envelope biogenesis, outer membrane]

 Score = 49.4 bits (118), Expect = 4e-07
 Identities = 26/77 (33%), Positives = 36/77 (46%)

Query: 193 KKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEK 252
             EE + E E  EE+ K   + +   +    K KEK K +KK K+ K K K K K K + 
Sbjct: 52  PTEEPQPEPEPPEEQPKPPTEPETPPEPTPPKPKEKPKPEKKPKKPKPKPKPKPKPKPKV 111

Query: 253 KKEKKKKKKKKEKKKKK 269
           K + K KK   +   K 
Sbjct: 112 KPQPKPKKPPSKTAAKA 128

Length = 244

>gnl|CDD|220252 pfam09468, RNase_H2-Ydr279, Ydr279p protein family (RNase H2 complex component)

 Score = 49.6 bits (119), Expect = 4e-07
 Identities = 25/74 (33%), Positives = 41/74 (55%), Gaps = 2/74 (2%)

Query: 190 RKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKE--KKKEKKKKKKKKKEKKKKKKEKKK 247
           ++  K     E +  ++  KE KK+K++ ++  E  + + +KK+K K++ KKKK KE K 
Sbjct: 209 KELLKSLLIPEFKPLDKYLKESKKKKRETEEDVEAAESRAEKKRKSKEEIKKKKPKESKG 268

Query: 248 KKEEKKKEKKKKKK 261
            K  KK   K  KK
Sbjct: 269 VKALKKVVAKGMKK 282

RNases H are enzymes that specifically hydrolyse RNA when annealed to a complementary DNA and are present in all living organisms. In yeast RNase H2 is composed of a complex of three proteins (Rnh2Ap, Ydr279p and Ylr154p), this family represents the homologues of Ydr279p. It is not known whether non yeast proteins in this family fulfil the same function. Length = 287

>gnl|CDD|114011 pfam05262, Borrelia_P83, Borrelia P83/100 protein

 Score = 50.4 bits (120), Expect = 4e-07
 Identities = 23/90 (25%), Positives = 49/90 (54%), Gaps = 1/90 (1%)

Query: 178 KERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKE-KKKEKKKKKKKKK 236
           KER  Q   KR ++ K+E ++K+ +  + ++K    +   +K++ E ++K+++ K   K 
Sbjct: 204 KERESQEDAKRAQQLKEELDKKQIDADKAQQKADFAQDNADKQRDEVRQKQQEAKNLPKP 263

Query: 237 EKKKKKKEKKKKKEEKKKEKKKKKKKKEKK 266
                 KE K+  E +K+E +K + + +K 
Sbjct: 264 ADTSSPKEDKQVAENQKREIEKAQIEIKKN 293

This family consists of several Borrelia P83/P100 antigen proteins. Length = 489

>gnl|CDD|219655 pfam07946, DUF1682, Protein of unknown function (DUF1682)

 Score = 49.6 bits (119), Expect = 5e-07
 Identities = 17/60 (28%), Positives = 40/60 (66%)

Query: 177 KKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKK 236
            K R ++  +  K   ++ +EE +E+K+E+KK+E++ +  K   ++++K E+K++KK+ +
Sbjct: 262 DKTREEEEEKILKAAEEERQEEAQEKKEEKKKEEREAKLAKLSPEEQRKLEEKERKKQAR 321

The members of this family are all hypothetical eukaryotic proteins of unknown function. One member is described as being an adipocyte-specific protein, but no evidence of this was found. Length = 322

>gnl|CDD|221641 pfam12569, NARP1, NMDA receptor-regulated protein 1

 Score = 50.3 bits (121), Expect = 5e-07
 Identities = 22/67 (32%), Positives = 35/67 (52%), Gaps = 3/67 (4%)

Query: 189 KRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKK 248
             + ++EE E       E+KK +KK++K EKK    +KE+ +K   KK+ +   K+ K  
Sbjct: 393 LAEGEEEEGENGNLSPAERKKLRKKQRKAEKK---AEKEEAEKAAAKKKAEAAAKKAKGP 449

Query: 249 KEEKKKE 255
             E KK 
Sbjct: 450 DGETKKV 456

This domain family is found in eukaryotes, and is approximately 40 amino acids in length. The family is found in association with pfam07719, pfam00515. There is a single completely conserved residue L that may be functionally important. NARP1 is the mammalian homologue of a yeast N-terminal acetyltransferase that regulates entry into the G(0) phase of the cell cycle. Length = 516

>gnl|CDD|234017 TIGR02794, tolA_full, TolA protein

 Score = 49.4 bits (118), Expect = 6e-07
 Identities = 23/99 (23%), Positives = 59/99 (59%)

Query: 177 KKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKK 236
           + E  +++R   + ++K+ E+    EK  ++ ++  K+ ++++K+ E+ K K+  + K K
Sbjct: 76  QAEEAEKQRAAEQARQKELEQRAAAEKAAKQAEQAAKQAEEKQKQAEEAKAKQAAEAKAK 135

Query: 237 EKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDEGRRR 275
            + + +K+ K++ +++ +E+ K K   E KKK  E +++
Sbjct: 136 AEAEAEKKAKEEAKKQAEEEAKAKAAAEAKKKAAEAKKK 174

TolA couples the inner membrane complex of itself with TolQ and TolR to the outer membrane complex of TolB and OprL (also called Pal). Most of the length of the protein consists of low-complexity sequence that may differ in both length and composition from one species to another, complicating efforts to discriminate TolA (the most divergent gene in the tol-pal system) from paralogs such as TonB. Selection of members of the seed alignment and criteria for setting scoring cutoffs are based largely conserved operon struction. //The Tol-Pal complex is required for maintaining outer membrane integrity. Also involved in transport (uptake) of colicins and filamentous DNA, and implicated in pathogenesis. Transport is energized by the proton motive force. TolA is an inner membrane protein that interacts with periplasmic TolB and with outer membrane porins ompC, phoE and lamB [Transport and binding proteins, Other, Cellular processes, Pathogenesis]. Length = 346

>gnl|CDD|219655 pfam07946, DUF1682, Protein of unknown function (DUF1682)

 Score = 49.6 bits (119), Expect = 6e-07
 Identities = 19/69 (27%), Positives = 46/69 (66%), Gaps = 3/69 (4%)

Query: 209 KEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKKKEKK---KKKKKKEK 265
             +   K  + +++E++K  K  +++++E+ ++KKE+KKK+E + K  K   ++++K E+
Sbjct: 254 SPEVLRKVDKTREEEEEKILKAAEEERQEEAQEKKEEKKKEEREAKLAKLSPEEQRKLEE 313

Query: 266 KKKKDEGRR 274
           K++K + R+
Sbjct: 314 KERKKQARK 322

The members of this family are all hypothetical eukaryotic proteins of unknown function. One member is described as being an adipocyte-specific protein, but no evidence of this was found. Length = 322

>gnl|CDD|220648 pfam10243, MIP-T3, Microtubule-binding protein MIP-T3

 Score = 49.9 bits (119), Expect = 6e-07
 Identities = 30/87 (34%), Positives = 63/87 (72%)

Query: 187 KRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKK 246
              + +  +E + E  K+EEK+KE+ KE+KK+KK+K K++ K +K K++ ++K+  KEK+
Sbjct: 88  PAAKTKPAKEPKNESGKEEEKEKEQVKEEKKKKKEKPKEEPKDRKPKEEAKEKRPPKEKE 147

Query: 247 KKKEEKKKEKKKKKKKKEKKKKKDEGR 273
           K+KE+K +E + ++++K++++ + + R
Sbjct: 148 KEKEKKVEEPRDREEEKKRERVRAKSR 174

This protein, which interacts with both microtubules and TRAF3 (tumour necrosis factor receptor-associated factor 3), is conserved from worms to humans. The N-terminal region is the microtubule binding domain and is well-conserved; the C-terminal 100 residues, also well-conserved, constitute the coiled-coil region which binds to TRAF3. The central region of the protein is rich in lysine and glutamic acid and carries KKE motifs which may also be necessary for tubulin-binding, but this region is the least well-conserved. Length = 506

>gnl|CDD|220648 pfam10243, MIP-T3, Microtubule-binding protein MIP-T3

 Score = 49.9 bits (119), Expect = 6e-07
 Identities = 36/98 (36%), Positives = 60/98 (61%), Gaps = 4/98 (4%)

Query: 177 KKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKK 236
            K    +   K K + K+E+++K+E+ KEE K  K KE+ KEK+   K+KEK+K+KK ++
Sbjct: 98  PKNESGKEEEKEKEQVKEEKKKKKEKPKEEPKDRKPKEEAKEKRPP-KEKEKEKEKKVEE 156

Query: 237 EKKK---KKKEKKKKKEEKKKEKKKKKKKKEKKKKKDE 271
            + +   KK+E+ + K   KK  KKK   K+K+  ++E
Sbjct: 157 PRDREEEKKRERVRAKSRPKKPPKKKPPNKKKEPPEEE 194

This protein, which interacts with both microtubules and TRAF3 (tumour necrosis factor receptor-associated factor 3), is conserved from worms to humans. The N-terminal region is the microtubule binding domain and is well-conserved; the C-terminal 100 residues, also well-conserved, constitute the coiled-coil region which binds to TRAF3. The central region of the protein is rich in lysine and glutamic acid and carries KKE motifs which may also be necessary for tubulin-binding, but this region is the least well-conserved. Length = 506

>gnl|CDD|226894 COG4499, COG4499, Predicted membrane protein [Function unknown]

 Score = 49.8 bits (119), Expect = 6e-07
 Identities = 23/70 (32%), Positives = 43/70 (61%), Gaps = 3/70 (4%)

Query: 187 KRKRKRKKEEEEKEEE---KKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKK 243
            ++++  KE  +K ++   K  E K E    ++ E K KE+K ++++ +KK+KE+  + K
Sbjct: 365 DKRQELLKEYNKKLQDYTKKLGEVKDETDASEEAEAKAKEEKLKQEENEKKQKEQADEDK 424

Query: 244 EKKKKKEEKK 253
           EK++K E KK
Sbjct: 425 EKRQKDERKK 434

Length = 434

>gnl|CDD|235640 PRK05901, PRK05901, RNA polymerase sigma factor; Provisional

 Score = 49.6 bits (119), Expect = 7e-07
 Identities = 19/95 (20%), Positives = 36/95 (37%)

Query: 177 KKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKK 236
            KE  + +++  ++  +         K  +   E    KKK K   +    K   KKK K
Sbjct: 38  IKEALESKKKTPEQIDQVLIFLSGMVKDTDDATESDIPKKKTKTAAKAAAAKAPAKKKLK 97

Query: 237 EKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDE 271
           ++    K+ +KK    K +     K  +   + D+
Sbjct: 98  DELDSSKKAEKKNALDKDDDLNYVKDIDVLNQADD 132

Length = 509

>gnl|CDD|234750 PRK00409, PRK00409, recombination and DNA strand exchange inhibitor protein; Reviewed

 Score = 49.8 bits (120), Expect = 7e-07
 Identities = 25/96 (26%), Positives = 55/96 (57%), Gaps = 4/96 (4%)

Query: 178 KERRKQRRRKRKRKRKKEEEEKEEEKK----EEKKKEKKKEKKKEKKKKEKKKEKKKKKK 233
              ++  + K + + KKE+ ++EE+K     E++ ++  KE KKE  +  K+  + +K  
Sbjct: 541 ALLKEAEKLKEELEEKKEKLQEEEDKLLEEAEKEAQQAIKEAKKEADEIIKELRQLQKGG 600

Query: 234 KKKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKK 269
               K  +  E +K+  +  ++K+KKKKK+++K+++
Sbjct: 601 YASVKAHELIEARKRLNKANEKKEKKKKKQKEKQEE 636

Length = 782

>gnl|CDD|219655 pfam07946, DUF1682, Protein of unknown function (DUF1682)

 Score = 48.8 bits (117), Expect = 9e-07
 Identities = 17/69 (24%), Positives = 48/69 (69%)

Query: 199 KEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKKKEKKK 258
             E  ++  K  +++E+K  K  +E+++E+ ++KK++K+K++++ +  K   E++++ ++
Sbjct: 254 SPEVLRKVDKTREEEEEKILKAAEEERQEEAQEKKEEKKKEEREAKLAKLSPEEQRKLEE 313

Query: 259 KKKKKEKKK 267
           K++KK+ +K
Sbjct: 314 KERKKQARK 322

The members of this family are all hypothetical eukaryotic proteins of unknown function. One member is described as being an adipocyte-specific protein, but no evidence of this was found. Length = 322

>gnl|CDD|220648 pfam10243, MIP-T3, Microtubule-binding protein MIP-T3

 Score = 49.5 bits (118), Expect = 9e-07
 Identities = 31/89 (34%), Positives = 62/89 (69%)

Query: 186 RKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEK 245
           ++ ++   K    K +  KE K +  K+E+K++++ KE+KK+KK+K K++ + +K K+E 
Sbjct: 78  KRVEKGGSKGPAAKTKPAKEPKNESGKEEEKEKEQVKEEKKKKKEKPKEEPKDRKPKEEA 137

Query: 246 KKKKEEKKKEKKKKKKKKEKKKKKDEGRR 274
           K+K+  K+KEK+K+KK +E + +++E +R
Sbjct: 138 KEKRPPKEKEKEKEKKVEEPRDREEEKKR 166

This protein, which interacts with both microtubules and TRAF3 (tumour necrosis factor receptor-associated factor 3), is conserved from worms to humans. The N-terminal region is the microtubule binding domain and is well-conserved; the C-terminal 100 residues, also well-conserved, constitute the coiled-coil region which binds to TRAF3. The central region of the protein is rich in lysine and glutamic acid and carries KKE motifs which may also be necessary for tubulin-binding, but this region is the least well-conserved. Length = 506

>gnl|CDD|234750 PRK00409, PRK00409, recombination and DNA strand exchange inhibitor protein; Reviewed

 Score = 49.4 bits (119), Expect = 9e-07
 Identities = 29/103 (28%), Positives = 53/103 (51%), Gaps = 16/103 (15%)

Query: 183 QRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKK----KKE- 237
           +  R+ ++K ++ E   +E +K +++ E+KKEK +E++ K  ++ +K+ ++     KKE 
Sbjct: 527 ELERELEQKAEEAEALLKEAEKLKEELEEKKEKLQEEEDKLLEEAEKEAQQAIKEAKKEA 586

Query: 238 -----------KKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKK 269
                      K      K  +  E +K   K  +KKEKKKKK
Sbjct: 587 DEIIKELRQLQKGGYASVKAHELIEARKRLNKANEKKEKKKKK 629

Length = 782

>gnl|CDD|215521 PLN02967, PLN02967, kinase

 Score = 49.3 bits (117), Expect = 9e-07
 Identities = 27/103 (26%), Positives = 42/103 (40%), Gaps = 16/103 (15%)

Query: 185 RRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEK---------------- 228
            RK+       +EE +E     KKK  +  K+  KK   +  E                 
Sbjct: 48  SRKKIESALAVDEEPDENGAVSKKKPTRSVKRATKKTVVEISEPLEEGSELVVNEDAALD 107

Query: 229 KKKKKKKKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDE 271
           K+ KK  +  ++K        EE+K EKK +K++K KK  +D 
Sbjct: 108 KESKKTPRRTRRKAAAASSDVEEEKTEKKVRKRRKVKKMDEDV 150

Length = 581

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 49.0 bits (116), Expect = 1e-06
 Identities = 35/96 (36%), Positives = 63/96 (65%)

Query: 180  RRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKK 239
            R+ +  +K +  R +E  +  EE+K+ K +E KK ++ + K +E KK +++KKK ++ KK
Sbjct: 1581 RKAEEAKKAEEARIEEVMKLYEEEKKMKAEEAKKAEEAKIKAEELKKAEEEKKKVEQLKK 1640

Query: 240  KKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDEGRRR 275
            K+ +EKKK +E KK E++ K K  E+ KK +E +++
Sbjct: 1641 KEAEEKKKAEELKKAEEENKIKAAEEAKKAEEDKKK 1676

Length = 2084

>gnl|CDD|215214 PLN02381, PLN02381, valyl-tRNA synthetase

 Score = 49.5 bits (118), Expect = 1e-06
 Identities = 23/68 (33%), Positives = 40/68 (58%)

Query: 190 RKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKK 249
            + + E E+K   ++E ++K+KK+EK KEK+ K+ K  +K+ K K + ++        KK
Sbjct: 2   SRTESEAEKKILTEEELERKKKKEEKAKEKELKKLKAAQKEAKAKLQAQQASDGTNVPKK 61

Query: 250 EEKKKEKK 257
            EKK  K+
Sbjct: 62  SEKKSRKR 69

Length = 1066

>gnl|CDD|226894 COG4499, COG4499, Predicted membrane protein [Function unknown]

 Score = 49.0 bits (117), Expect = 1e-06
 Identities = 20/82 (24%), Positives = 47/82 (57%)

Query: 188 RKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKK 247
           +  +  K   +   +K++E  KE  K+ +   KK  + K++    ++ + K K++K K++
Sbjct: 351 KLYEEVKSNTDLSGDKRQELLKEYNKKLQDYTKKLGEVKDETDASEEAEAKAKEEKLKQE 410

Query: 248 KKEEKKKEKKKKKKKKEKKKKK 269
           + E+K+KE+  + K+K +K ++
Sbjct: 411 ENEKKQKEQADEDKEKRQKDER 432

Length = 434

>gnl|CDD|217051 pfam02463, SMC_N, RecF/RecN/SMC N terminal domain

 Score = 49.2 bits (117), Expect = 1e-06
 Identities = 26/95 (27%), Positives = 56/95 (58%)

Query: 177 KKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKK 236
           ++     +   R  + + E  ++E EK+EE   +  KE K+E+K+K+ ++E+ K   K++
Sbjct: 237 EERIDLLQELLRDEQEEIESSKQELEKEEEILAQVLKENKEEEKEKKLQEEELKLLAKEE 296

Query: 237 EKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDE 271
           E+ K +  K ++++   +EK K+ +K+ KK +K+ 
Sbjct: 297 EELKSELLKLERRKVDDEEKLKESEKELKKLEKEL 331

This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination. Length = 1162

>gnl|CDD|217051 pfam02463, SMC_N, RecF/RecN/SMC N terminal domain

 Score = 49.2 bits (117), Expect = 1e-06
 Identities = 22/92 (23%), Positives = 56/92 (60%)

Query: 178 KERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKE 237
           K   ++    ++  R ++EE +  +++ EK++E   +  KE K++EK+K+ ++++ K   
Sbjct: 234 KLNEERIDLLQELLRDEQEEIESSKQELEKEEEILAQVLKENKEEEKEKKLQEEELKLLA 293

Query: 238 KKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKK 269
           K++++ + +  K E++K   ++K K+ +K+ K
Sbjct: 294 KEEEELKSELLKLERRKVDDEEKLKESEKELK 325

This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination. Length = 1162

>gnl|CDD|240271 PTZ00108, PTZ00108, DNA topoisomerase 2-like protein; Provisional

 Score = 49.7 bits (119), Expect = 1e-06
 Identities = 31/81 (38%), Positives = 43/81 (53%), Gaps = 3/81 (3%)

Query: 195  EEEEKEEEK---KEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEE 251
            EE+E+ EEK   KE++ K K K K  + +K + KK++KKKKK   +K KK       K  
Sbjct: 1142 EEQEEVEEKEIAKEQRLKSKTKGKASKLRKPKLKKKEKKKKKSSADKSKKASVVGNSKRV 1201

Query: 252  KKKEKKKKKKKKEKKKKKDEG 272
               EK+K   K + KK    G
Sbjct: 1202 DSDEKRKLDDKPDNKKSNSSG 1222

Length = 1388

>gnl|CDD|240271 PTZ00108, PTZ00108, DNA topoisomerase 2-like protein; Provisional

 Score = 48.9 bits (117), Expect = 1e-06
 Identities = 25/134 (18%), Positives = 43/134 (32%)

Query: 138  KDGSLPSCGCSRTARPKDLKREWLWGGCGDNLEYGYKGGKKERRKQRRRKRKRKRKKEEE 197
            K                    E       D+L    K     +R    +       K  +
Sbjct: 1234 KPKKSSVKRLKSKKNNSSKSSEDNDEFSSDDLSKEGKPKNAPKRVSAVQYSPPPPSKRPD 1293

Query: 198  EKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKKKEKK 257
             +     +     KKK KK+ +      K+KKK +KK   KKK K   K+    +     
Sbjct: 1294 GESNGGSKPSSPTKKKVKKRLEGSLAALKKKKKSEKKTARKKKSKTRVKQASASQSSRLL 1353

Query: 258  KKKKKKEKKKKKDE 271
            ++ +KK+     ++
Sbjct: 1354 RRPRKKKSDSSSED 1367

Length = 1388

>gnl|CDD|235640 PRK05901, PRK05901, RNA polymerase sigma factor; Provisional

 Score = 49.2 bits (118), Expect = 1e-06
 Identities = 16/96 (16%), Positives = 36/96 (37%)

Query: 177 KKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKK 236
           K + +    ++  ++  + +++  E+  +         K  +   +    +KK K   K 
Sbjct: 26  KSKSKGFITKEEIKEALESKKKTPEQIDQVLIFLSGMVKDTDDATESDIPKKKTKTAAKA 85

Query: 237 EKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDEG 272
              K   +KK K E    +K +KK   +K    +  
Sbjct: 86  AAAKAPAKKKLKDELDSSKKAEKKNALDKDDDLNYV 121

Length = 509

>gnl|CDD|221641 pfam12569, NARP1, NMDA receptor-regulated protein 1

 Score = 48.8 bits (117), Expect = 1e-06
 Identities = 22/61 (36%), Positives = 32/61 (52%)

Query: 196 EEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKKKE 255
                 E+K+ +KK++K EKK EK++ EK   KKK +   K+ K    E KK   +   E
Sbjct: 404 GNLSPAERKKLRKKQRKAEKKAEKEEAEKAAAKKKAEAAAKKAKGPDGETKKVDPDPLGE 463

Query: 256 K 256
           K
Sbjct: 464 K 464

This domain family is found in eukaryotes, and is approximately 40 amino acids in length. The family is found in association with pfam07719, pfam00515. There is a single completely conserved residue L that may be functionally important. NARP1 is the mammalian homologue of a yeast N-terminal acetyltransferase that regulates entry into the G(0) phase of the cell cycle. Length = 516

>gnl|CDD|221641 pfam12569, NARP1, NMDA receptor-regulated protein 1

 Score = 48.8 bits (117), Expect = 1e-06
 Identities = 19/61 (31%), Positives = 32/61 (52%)

Query: 212 KKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDE 271
           K    + ++++ +       ++KK  KK++K EKK +KEE +K   KKK +   KK K  
Sbjct: 390 KPLLAEGEEEEGENGNLSPAERKKLRKKQRKAEKKAEKEEAEKAAAKKKAEAAAKKAKGP 449

Query: 272 G 272
            
Sbjct: 450 D 450

This domain family is found in eukaryotes, and is approximately 40 amino acids in length. The family is found in association with pfam07719, pfam00515. There is a single completely conserved residue L that may be functionally important. NARP1 is the mammalian homologue of a yeast N-terminal acetyltransferase that regulates entry into the G(0) phase of the cell cycle. Length = 516

>gnl|CDD|220252 pfam09468, RNase_H2-Ydr279, Ydr279p protein family (RNase H2 complex component)

 Score = 48.1 bits (115), Expect = 1e-06
 Identities = 21/73 (28%), Positives = 39/73 (53%)

Query: 199 KEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKKKEKKK 258
            +  K+  K     + K  +K  KE KK+K++ ++  +  + + ++K+K KEE KK+K K
Sbjct: 205 PDLYKELLKSLLIPEFKPLDKYLKESKKKKRETEEDVEAAESRAEKKRKSKEEIKKKKPK 264

Query: 259 KKKKKEKKKKKDE 271
           + K  +  KK   
Sbjct: 265 ESKGVKALKKVVA 277

RNases H are enzymes that specifically hydrolyse RNA when annealed to a complementary DNA and are present in all living organisms. In yeast RNase H2 is composed of a complex of three proteins (Rnh2Ap, Ydr279p and Ylr154p), this family represents the homologues of Ydr279p. It is not known whether non yeast proteins in this family fulfil the same function. Length = 287

>gnl|CDD|235401 PRK05306, infB, translation initiation factor IF-2; Validated

 Score = 49.5 bits (119), Expect = 1e-06
 Identities = 12/81 (14%), Positives = 36/81 (44%)

Query: 195 EEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKKK 254
           EEEE  +E+ + + +E+ K + +E    E ++E K +       ++  +     +   + 
Sbjct: 39  EEEEARKEEAKREAEEEAKAEAEEAAAAEAEEEAKAEAAAAAPAEEAAEAAAAAEAAARP 98

Query: 255 EKKKKKKKKEKKKKKDEGRRR 275
            + +  +  E   ++ + ++ 
Sbjct: 99  AEDEAARPAEAAARRPKAKKA 119

Length = 746

>gnl|CDD|214661 smart00435, TOPEUc, DNA Topoisomerase I (eukaryota)

 Score = 48.9 bits (117), Expect = 1e-06
 Identities = 25/86 (29%), Positives = 48/86 (55%)

Query: 182 KQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKK 241
           K   + +++ +  + + K  +K     +     K+K K K E+  EK   + K+K+K+KK
Sbjct: 277 KSMEKLQEKIKALKYQLKRLKKMILLFEMISDLKRKLKSKFERDNEKLDAEVKEKKKEKK 336

Query: 242 KKEKKKKKEEKKKEKKKKKKKKEKKK 267
           K+EKKKK+ E+ +E+ +K + +   K
Sbjct: 337 KEEKKKKQIERLEERIEKLEVQATDK 362

DNA Topoisomerase I (eukaryota), DNA topoisomerase V, Vaccina virus topoisomerase, Variola virus topoisomerase, Shope fibroma virus topoisomeras. Length = 391

>gnl|CDD|214661 smart00435, TOPEUc, DNA Topoisomerase I (eukaryota)

 Score = 48.9 bits (117), Expect = 1e-06
 Identities = 26/72 (36%), Positives = 44/72 (61%), Gaps = 1/72 (1%)

Query: 198 EKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKK-KKKKKKEKKKKKKEKKKKKEEKKKEK 256
           EK +EK +  K + K+ KK     +     K+K K K +++ +K   E K+KK+EKKKE+
Sbjct: 280 EKLQEKIKALKYQLKRLKKMILLFEMISDLKRKLKSKFERDNEKLDAEVKEKKKEKKKEE 339

Query: 257 KKKKKKKEKKKK 268
           KKKK+ +  +++
Sbjct: 340 KKKKQIERLEER 351

DNA Topoisomerase I (eukaryota), DNA topoisomerase V, Vaccina virus topoisomerase, Variola virus topoisomerase, Shope fibroma virus topoisomeras. Length = 391

>gnl|CDD|221952 pfam13166, AAA_13, AAA domain

 Score = 48.9 bits (117), Expect = 1e-06
 Identities = 26/81 (32%), Positives = 42/81 (51%)

Query: 191 KRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKE 250
           +   E E + EE K+E KK ++K ++ E + ++K++E +K K K  +K  KK  KK    
Sbjct: 88  EENIEIEAQIEELKKELKKLEEKIEQLEAEIEKKEEELEKAKNKFLDKAWKKLAKKYDSN 147

Query: 251 EKKKEKKKKKKKKEKKKKKDE 271
             +  K    KK  K+K   E
Sbjct: 148 LSEALKGLNYKKNFKEKLLKE 168

This family of domains contain a P-loop motif that is characteristic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins. This family includes the PrrC protein that is thought to be the active component of the anticodon nuclease. Length = 713

>gnl|CDD|219655 pfam07946, DUF1682, Protein of unknown function (DUF1682)

 Score = 48.0 bits (115), Expect = 2e-06
 Identities = 19/69 (27%), Positives = 47/69 (68%), Gaps = 3/69 (4%)

Query: 204 KEEKKKEKKKEKKKEKKKKEKKKEKKKK---KKKKKEKKKKKKEKKKKKEEKKKEKKKKK 260
             E  ++  K +++E++K  K  E++++   ++KK+EKKK+++E K  K   ++++K ++
Sbjct: 254 SPEVLRKVDKTREEEEEKILKAAEEERQEEAQEKKEEKKKEEREAKLAKLSPEEQRKLEE 313

Query: 261 KKKEKKKKK 269
           K+++K+ +K
Sbjct: 314 KERKKQARK 322

The members of this family are all hypothetical eukaryotic proteins of unknown function. One member is described as being an adipocyte-specific protein, but no evidence of this was found. Length = 322

>gnl|CDD|220648 pfam10243, MIP-T3, Microtubule-binding protein MIP-T3

 Score = 48.3 bits (115), Expect = 2e-06
 Identities = 30/85 (35%), Positives = 55/85 (64%)

Query: 191 KRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKE 250
           KR ++   K    K +  KE K E  KE++K++++ +++KKKKK+K K++ K  K K++ 
Sbjct: 78  KRVEKGGSKGPAAKTKPAKEPKNESGKEEEKEKEQVKEEKKKKKEKPKEEPKDRKPKEEA 137

Query: 251 EKKKEKKKKKKKKEKKKKKDEGRRR 275
           ++K+  K+K+K+KEKK ++   R  
Sbjct: 138 KEKRPPKEKEKEKEKKVEEPRDREE 162

This protein, which interacts with both microtubules and TRAF3 (tumour necrosis factor receptor-associated factor 3), is conserved from worms to humans. The N-terminal region is the microtubule binding domain and is well-conserved; the C-terminal 100 residues, also well-conserved, constitute the coiled-coil region which binds to TRAF3. The central region of the protein is rich in lysine and glutamic acid and carries KKE motifs which may also be necessary for tubulin-binding, but this region is the least well-conserved. Length = 506

>gnl|CDD|220648 pfam10243, MIP-T3, Microtubule-binding protein MIP-T3

 Score = 48.3 bits (115), Expect = 2e-06
 Identities = 30/87 (34%), Positives = 61/87 (70%)

Query: 189 KRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKK 248
           K    K +  KE + +  K++EK+KE+ KE+KKK+K+K K++ K +K +++ K+K   K+
Sbjct: 86  KGPAAKTKPAKEPKNESGKEEEKEKEQVKEEKKKKKEKPKEEPKDRKPKEEAKEKRPPKE 145

Query: 249 KEEKKKEKKKKKKKKEKKKKKDEGRRR 275
           KE++K++K ++ + +E++KK++  R +
Sbjct: 146 KEKEKEKKVEEPRDREEEKKRERVRAK 172

This protein, which interacts with both microtubules and TRAF3 (tumour necrosis factor receptor-associated factor 3), is conserved from worms to humans. The N-terminal region is the microtubule binding domain and is well-conserved; the C-terminal 100 residues, also well-conserved, constitute the coiled-coil region which binds to TRAF3. The central region of the protein is rich in lysine and glutamic acid and carries KKE motifs which may also be necessary for tubulin-binding, but this region is the least well-conserved. Length = 506

>gnl|CDD|237177 PRK12704, PRK12704, phosphodiesterase; Provisional

 Score = 47.9 bits (115), Expect = 2e-06
 Identities = 23/93 (24%), Positives = 59/93 (63%)

Query: 179 ERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEK 238
           ++  +  +K      KEE  K   + E++ +E++ E +K +K+  +K+E   +K +  EK
Sbjct: 48  KKEAEAIKKEALLEAKEEIHKLRNEFEKELRERRNELQKLEKRLLQKEENLDRKLELLEK 107

Query: 239 KKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDE 271
           ++++ EKK+K+ E+K+++ +KK+++ ++  +++
Sbjct: 108 REEELEKKEKELEQKQQELEKKEEELEELIEEQ 140

Length = 520

>gnl|CDD|240271 PTZ00108, PTZ00108, DNA topoisomerase 2-like protein; Provisional

 Score = 48.1 bits (115), Expect = 2e-06
 Identities = 32/105 (30%), Positives = 52/105 (49%), Gaps = 6/105 (5%)

Query: 177  KKERRKQRRRKRKRKRK------KEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKK 230
              E  K+ +   K K         E+ +K EE  EE+++ ++KE  KE++ K K K K  
Sbjct: 1108 NAELEKKEKELEKLKNTTPKDMWLEDLDKFEEALEEQEEVEEKEIAKEQRLKSKTKGKAS 1167

Query: 231  KKKKKKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDEGRRR 275
            K +K K KKK+KK+KK   ++ KK       K+    +K +   +
Sbjct: 1168 KLRKPKLKKKEKKKKKSSADKSKKASVVGNSKRVDSDEKRKLDDK 1212

Length = 1388

>gnl|CDD|235640 PRK05901, PRK05901, RNA polymerase sigma factor; Provisional

 Score = 48.5 bits (116), Expect = 2e-06
 Identities = 19/95 (20%), Positives = 33/95 (34%)

Query: 177 KKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKK 236
            + ++K   +  +         K+ +   E    KKK K   K    K   KKK K +  
Sbjct: 42  LESKKKTPEQIDQVLIFLSGMVKDTDDATESDIPKKKTKTAAKAAAAKAPAKKKLKDELD 101

Query: 237 EKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDE 271
             KK +K+    K++     K      +     D+
Sbjct: 102 SSKKAEKKNALDKDDDLNYVKDIDVLNQADDDDDD 136

Length = 509

>gnl|CDD|235640 PRK05901, PRK05901, RNA polymerase sigma factor; Provisional

 Score = 48.1 bits (115), Expect = 2e-06
 Identities = 22/96 (22%), Positives = 32/96 (33%)

Query: 174 KGGKKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKK 233
           K   K    +   K   + KK+  E+ ++         K      +    KKK K   K 
Sbjct: 26  KSKSKGFITKEEIKEALESKKKTPEQIDQVLIFLSGMVKDTDDATESDIPKKKTKTAAKA 85

Query: 234 KKKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKK 269
              +   KKK K +    KK EKK    K +     
Sbjct: 86  AAAKAPAKKKLKDELDSSKKAEKKNALDKDDDLNYV 121

Length = 509

>gnl|CDD|214661 smart00435, TOPEUc, DNA Topoisomerase I (eukaryota)

 Score = 47.7 bits (114), Expect = 2e-06
 Identities = 28/71 (39%), Positives = 41/71 (57%)

Query: 199 KEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKKKEKKK 258
           K  EK  EK +EK K  K + K+ +K     +     K K K K E+  +K + + ++KK
Sbjct: 273 KTHEKSMEKLQEKIKALKYQLKRLKKMILLFEMISDLKRKLKSKFERDNEKLDAEVKEKK 332

Query: 259 KKKKKEKKKKK 269
           K+KKKE+KKKK
Sbjct: 333 KEKKKEEKKKK 343

DNA Topoisomerase I (eukaryota), DNA topoisomerase V, Vaccina virus topoisomerase, Variola virus topoisomerase, Shope fibroma virus topoisomeras. Length = 391

>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]

 Score = 48.6 bits (116), Expect = 2e-06
 Identities = 17/96 (17%), Positives = 46/96 (47%)

Query: 180 RRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKK 239
              + R +      +E EE+ EE KE+ +  K++ +++E   +E ++   + ++ K+E +
Sbjct: 305 SLLRERLEELENELEELEERLEELKEKIEALKEELEERETLLEELEQLLAELEEAKEELE 364

Query: 240 KKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDEGRRR 275
           +K     ++ EE  +  +++  + E +  +      
Sbjct: 365 EKLSALLEELEELFEALREELAELEAELAEIRNELE 400

Length = 1163

>gnl|CDD|237753 PRK14552, PRK14552, C/D box methylation guide ribonucleoprotein complex aNOP56 subunit; Provisional

 Score = 48.0 bits (115), Expect = 2e-06
 Identities = 23/50 (46%), Positives = 38/50 (76%)

Query: 220 KKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKK 269
           K++  K+ ++ K+K  K  KKK++EKK +K +KKK++KKK KK++KK +K
Sbjct: 365 KEELNKRIEEIKEKYPKPPKKKREEKKPQKRKKKKKRKKKGKKRKKKGRK 414

Length = 414

>gnl|CDD|237753 PRK14552, PRK14552, C/D box methylation guide ribonucleoprotein complex aNOP56 subunit; Provisional

 Score = 48.0 bits (115), Expect = 2e-06
 Identities = 23/50 (46%), Positives = 38/50 (76%)

Query: 193 KKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKK 242
           K+E  ++ EE KE+  K  KK+++++K +K KKK+K+KKK KK++KK +K
Sbjct: 365 KEELNKRIEEIKEKYPKPPKKKREEKKPQKRKKKKKRKKKGKKRKKKGRK 414

Length = 414

>gnl|CDD|233467 TIGR01554, major_cap_HK97, phage major capsid protein, HK97 family

 Score = 47.7 bits (114), Expect = 2e-06
 Identities = 18/97 (18%), Positives = 42/97 (43%)

Query: 178 KERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKE 237
           KE R+      K  RK  E+EK  E +EEK +    +++ +K   E  + ++   + + +
Sbjct: 2   KELREALAELAKELRKLTEDEKLAEAEEEKAEYDALKEEIDKLDAEIDRLEELLDELEAK 61

Query: 238 KKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDEGRR 274
                +    ++EE++ + +  + +   +   D    
Sbjct: 62  PAASGEGGGGEEEEEEAKAEAAEFRAYLRGGDDALAE 98

This model family represents the major capsid protein component of the heads (capsids) of bacteriophage HK97, phi-105, P27, and related phage. This model represents one of several analogous families lacking detectable sequence similarity. The gene encoding this component is typically located in an operon encoding the small and large terminase subunits, the portal protein and the prohead or maturation protease [Mobile and extrachromosomal element functions, Prophage functions]. Length = 384

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 48.2 bits (114), Expect = 3e-06
 Identities = 33/98 (33%), Positives = 64/98 (65%)

Query: 178  KERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKE 237
            K   ++++ K +  +K EE + + E+ ++ ++EKKK ++ +KK+ E+KK+ ++ KK ++E
Sbjct: 1599 KLYEEEKKMKAEEAKKAEEAKIKAEELKKAEEEKKKVEQLKKKEAEEKKKAEELKKAEEE 1658

Query: 238  KKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDEGRRR 275
             K K  E+ KK EE KK+ ++ KK +E +KK  E  ++
Sbjct: 1659 NKIKAAEEAKKAEEDKKKAEEAKKAEEDEKKAAEALKK 1696

Length = 2084

>gnl|CDD|234017 TIGR02794, tolA_full, TolA protein

 Score = 47.5 bits (113), Expect = 3e-06
 Identities = 23/94 (24%), Positives = 56/94 (59%)

Query: 178 KERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKE 237
           +ER+K+  ++ +   K+   E+  +K+ E++   +K  K+ ++  ++ +EK+K+ ++ K 
Sbjct: 67  QERQKKLEQQAEEAEKQRAAEQARQKELEQRAAAEKAAKQAEQAAKQAEEKQKQAEEAKA 126

Query: 238 KKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDE 271
           K+  + + K + E +KK K++ KK+ E++ K   
Sbjct: 127 KQAAEAKAKAEAEAEKKAKEEAKKQAEEEAKAKA 160

TolA couples the inner membrane complex of itself with TolQ and TolR to the outer membrane complex of TolB and OprL (also called Pal). Most of the length of the protein consists of low-complexity sequence that may differ in both length and composition from one species to another, complicating efforts to discriminate TolA (the most divergent gene in the tol-pal system) from paralogs such as TonB. Selection of members of the seed alignment and criteria for setting scoring cutoffs are based largely conserved operon struction. //The Tol-Pal complex is required for maintaining outer membrane integrity. Also involved in transport (uptake) of colicins and filamentous DNA, and implicated in pathogenesis. Transport is energized by the proton motive force. TolA is an inner membrane protein that interacts with periplasmic TolB and with outer membrane porins ompC, phoE and lamB [Transport and binding proteins, Other, Cellular processes, Pathogenesis]. Length = 346

>gnl|CDD|217051 pfam02463, SMC_N, RecF/RecN/SMC N terminal domain

 Score = 48.0 bits (114), Expect = 3e-06
 Identities = 28/94 (29%), Positives = 59/94 (62%)

Query: 177 KKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKK 236
           K E  K  RRK   + K +E EKE +K E++ K++K+E ++ +K+ ++ + K++ +++++
Sbjct: 300 KSELLKLERRKVDDEEKLKESEKELKKLEKELKKEKEEIEELEKELKELEIKREAEEEEE 359

Query: 237 EKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKD 270
           E+ +K +EK ++ EE+   KKK + ++     K 
Sbjct: 360 EQLEKLQEKLEQLEEELLAKKKLESERLSSAAKL 393

This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination. Length = 1162

>gnl|CDD|223880 COG0810, TonB, Periplasmic protein TonB, links inner and outer membranes [Cell envelope biogenesis, outer membrane]

 Score = 47.1 bits (112), Expect = 3e-06
 Identities = 22/76 (28%), Positives = 36/76 (47%)

Query: 195 EEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKKK 254
           E   +E + + E  +E+ K   + +   E    K K+K K ++K KK K K K K + K 
Sbjct: 50  EAPTEEPQPEPEPPEEQPKPPTEPETPPEPTPPKPKEKPKPEKKPKKPKPKPKPKPKPKP 109

Query: 255 EKKKKKKKKEKKKKKD 270
           + K + K K+   K  
Sbjct: 110 KVKPQPKPKKPPSKTA 125

Length = 244

>gnl|CDD|234750 PRK00409, PRK00409, recombination and DNA strand exchange inhibitor protein; Reviewed

 Score = 47.9 bits (115), Expect = 3e-06
 Identities = 32/110 (29%), Positives = 59/110 (53%), Gaps = 15/110 (13%)

Query: 177 KKERRKQRRRKRKRKRKKEE-EEKEEEKKEEKKKEKKKEKKKEKKK-KEKKKE------- 227
           +++  +     ++ ++ KEE EEK+E+ +EE+ K  ++ +K+ ++  KE KKE       
Sbjct: 533 EQKAEEAEALLKEAEKLKEELEEKKEKLQEEEDKLLEEAEKEAQQAIKEAKKEADEIIKE 592

Query: 228 ------KKKKKKKKKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDE 271
                       K  E  + +K   K  E+K+K+KKK+K+K+E+ K  DE
Sbjct: 593 LRQLQKGGYASVKAHELIEARKRLNKANEKKEKKKKKQKEKQEELKVGDE 642

Length = 782

>gnl|CDD|214661 smart00435, TOPEUc, DNA Topoisomerase I (eukaryota)

 Score = 47.7 bits (114), Expect = 3e-06
 Identities = 24/84 (28%), Positives = 49/84 (58%)

Query: 187 KRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKK 246
           K + K K  + + +  KK     E   + K++ K K ++  +K   + K++KK+KKKE+K
Sbjct: 281 KLQEKIKALKYQLKRLKKMILLFEMISDLKRKLKSKFERDNEKLDAEVKEKKKEKKKEEK 340

Query: 247 KKKEEKKKEKKKKKKKKEKKKKKD 270
           KKK+ ++ E++ +K + +   K++
Sbjct: 341 KKKQIERLEERIEKLEVQATDKEE 364

DNA Topoisomerase I (eukaryota), DNA topoisomerase V, Vaccina virus topoisomerase, Variola virus topoisomerase, Shope fibroma virus topoisomeras. Length = 391

>gnl|CDD|237753 PRK14552, PRK14552, C/D box methylation guide ribonucleoprotein complex aNOP56 subunit; Provisional

 Score = 47.7 bits (114), Expect = 3e-06
 Identities = 22/50 (44%), Positives = 38/50 (76%)

Query: 219 KKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKK 268
           K++  K+ E+ K+K  K  KKK++++K +K+++KKK KKK KK+K+K +K
Sbjct: 365 KEELNKRIEEIKEKYPKPPKKKREEKKPQKRKKKKKRKKKGKKRKKKGRK 414

Length = 414

>gnl|CDD|237753 PRK14552, PRK14552, C/D box methylation guide ribonucleoprotein complex aNOP56 subunit; Provisional

 Score = 47.7 bits (114), Expect = 3e-06
 Identities = 22/53 (41%), Positives = 41/53 (77%)

Query: 206 EKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKKKEKKK 258
           ++ KE+  ++ +E K+K  K  KKK+++KK +K+KKKK++KKK +++KK+ +K
Sbjct: 362 DELKEELNKRIEEIKEKYPKPPKKKREEKKPQKRKKKKKRKKKGKKRKKKGRK 414

Length = 414

>gnl|CDD|237753 PRK14552, PRK14552, C/D box methylation guide ribonucleoprotein complex aNOP56 subunit; Provisional

 Score = 47.7 bits (114), Expect = 3e-06
 Identities = 22/53 (41%), Positives = 41/53 (77%)

Query: 210 EKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKKKEKKKKKKK 262
           ++ KE+  ++ ++ K+K  K  KKK++EKK +K++KKKK+++K K++KKK +K
Sbjct: 362 DELKEELNKRIEEIKEKYPKPPKKKREEKKPQKRKKKKKRKKKGKKRKKKGRK 414

Length = 414

>gnl|CDD|236944 PRK11642, PRK11642, exoribonuclease R; Provisional

 Score = 48.2 bits (115), Expect = 3e-06
 Identities = 21/71 (29%), Positives = 34/71 (47%)

Query: 174 KGGKKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKK 233
           K G   ++  +RR+  +K   E +     +K+ K K  KK+ +K KK   K ++     K
Sbjct: 743 KKGDAGKKGGKRRQVGKKVNFEPDSAFRGEKKAKPKAAKKDARKAKKPSAKTQKIAAATK 802

Query: 234 KKKEKKKKKKE 244
            K+  KKK  E
Sbjct: 803 AKRAAKKKVAE 813

Length = 813

>gnl|CDD|236944 PRK11642, PRK11642, exoribonuclease R; Provisional

 Score = 47.8 bits (114), Expect = 3e-06
 Identities = 23/86 (26%), Positives = 37/86 (43%), Gaps = 5/86 (5%)

Query: 191 KRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKE 250
           +R      K   +K +K    KK  K+ +  K+   E     + +K+ K K  +K  +K 
Sbjct: 728 ERAPRNVGKTAREKAKKGDAGKKGGKRRQVGKKVNFEPDSAFRGEKKAKPKAAKKDARKA 787

Query: 251 EKKKEKKKK-----KKKKEKKKKKDE 271
           +K   K +K     K K+  KKK  E
Sbjct: 788 KKPSAKTQKIAAATKAKRAAKKKVAE 813

Length = 813

>gnl|CDD|219924 pfam08597, eIF3_subunit, Translation initiation factor eIF3 subunit

 Score = 47.0 bits (112), Expect = 3e-06
 Identities = 19/76 (25%), Positives = 48/76 (63%)

Query: 195 EEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKKK 254
           +++ K+   +EE +++++++ K   K K KK  K K ++K+K K++K+++  ++ EE   
Sbjct: 30  DDDVKDSWDEEEDEEKEEEKAKVAAKAKAKKALKAKIEEKEKAKREKEEKGLRELEEDTP 89

Query: 255 EKKKKKKKKEKKKKKD 270
           E +  +K + +K +++
Sbjct: 90  EDELAEKLRLRKLQEE 105

This is a family of proteins which are subunits of the eukaryotic translation initiation factor 3 (eIF3). In yeast it is called Hcr1. The Saccharomyces cerevisiae protein eIF3j (HCR1) has been shown to be required for processing of 20S pre-rRNA and binds to 18S rRNA and eIF3 subunits Rpg1p and Prt1p. Length = 242

>gnl|CDD|130141 TIGR01069, mutS2, MutS2 family protein

 Score = 47.9 bits (114), Expect = 3e-06
 Identities = 29/95 (30%), Positives = 52/95 (54%), Gaps = 2/95 (2%)

Query: 175 GGKKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKK 234
           G  KE       K     K+ E++ E    E+  KE++K KK+ +++ E+ KE+++ KK 
Sbjct: 507 GEFKEEINVLIEKLSALEKELEQKNE--HLEKLLKEQEKLKKELEQEMEELKERERNKKL 564

Query: 235 KKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKK 269
           + EK+ ++  K  KKE +   ++ K+KK  K K+ 
Sbjct: 565 ELEKEAQEALKALKKEVESIIRELKEKKIHKAKEI 599

Function of MutS2 is unknown. It should not be considered a DNA mismatch repair protein. It is likely a DNA mismatch binding protein of unknown cellular function [DNA metabolism, Other]. Length = 771

>gnl|CDD|234017 TIGR02794, tolA_full, TolA protein

 Score = 47.1 bits (112), Expect = 4e-06
 Identities = 23/89 (25%), Positives = 58/89 (65%)

Query: 181 RKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKK 240
           R Q+++K   K+++E ++K E++ EE +K++  E+ ++K+ +++   +K  K+ ++  K+
Sbjct: 54  RIQQQKKPAAKKEQERQKKLEQQAEEAEKQRAAEQARQKELEQRAAAEKAAKQAEQAAKQ 113

Query: 241 KKKEKKKKKEEKKKEKKKKKKKKEKKKKK 269
            ++++K+ +E K K+  + K K E + +K
Sbjct: 114 AEEKQKQAEEAKAKQAAEAKAKAEAEAEK 142

TolA couples the inner membrane complex of itself with TolQ and TolR to the outer membrane complex of TolB and OprL (also called Pal). Most of the length of the protein consists of low-complexity sequence that may differ in both length and composition from one species to another, complicating efforts to discriminate TolA (the most divergent gene in the tol-pal system) from paralogs such as TonB. Selection of members of the seed alignment and criteria for setting scoring cutoffs are based largely conserved operon struction. //The Tol-Pal complex is required for maintaining outer membrane integrity. Also involved in transport (uptake) of colicins and filamentous DNA, and implicated in pathogenesis. Transport is energized by the proton motive force. TolA is an inner membrane protein that interacts with periplasmic TolB and with outer membrane porins ompC, phoE and lamB [Transport and binding proteins, Other, Cellular processes, Pathogenesis]. Length = 346

>gnl|CDD|234017 TIGR02794, tolA_full, TolA protein

 Score = 47.1 bits (112), Expect = 4e-06
 Identities = 29/93 (31%), Positives = 49/93 (52%)

Query: 177 KKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKK 236
           +K+  + + ++    + K E E E++ KEE KK+ ++E K +   + KKK  + KKK + 
Sbjct: 118 QKQAEEAKAKQAAEAKAKAEAEAEKKAKEEAKKQAEEEAKAKAAAEAKKKAAEAKKKAEA 177

Query: 237 EKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKK 269
           E K K + K K K E+ K K +  K K   +  
Sbjct: 178 EAKAKAEAKAKAKAEEAKAKAEAAKAKAAAEAA 210

TolA couples the inner membrane complex of itself with TolQ and TolR to the outer membrane complex of TolB and OprL (also called Pal). Most of the length of the protein consists of low-complexity sequence that may differ in both length and composition from one species to another, complicating efforts to discriminate TolA (the most divergent gene in the tol-pal system) from paralogs such as TonB. Selection of members of the seed alignment and criteria for setting scoring cutoffs are based largely conserved operon struction. //The Tol-Pal complex is required for maintaining outer membrane integrity. Also involved in transport (uptake) of colicins and filamentous DNA, and implicated in pathogenesis. Transport is energized by the proton motive force. TolA is an inner membrane protein that interacts with periplasmic TolB and with outer membrane porins ompC, phoE and lamB [Transport and binding proteins, Other, Cellular processes, Pathogenesis]. Length = 346

>gnl|CDD|220648 pfam10243, MIP-T3, Microtubule-binding protein MIP-T3

 Score = 47.2 bits (112), Expect = 4e-06
 Identities = 31/89 (34%), Positives = 60/89 (67%)

Query: 187 KRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKK 246
           KR  K   +    + +  +E K E  KE++KEK++ +++K+KKK+K K++ K +K KE+ 
Sbjct: 78  KRVEKGGSKGPAAKTKPAKEPKNESGKEEEKEKEQVKEEKKKKKEKPKEEPKDRKPKEEA 137

Query: 247 KKKEEKKKEKKKKKKKKEKKKKKDEGRRR 275
           K+K   K+++K+K+KK E+ + ++E ++R
Sbjct: 138 KEKRPPKEKEKEKEKKVEEPRDREEEKKR 166

This protein, which interacts with both microtubules and TRAF3 (tumour necrosis factor receptor-associated factor 3), is conserved from worms to humans. The N-terminal region is the microtubule binding domain and is well-conserved; the C-terminal 100 residues, also well-conserved, constitute the coiled-coil region which binds to TRAF3. The central region of the protein is rich in lysine and glutamic acid and carries KKE motifs which may also be necessary for tubulin-binding, but this region is the least well-conserved. Length = 506

>gnl|CDD|226894 COG4499, COG4499, Predicted membrane protein [Function unknown]

 Score = 47.5 bits (113), Expect = 4e-06
 Identities = 21/77 (27%), Positives = 41/77 (53%)

Query: 199 KEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKKKEKKK 258
            EE K        K+++  ++  K+ +   KK  + K E    ++ + K KEEK K+++ 
Sbjct: 353 YEEVKSNTDLSGDKRQELLKEYNKKLQDYTKKLGEVKDETDASEEAEAKAKEEKLKQEEN 412

Query: 259 KKKKKEKKKKKDEGRRR 275
           +KK+KE+  +  E R++
Sbjct: 413 EKKQKEQADEDKEKRQK 429

Length = 434

>gnl|CDD|219746 pfam08208, RNA_polI_A34, DNA-directed RNA polymerase I subunit RPA34

 Score = 46.2 bits (110), Expect = 4e-06
 Identities = 34/69 (49%), Positives = 48/69 (69%), Gaps = 1/69 (1%)

Query: 193 KKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEK 252
            +   E E  +KE   K +K+ + +E++KKEKKK KK+ KK+KKEKK KK++  + K  K
Sbjct: 126 SELGSESETSEKETTAKVEKEAEVEEEEKKEKKK-KKEVKKEKKEKKDKKEKMVEPKGSK 184

Query: 253 KKEKKKKKK 261
           KK+KKKKKK
Sbjct: 185 KKKKKKKKK 193

5. This is a family of proteins conserved from yeasts to human. Subunit A34.5 of RNA polymerase I is a non-essential subunit which is thought to help Pol I overcome topological constraints imposed on ribosomal DNA during the process of transcription. Length = 193

>gnl|CDD|237753 PRK14552, PRK14552, C/D box methylation guide ribonucleoprotein complex aNOP56 subunit; Provisional

 Score = 47.3 bits (113), Expect = 4e-06
 Identities = 24/49 (48%), Positives = 38/49 (77%), Gaps = 1/49 (2%)

Query: 202 EKKEEKKKE-KKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKK 249
           E+  ++ +E K+K  K  KKK+E+KK +K+KKKKK++KK KK++KK +K
Sbjct: 366 EELNKRIEEIKEKYPKPPKKKREEKKPQKRKKKKKRKKKGKKRKKKGRK 414

Length = 414

>gnl|CDD|237753 PRK14552, PRK14552, C/D box methylation guide ribonucleoprotein complex aNOP56 subunit; Provisional

 Score = 47.3 bits (113), Expect = 4e-06
 Identities = 24/49 (48%), Positives = 35/49 (71%)

Query: 197 EEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEK 245
           EE  +  +E K+K  K  KKK ++KK +K++KKKK+KKK +K+KKK  K
Sbjct: 366 EELNKRIEEIKEKYPKPPKKKREEKKPQKRKKKKKRKKKGKKRKKKGRK 414

Length = 414

>gnl|CDD|219838 pfam08432, DUF1742, Fungal protein of unknown function (DUF1742)

 Score = 45.8 bits (109), Expect = 5e-06
 Identities = 26/87 (29%), Positives = 49/87 (56%)

Query: 173 YKGGKKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKK 232
           Y   KK++++      K K++ EE++K + KK++ KK+K K+K K+  KK+ K EKK +K
Sbjct: 57  YTEAKKKKKELAEEIEKVKKEYEEKQKWKWKKKKSKKKKDKDKDKKDDKKDDKSEKKDEK 116

Query: 233 KKKKEKKKKKKEKKKKKEEKKKEKKKK 259
           + + + +   K   +      + K +K
Sbjct: 117 EAEDKLEDLTKSYSETLSTLSELKPRK 143

This is a family of fungal proteins of unknown function. Length = 182

>gnl|CDD|220648 pfam10243, MIP-T3, Microtubule-binding protein MIP-T3

 Score = 47.2 bits (112), Expect = 5e-06
 Identities = 28/98 (28%), Positives = 57/98 (58%)

Query: 177 KKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKK 236
            KE  K R+ K + K K+  +EKE+EK+++ ++ + +E++K++++   K   KK  KKK 
Sbjct: 124 PKEEPKDRKPKEEAKEKRPPKEKEKEKEKKVEEPRDREEEKKRERVRAKSRPKKPPKKKP 183

Query: 237 EKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDEGRR 274
             KKK+  +++K+ +  +E  K K ++    ++ E   
Sbjct: 184 PNKKKEPPEEEKQRQAAREAVKGKPEEPDVNEEREKEE 221

This protein, which interacts with both microtubules and TRAF3 (tumour necrosis factor receptor-associated factor 3), is conserved from worms to humans. The N-terminal region is the microtubule binding domain and is well-conserved; the C-terminal 100 residues, also well-conserved, constitute the coiled-coil region which binds to TRAF3. The central region of the protein is rich in lysine and glutamic acid and carries KKE motifs which may also be necessary for tubulin-binding, but this region is the least well-conserved. Length = 506

>gnl|CDD|219746 pfam08208, RNA_polI_A34, DNA-directed RNA polymerase I subunit RPA34

 Score = 45.9 bits (109), Expect = 5e-06
 Identities = 29/64 (45%), Positives = 46/64 (71%)

Query: 191 KRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKE 250
              +  E++   K E++ + +++EKK++KKKKE KKEKK+KK KK++  + K  KKKKK+
Sbjct: 130 SESETSEKETTAKVEKEAEVEEEEKKEKKKKKEVKKEKKEKKDKKEKMVEPKGSKKKKKK 189

Query: 251 EKKK 254
           +KKK
Sbjct: 190 KKKK 193

5. This is a family of proteins conserved from yeasts to human. Subunit A34.5 of RNA polymerase I is a non-essential subunit which is thought to help Pol I overcome topological constraints imposed on ribosomal DNA during the process of transcription. Length = 193

>gnl|CDD|221641 pfam12569, NARP1, NMDA receptor-regulated protein 1

 Score = 47.2 bits (113), Expect = 5e-06
 Identities = 18/62 (29%), Positives = 35/62 (56%)

Query: 211 KKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKD 270
           K    + E+++ E       ++KK ++K++K ++K +K+E +K   KKK +   KK K  
Sbjct: 390 KPLLAEGEEEEGENGNLSPAERKKLRKKQRKAEKKAEKEEAEKAAAKKKAEAAAKKAKGP 449

Query: 271 EG 272
           +G
Sbjct: 450 DG 451

This domain family is found in eukaryotes, and is approximately 40 amino acids in length. The family is found in association with pfam07719, pfam00515. There is a single completely conserved residue L that may be functionally important. NARP1 is the mammalian homologue of a yeast N-terminal acetyltransferase that regulates entry into the G(0) phase of the cell cycle. Length = 516

>gnl|CDD|214395 CHL00204, ycf1, Ycf1; Provisional

 Score = 47.4 bits (113), Expect = 5e-06
 Identities = 22/86 (25%), Positives = 36/86 (41%), Gaps = 2/86 (2%)

Query: 168  NLEYGYKGGKKERRKQRRRKRKR--KRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKK 225
            N+       KK       +K      R +EE+E   + + E  KEKK   +     +EK 
Sbjct: 1497 NVNKKINQKKKGFIPSNEKKSIEIENRNQEEKEPAGQGELESDKEKKGNLESVLSNQEKN 1556

Query: 226  KEKKKKKKKKKEKKKKKKEKKKKKEE 251
             E+   +   K++K KK+ K   + E
Sbjct: 1557 IEEDYAESDIKKRKNKKQYKSNTEAE 1582

Length = 1832

>gnl|CDD|237258 PRK12903, secA, preprotein translocase subunit SecA; Reviewed

 Score = 47.4 bits (113), Expect = 5e-06
 Identities = 26/109 (23%), Positives = 51/109 (46%), Gaps = 15/109 (13%)

Query: 178 KERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKE 237
           +ER K  R +R+    + EE +   ++++  K++ K +  E ++ E++ +   + K +  
Sbjct: 816 EERLKALRIQREEMLMRPEELELINEEQKNLKQEIKLELSEIQEAEEEIQNINENKNEFV 875

Query: 238 KKKKKKEKKKKK---------------EEKKKEKKKKKKKKEKKKKKDE 271
           + K   +K  K                E K+ EK  KKKKK+ +K  +E
Sbjct: 876 EFKNDPKKLNKLIIAKDVLIKLVISSDEIKQDEKTTKKKKKDLEKTDEE 924

Length = 925

>gnl|CDD|240271 PTZ00108, PTZ00108, DNA topoisomerase 2-like protein; Provisional

 Score = 47.0 bits (112), Expect = 6e-06
 Identities = 25/79 (31%), Positives = 37/79 (46%), Gaps = 1/79 (1%)

Query: 192  RKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEE 251
             + EE+E  +E++  K K K K  K  K K +KK++KKKK    K KK       K+ + 
Sbjct: 1145 EEVEEKEIAKEQRL-KSKTKGKASKLRKPKLKKKEKKKKKSSADKSKKASVVGNSKRVDS 1203

Query: 252  KKKEKKKKKKKKEKKKKKD 270
             +K K   K   +K     
Sbjct: 1204 DEKRKLDDKPDNKKSNSSG 1222

Length = 1388

>gnl|CDD|235640 PRK05901, PRK05901, RNA polymerase sigma factor; Provisional

 Score = 46.9 bits (112), Expect = 6e-06
 Identities = 20/95 (21%), Positives = 37/95 (38%)

Query: 177 KKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKK 236
             +       + K+K KK   + + +    K++ K+  + K+K  ++  +         K
Sbjct: 5   STKAELAAEEEAKKKLKKLAAKSKSKGFITKEEIKEALESKKKTPEQIDQVLIFLSGMVK 64

Query: 237 EKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDE 271
           +     +    KK+ K   K    K   KKK KDE
Sbjct: 65  DTDDATESDIPKKKTKTAAKAAAAKAPAKKKLKDE 99

Length = 509

>gnl|CDD|237753 PRK14552, PRK14552, C/D box methylation guide ribonucleoprotein complex aNOP56 subunit; Provisional

 Score = 46.5 bits (111), Expect = 6e-06
 Identities = 22/53 (41%), Positives = 41/53 (77%)

Query: 195 EEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKK 247
           +E ++E  K+ E+ KEK  +  K+K++++K +++KKKKK+KK+ KK+KK+ +K
Sbjct: 362 DELKEELNKRIEEIKEKYPKPPKKKREEKKPQKRKKKKKRKKKGKKRKKKGRK 414

Length = 414

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 47.1 bits (111), Expect = 7e-06
 Identities = 38/103 (36%), Positives = 63/103 (61%), Gaps = 6/103 (5%)

Query: 178  KERRKQRRRKRKRKRKKEEEEKEEE---KKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKK 234
            K++ ++ ++  + K+K EE +K +E   K EE KK+  + KK  + KK+  + KK ++ K
Sbjct: 1463 KKKAEEAKKADEAKKKAEEAKKADEAKKKAEEAKKKADEAKKAAEAKKKADEAKKAEEAK 1522

Query: 235  KKEKKKKKKEKKKKKEEKKKEKKKKK---KKKEKKKKKDEGRR 274
            K ++ KK +E KK  E KK E+KKK    KK E+ KK +E ++
Sbjct: 1523 KADEAKKAEEAKKADEAKKAEEKKKADELKKAEELKKAEEKKK 1565

Length = 2084

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 47.1 bits (111), Expect = 7e-06
 Identities = 35/100 (35%), Positives = 61/100 (61%), Gaps = 2/100 (2%)

Query: 177  KKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKK 236
            KK    ++  + K+K ++ +++ +E KK  + K+K  E KK ++ K+  + KK ++ KK 
Sbjct: 1477 KKAEEAKKADEAKKKAEEAKKKADEAKKAAEAKKKADEAKKAEEAKKADEAKKAEEAKKA 1536

Query: 237  EKKKKKKEKKKKKEEKKKE--KKKKKKKKEKKKKKDEGRR 274
            ++ KK +EKKK  E KK E  KK ++KKK ++ KK E  +
Sbjct: 1537 DEAKKAEEKKKADELKKAEELKKAEEKKKAEEAKKAEEDK 1576

Length = 2084

>gnl|CDD|220648 pfam10243, MIP-T3, Microtubule-binding protein MIP-T3

 Score = 46.8 bits (111), Expect = 7e-06
 Identities = 30/102 (29%), Positives = 65/102 (63%), Gaps = 1/102 (0%)

Query: 174 KGGKKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKK 233
           K  +K + + + RK K + K++   KE+EK++EKK E+ +++++E KK+E+ + K + KK
Sbjct: 119 KKKEKPKEEPKDRKPKEEAKEKRPPKEKEKEKEKKVEEPRDREEE-KKRERVRAKSRPKK 177

Query: 234 KKKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDEGRRR 275
             K+K   KK++  ++E++++  ++  K K ++   +E R +
Sbjct: 178 PPKKKPPNKKKEPPEEEKQRQAAREAVKGKPEEPDVNEEREK 219

This protein, which interacts with both microtubules and TRAF3 (tumour necrosis factor receptor-associated factor 3), is conserved from worms to humans. The N-terminal region is the microtubule binding domain and is well-conserved; the C-terminal 100 residues, also well-conserved, constitute the coiled-coil region which binds to TRAF3. The central region of the protein is rich in lysine and glutamic acid and carries KKE motifs which may also be necessary for tubulin-binding, but this region is the least well-conserved. Length = 506

>gnl|CDD|237177 PRK12704, PRK12704, phosphodiesterase; Provisional

 Score = 46.3 bits (111), Expect = 7e-06
 Identities = 20/80 (25%), Positives = 51/80 (63%)

Query: 177 KKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKK 236
            K R +  +  R+R+ + ++ EK   +KEE    K +  +K +++ EKK+++ ++K+++ 
Sbjct: 67  HKLRNEFEKELRERRNELQKLEKRLLQKEENLDRKLELLEKREEELEKKEKELEQKQQEL 126

Query: 237 EKKKKKKEKKKKKEEKKKEK 256
           EKK+++ E+  +++ ++ E+
Sbjct: 127 EKKEEELEELIEEQLQELER 146

Length = 520

>gnl|CDD|215214 PLN02381, PLN02381, valyl-tRNA synthetase

 Score = 46.8 bits (111), Expect = 7e-06
 Identities = 27/76 (35%), Positives = 38/76 (50%), Gaps = 5/76 (6%)

Query: 185 RRKRKRKRKKEEEEKEEE---KKEEKKKEK--KKEKKKEKKKKEKKKEKKKKKKKKKEKK 239
            R      KK   E+E E   KKEEK KEK  KK K  +K+ K K + ++        KK
Sbjct: 2   SRTESEAEKKILTEEELERKKKKEEKAKEKELKKLKAAQKEAKAKLQAQQASDGTNVPKK 61

Query: 240 KKKKEKKKKKEEKKKE 255
            +KK +K+  E++  E
Sbjct: 62  SEKKSRKRDVEDENPE 77

Length = 1066

>gnl|CDD|235640 PRK05901, PRK05901, RNA polymerase sigma factor; Provisional

 Score = 46.5 bits (111), Expect = 7e-06
 Identities = 17/86 (19%), Positives = 33/86 (38%)

Query: 187 KRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKK 246
            + + +    +E+ +E  E KKK  ++  +         K+     +    KKK K   K
Sbjct: 25  AKSKSKGFITKEEIKEALESKKKTPEQIDQVLIFLSGMVKDTDDATESDIPKKKTKTAAK 84

Query: 247 KKKEEKKKEKKKKKKKKEKKKKKDEG 272
               +   +KK K +    KK + + 
Sbjct: 85  AAAAKAPAKKKLKDELDSSKKAEKKN 110

Length = 509

>gnl|CDD|236944 PRK11642, PRK11642, exoribonuclease R; Provisional

 Score = 46.7 bits (111), Expect = 7e-06
 Identities = 24/79 (30%), Positives = 36/79 (45%), Gaps = 3/79 (3%)

Query: 176 GKKERRKQRR---RKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKK 232
           GK  R K ++    K+  KR++  ++   E     + EKK + K  KK   K K+   K 
Sbjct: 735 GKTAREKAKKGDAGKKGGKRRQVGKKVNFEPDSAFRGEKKAKPKAAKKDARKAKKPSAKT 794

Query: 233 KKKKEKKKKKKEKKKKKEE 251
           +K     K K+  KKK  E
Sbjct: 795 QKIAAATKAKRAAKKKVAE 813

Length = 813

>gnl|CDD|215774 pfam00183, HSP90, Hsp90 protein

 Score = 46.7 bits (111), Expect = 7e-06
 Identities = 23/63 (36%), Positives = 46/63 (73%)

Query: 194 KEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKK 253
           KE E++  +++EE++KE+KKE++++   KE++ +++++K++KK+K KK KE   + E   
Sbjct: 29  KEVEKEVPDEEEEEEKEEKKEEEEKTTDKEEEVDEEEEKEEKKKKTKKVKETTTEWELLN 88

Query: 254 KEK 256
           K K
Sbjct: 89  KTK 91

Length = 529

>gnl|CDD|220648 pfam10243, MIP-T3, Microtubule-binding protein MIP-T3

 Score = 46.4 bits (110), Expect = 8e-06
 Identities = 27/98 (27%), Positives = 58/98 (59%)

Query: 178 KERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKE 237
           KE  K++R  ++++++KE++ +E   +EE+KK ++   K   KK  KKK   KKK+  +E
Sbjct: 134 KEEAKEKRPPKEKEKEKEKKVEEPRDREEEKKRERVRAKSRPKKPPKKKPPNKKKEPPEE 193

Query: 238 KKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDEGRRR 275
           +K+++  ++  K + ++    ++++KE+   KD     
Sbjct: 194 EKQRQAAREAVKGKPEEPDVNEEREKEEDDGKDRETTT 231

This protein, which interacts with both microtubules and TRAF3 (tumour necrosis factor receptor-associated factor 3), is conserved from worms to humans. The N-terminal region is the microtubule binding domain and is well-conserved; the C-terminal 100 residues, also well-conserved, constitute the coiled-coil region which binds to TRAF3. The central region of the protein is rich in lysine and glutamic acid and carries KKE motifs which may also be necessary for tubulin-binding, but this region is the least well-conserved. Length = 506

>gnl|CDD|172341 PRK13808, PRK13808, adenylate kinase; Provisional

 Score = 46.0 bits (109), Expect = 8e-06
 Identities = 30/101 (29%), Positives = 40/101 (39%)

Query: 174 KGGKKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKK 233
           K  K    K   +K   K K   ++  ++K  +     KK  K   K  +K K+  KK  
Sbjct: 201 KAAKTPAAKSGAKKASAKAKSAAKKVSKKKAAKTAVSAKKAAKTAAKAAKKAKKTAKKAL 260

Query: 234 KKKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDEGRR 274
           KK  K  KK  KK  K   K  K   K  K K K K +  +
Sbjct: 261 KKAAKAVKKAAKKAAKAAAKAAKGAAKATKGKAKAKKKAGK 301

Length = 333

>gnl|CDD|202833 pfam03962, Mnd1, Mnd1 family

 Score = 44.9 bits (107), Expect = 8e-06
 Identities = 21/89 (23%), Positives = 52/89 (58%)

Query: 177 KKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKK 236
             +   + + + ++ +K+ EE K+   + + + EK K+ ++E +++ +  E+ K+ +K+ 
Sbjct: 60  PSQALNKLKTRLEKLKKELEELKQRIAELQAQIEKLKKGREETEERTELLEELKQLEKEL 119

Query: 237 EKKKKKKEKKKKKEEKKKEKKKKKKKKEK 265
           +K K + EK +K + ++ EK K++ K  K
Sbjct: 120 KKLKAELEKYEKNDPERIEKLKEETKVAK 148

This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair. Length = 188

>gnl|CDD|236545 PRK09510, tolA, cell envelope integrity inner membrane protein TolA; Provisional

 Score = 46.3 bits (110), Expect = 8e-06
 Identities = 25/94 (26%), Positives = 53/94 (56%)

Query: 178 KERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKE 237
           ++R+K+ +++ +  ++K+  E+E  K+ EK++   +E+KK+ ++  K+   K+K+ ++  
Sbjct: 79  EQRKKKEQQQAEELQQKQAAEQERLKQLEKERLAAQEQKKQAEEAAKQAALKQKQAEEAA 138

Query: 238 KKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDE 271
            K     K K + E K+     KK   + KKK E
Sbjct: 139 AKAAAAAKAKAEAEAKRAAAAAKKAAAEAKKKAE 172

Length = 387

>gnl|CDD|240246 PTZ00053, PTZ00053, methionine aminopeptidase 2; Provisional

 Score = 46.2 bits (110), Expect = 8e-06
 Identities = 20/81 (24%), Positives = 38/81 (46%)

Query: 191 KRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKE 250
            ++++++ K++  K++ KK KK     +    E   E ++ + K+  KKKKKK+KKKKK+
Sbjct: 10  VKQQKQQNKQKGTKKKNKKSKKDVDDDDAFLAELISENQEAENKQNNKKKKKKKKKKKKK 69

Query: 251 EKKKEKKKKKKKKEKKKKKDE 271
              +                 
Sbjct: 70  NLGEAYDLAYDLPVVWSSAAF 90

Length = 470

>gnl|CDD|240388 PTZ00372, PTZ00372, endonuclease 4-like protein; Provisional

 Score = 46.2 bits (110), Expect = 9e-06
 Identities = 21/76 (27%), Positives = 37/76 (48%)

Query: 193 KKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEK 252
           +K + +             K+      +++ K      KK KK++K  + K+K +KK++K
Sbjct: 17  QKSKLQPISYIYSNVLVLSKEILSTFSEEENKVATTSTKKDKKEDKNNESKKKSEKKKKK 76

Query: 253 KKEKKKKKKKKEKKKK 268
           KKEKK+ K + E K  
Sbjct: 77  KKEKKEPKSEGETKLG 92

Length = 413

>gnl|CDD|226894 COG4499, COG4499, Predicted membrane protein [Function unknown]

 Score = 46.3 bits (110), Expect = 9e-06
 Identities = 20/70 (28%), Positives = 47/70 (67%)

Query: 179 ERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEK 238
           ++R++  ++  +K +   ++  E K E    E+ + K KE+K K+++ EKK+K++  ++K
Sbjct: 365 DKRQELLKEYNKKLQDYTKKLGEVKDETDASEEAEAKAKEEKLKQEENEKKQKEQADEDK 424

Query: 239 KKKKKEKKKK 248
           +K++K+++KK
Sbjct: 425 EKRQKDERKK 434

Length = 434

>gnl|CDD|237753 PRK14552, PRK14552, C/D box methylation guide ribonucleoprotein complex aNOP56 subunit; Provisional

 Score = 46.1 bits (110), Expect = 9e-06
 Identities = 26/53 (49%), Positives = 40/53 (75%)

Query: 201 EEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKK 253
           +E KEE  K  ++ K+K  K  +KK+E+KK +K+KK+KK+KKK KK+KK+ +K
Sbjct: 362 DELKEELNKRIEEIKEKYPKPPKKKREEKKPQKRKKKKKRKKKGKKRKKKGRK 414

Length = 414

>gnl|CDD|237258 PRK12903, secA, preprotein translocase subunit SecA; Reviewed

 Score = 46.6 bits (111), Expect = 9e-06
 Identities = 24/115 (20%), Positives = 52/115 (45%), Gaps = 13/115 (11%)

Query: 170 EYGYKGGKKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKK---EKKKEKKKKEKKK 226
           +   +  ++  +  R ++ +   + EE E   E+++  K+E K    E ++ +++ +   
Sbjct: 809 DQIIESEEERLKALRIQREEMLMRPEELELINEEQKNLKQEIKLELSEIQEAEEEIQNIN 868

Query: 227 EKKKKKKKKKEKKKKKKEKK----------KKKEEKKKEKKKKKKKKEKKKKKDE 271
           E K +  + K   KK  +               +E K+++K  KKKK+  +K DE
Sbjct: 869 ENKNEFVEFKNDPKKLNKLIIAKDVLIKLVISSDEIKQDEKTTKKKKKDLEKTDE 923

Length = 925

>gnl|CDD|237035 PRK12280, rplW, 50S ribosomal protein L23; Reviewed

 Score = 44.4 bits (105), Expect = 9e-06
 Identities = 29/67 (43%), Positives = 42/67 (62%)

Query: 201 EEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKKKEKKKKK 260
            E+ E+++KE  KE ++++  K KK++K+KK+KK  EK  KKK  K  K   KK  KK  
Sbjct: 92  PEESEKEQKEVSKETEEKEAIKAKKEKKEKKEKKVAEKLAKKKSTKTTKNTTKKATKKTT 151

Query: 261 KKKEKKK 267
            KKE+ K
Sbjct: 152 TKKEEGK 158

Length = 158

>gnl|CDD|237035 PRK12280, rplW, 50S ribosomal protein L23; Reviewed

 Score = 44.4 bits (105), Expect = 9e-06
 Identities = 29/67 (43%), Positives = 42/67 (62%)

Query: 196 EEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKKKE 255
            EE E+E+KE  K+ ++KE  K KK+K++KKEKK  +K  K+K  K  +   KK  KK  
Sbjct: 92  PEESEKEQKEVSKETEEKEAIKAKKEKKEKKEKKVAEKLAKKKSTKTTKNTTKKATKKTT 151

Query: 256 KKKKKKK 262
            KK++ K
Sbjct: 152 TKKEEGK 158

Length = 158

>gnl|CDD|240388 PTZ00372, PTZ00372, endonuclease 4-like protein; Provisional

 Score = 45.9 bits (109), Expect = 1e-05
 Identities = 21/69 (30%), Positives = 33/69 (47%)

Query: 201 EEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKKKEKKKKK 260
           ++ K +             K+      +++ K      KK KKE K  + +KK EKKKKK
Sbjct: 17  QKSKLQPISYIYSNVLVLSKEILSTFSEEENKVATTSTKKDKKEDKNNESKKKSEKKKKK 76

Query: 261 KKKEKKKKK 269
           KK++K+ K 
Sbjct: 77  KKEKKEPKS 85

Length = 413

>gnl|CDD|240388 PTZ00372, PTZ00372, endonuclease 4-like protein; Provisional

 Score = 45.5 bits (108), Expect = 1e-05
 Identities = 20/79 (25%), Positives = 38/79 (48%)

Query: 197 EEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKKKEK 256
           ++ + +             K+      +++ K      KK+KK+ K  + KKK EKKK+K
Sbjct: 17  QKSKLQPISYIYSNVLVLSKEILSTFSEEENKVATTSTKKDKKEDKNNESKKKSEKKKKK 76

Query: 257 KKKKKKKEKKKKKDEGRRR 275
           KK+KK+ + + +   G + 
Sbjct: 77  KKEKKEPKSEGETKLGFKT 95

Length = 413

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 46.3 bits (109), Expect = 1e-05
 Identities = 32/99 (32%), Positives = 62/99 (62%)

Query: 177  KKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKK 236
            +    +  +   + K+ K EE K+ E+ + K +E KK ++++KK ++ KK++ ++KKK +
Sbjct: 1591 EARIEEVMKLYEEEKKMKAEEAKKAEEAKIKAEELKKAEEEKKKVEQLKKKEAEEKKKAE 1650

Query: 237  EKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDEGRRR 275
            E KK ++E K K  E+ K+ ++ KKK E+ KK +E  ++
Sbjct: 1651 ELKKAEEENKIKAAEEAKKAEEDKKKAEEAKKAEEDEKK 1689

Length = 2084

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 46.3 bits (109), Expect = 1e-05
 Identities = 34/102 (33%), Positives = 55/102 (53%)

Query: 174  KGGKKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKK 233
            K   +E +K    +   + +K EE +       +   K +E +K  + K+ +++KK  + 
Sbjct: 1236 KKDAEEAKKAEEERNNEEIRKFEEARMAHFARRQAAIKAEEARKADELKKAEEKKKADEA 1295

Query: 234  KKKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDEGRRR 275
            KK E+KKK  E KKK EE KK  + KKK +E KKK D  +++
Sbjct: 1296 KKAEEKKKADEAKKKAEEAKKADEAKKKAEEAKKKADAAKKK 1337

Length = 2084

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 46.3 bits (109), Expect = 1e-05
 Identities = 31/92 (33%), Positives = 63/92 (68%)

Query: 177  KKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKK 236
            +K+  +  +++ +  +K EE +K+E ++++K +E KK +++ K K E+ K++ ++ KKK 
Sbjct: 1687 EKKAAEALKKEAEEAKKAEELKKKEAEEKKKAEELKKAEEENKIKAEEAKKEAEEDKKKA 1746

Query: 237  EKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKK 268
            E+ KK +E+KKK    KKE++KK ++  K+K+
Sbjct: 1747 EEAKKDEEEKKKIAHLKKEEEKKAEEIRKEKE 1778

Length = 2084

>gnl|CDD|236877 PRK11192, PRK11192, ATP-dependent RNA helicase SrmB; Provisional

 Score = 45.7 bits (109), Expect = 1e-05
 Identities = 12/54 (22%), Positives = 29/54 (53%)

Query: 184 RRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKE 237
           + +    K+  +  +K   K+ EKK+++K++ K +K+ ++ K   K++K     
Sbjct: 379 KTKAPSEKKTGKPSKKVLAKRAEKKEKEKEKPKVKKRHRDTKNIGKRRKPSGTS 432

Length = 434

>gnl|CDD|234017 TIGR02794, tolA_full, TolA protein

 Score = 45.2 bits (107), Expect = 1e-05
 Identities = 23/93 (24%), Positives = 45/93 (48%)

Query: 177 KKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKK 236
             E + +   + ++K K+E +++ EE+ + K   + K+K  E KKK + + K K + K K
Sbjct: 129 AAEAKAKAEAEAEKKAKEEAKKQAEEEAKAKAAAEAKKKAAEAKKKAEAEAKAKAEAKAK 188

Query: 237 EKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKK 269
            K ++ K K +  + K   +   K + E     
Sbjct: 189 AKAEEAKAKAEAAKAKAAAEAAAKAEAEAAAAA 221

TolA couples the inner membrane complex of itself with TolQ and TolR to the outer membrane complex of TolB and OprL (also called Pal). Most of the length of the protein consists of low-complexity sequence that may differ in both length and composition from one species to another, complicating efforts to discriminate TolA (the most divergent gene in the tol-pal system) from paralogs such as TonB. Selection of members of the seed alignment and criteria for setting scoring cutoffs are based largely conserved operon struction. //The Tol-Pal complex is required for maintaining outer membrane integrity. Also involved in transport (uptake) of colicins and filamentous DNA, and implicated in pathogenesis. Transport is energized by the proton motive force. TolA is an inner membrane protein that interacts with periplasmic TolB and with outer membrane porins ompC, phoE and lamB [Transport and binding proteins, Other, Cellular processes, Pathogenesis]. Length = 346

>gnl|CDD|237177 PRK12704, PRK12704, phosphodiesterase; Provisional

 Score = 45.5 bits (109), Expect = 1e-05
 Identities = 30/99 (30%), Positives = 59/99 (59%), Gaps = 8/99 (8%)

Query: 185 RRKRKRKRKKEEEEKEEEKKEEKKKE---KKKEKKKEKKKK-EKKKEKKKKKKKKKEKKK 240
           R+K    + KE EE+ +   EE KKE    KKE   E K++  K + + +K+ +++  + 
Sbjct: 25  RKKIAEAKIKEAEEEAKRILEEAKKEAEAIKKEALLEAKEEIHKLRNEFEKELRERRNEL 84

Query: 241 KKKEKK-KKKEE---KKKEKKKKKKKKEKKKKKDEGRRR 275
           +K EK+  +KEE   +K E  +K++++ +KK+K+  +++
Sbjct: 85  QKLEKRLLQKEENLDRKLELLEKREEELEKKEKELEQKQ 123

Length = 520

>gnl|CDD|219746 pfam08208, RNA_polI_A34, DNA-directed RNA polymerase I subunit RPA34

 Score = 44.7 bits (106), Expect = 1e-05
 Identities = 32/58 (55%), Positives = 43/58 (74%)

Query: 188 RKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEK 245
            K    K E+E E E++E+K+K+KKKE KKEKK+K+ KKEK  + K  K+KKKKKK+K
Sbjct: 136 EKETTAKVEKEAEVEEEEKKEKKKKKEVKKEKKEKKDKKEKMVEPKGSKKKKKKKKKK 193

5. This is a family of proteins conserved from yeasts to human. Subunit A34.5 of RNA polymerase I is a non-essential subunit which is thought to help Pol I overcome topological constraints imposed on ribosomal DNA during the process of transcription. Length = 193

>gnl|CDD|219746 pfam08208, RNA_polI_A34, DNA-directed RNA polymerase I subunit RPA34

 Score = 44.3 bits (105), Expect = 1e-05
 Identities = 32/61 (52%), Positives = 44/61 (72%)

Query: 187 KRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKK 246
           +   K    + EKE E +EE+KKEKKK+K+ +K+KKEKK +K+K  + K  KKKKKK+KK
Sbjct: 133 ETSEKETTAKVEKEAEVEEEEKKEKKKKKEVKKEKKEKKDKKEKMVEPKGSKKKKKKKKK 192

Query: 247 K 247
           K
Sbjct: 193 K 193

5. This is a family of proteins conserved from yeasts to human. Subunit A34.5 of RNA polymerase I is a non-essential subunit which is thought to help Pol I overcome topological constraints imposed on ribosomal DNA during the process of transcription. Length = 193

>gnl|CDD|217051 pfam02463, SMC_N, RecF/RecN/SMC N terminal domain

 Score = 46.1 bits (109), Expect = 1e-05
 Identities = 25/95 (26%), Positives = 59/95 (62%)

Query: 177 KKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKK 236
           K+E  K+     +  ++ +EEEKE++ +EE+ K   KE+++ K +  K + +K   ++K 
Sbjct: 258 KQELEKEEEILAQVLKENKEEEKEKKLQEEELKLLAKEEEELKSELLKLERRKVDDEEKL 317

Query: 237 EKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDE 271
           ++ +K+ +K +K+ +K+KE+ ++ +K+ K+ +   
Sbjct: 318 KESEKELKKLEKELKKEKEEIEELEKELKELEIKR 352

This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination. Length = 1162

>gnl|CDD|217051 pfam02463, SMC_N, RecF/RecN/SMC N terminal domain

 Score = 45.7 bits (108), Expect = 1e-05
 Identities = 30/95 (31%), Positives = 62/95 (65%)

Query: 177 KKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKK 236
           K+E    +  K  ++ +KE++ +EEE K   K+E++ + +  K ++ K  +++K K+ +K
Sbjct: 263 KEEEILAQVLKENKEEEKEKKLQEEELKLLAKEEEELKSELLKLERRKVDDEEKLKESEK 322

Query: 237 EKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDE 271
           E KK +KE KK+KEE ++ +K+ K+ + K++ ++E
Sbjct: 323 ELKKLEKELKKEKEEIEELEKELKELEIKREAEEE 357

This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination. Length = 1162

>gnl|CDD|240271 PTZ00108, PTZ00108, DNA topoisomerase 2-like protein; Provisional

 Score = 46.6 bits (111), Expect = 1e-05
 Identities = 25/83 (30%), Positives = 47/83 (56%)

Query: 188  RKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKK 247
            +  K   E E+KE+E ++ K    K    ++  K E+  E++++ ++K+  K+++ + K 
Sbjct: 1103 KVEKLNAELEKKEKELEKLKNTTPKDMWLEDLDKFEEALEEQEEVEEKEIAKEQRLKSKT 1162

Query: 248  KKEEKKKEKKKKKKKKEKKKKKD 270
            K +  K  K K KKK++KKKK  
Sbjct: 1163 KGKASKLRKPKLKKKEKKKKKSS 1185

Length = 1388

>gnl|CDD|221641 pfam12569, NARP1, NMDA receptor-regulated protein 1

 Score = 45.7 bits (109), Expect = 1e-05
 Identities = 16/62 (25%), Positives = 34/62 (54%)

Query: 212 KKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDE 271
             E ++E+ +       ++KK +KK++K +KK +K++ E+   +KK +   K+ K    E
Sbjct: 393 LAEGEEEEGENGNLSPAERKKLRKKQRKAEKKAEKEEAEKAAAKKKAEAAAKKAKGPDGE 452

Query: 272 GR 273
            +
Sbjct: 453 TK 454

This domain family is found in eukaryotes, and is approximately 40 amino acids in length. The family is found in association with pfam07719, pfam00515. There is a single completely conserved residue L that may be functionally important. NARP1 is the mammalian homologue of a yeast N-terminal acetyltransferase that regulates entry into the G(0) phase of the cell cycle. Length = 516

>gnl|CDD|220252 pfam09468, RNase_H2-Ydr279, Ydr279p protein family (RNase H2 complex component)

 Score = 45.4 bits (108), Expect = 1e-05
 Identities = 25/77 (32%), Positives = 39/77 (50%), Gaps = 3/77 (3%)

Query: 196 EEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKK---KKKKKEKKKKKKEKKKKKEEK 252
            +  +E  K     E K   K  K+ K+KK+E ++     + + EKK+K KE+ KKK+ K
Sbjct: 205 PDLYKELLKSLLIPEFKPLDKYLKESKKKKRETEEDVEAAESRAEKKRKSKEEIKKKKPK 264

Query: 253 KKEKKKKKKKKEKKKKK 269
           + +  K  KK   K  K
Sbjct: 265 ESKGVKALKKVVAKGMK 281

RNases H are enzymes that specifically hydrolyse RNA when annealed to a complementary DNA and are present in all living organisms. In yeast RNase H2 is composed of a complex of three proteins (Rnh2Ap, Ydr279p and Ylr154p), this family represents the homologues of Ydr279p. It is not known whether non yeast proteins in this family fulfil the same function. Length = 287

>gnl|CDD|237753 PRK14552, PRK14552, C/D box methylation guide ribonucleoprotein complex aNOP56 subunit; Provisional

 Score = 45.7 bits (109), Expect = 1e-05
 Identities = 23/49 (46%), Positives = 36/49 (73%)

Query: 215 KKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKKKEKKKKKKKK 263
           ++  K+ +E K++  K  KKK+E+KK +K KKKKK +KK +K+KKK +K
Sbjct: 366 EELNKRIEEIKEKYPKPPKKKREEKKPQKRKKKKKRKKKGKKRKKKGRK 414

Length = 414

>gnl|CDD|237753 PRK14552, PRK14552, C/D box methylation guide ribonucleoprotein complex aNOP56 subunit; Provisional

 Score = 45.7 bits (109), Expect = 1e-05
 Identities = 24/50 (48%), Positives = 37/50 (74%)

Query: 215 KKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKKKEKKKKKKKKE 264
           K++  K+ E+ KEK  K  KKK ++KK +++KKKK+ KKK KK+KKK ++
Sbjct: 365 KEELNKRIEEIKEKYPKPPKKKREEKKPQKRKKKKKRKKKGKKRKKKGRK 414

Length = 414

>gnl|CDD|237753 PRK14552, PRK14552, C/D box methylation guide ribonucleoprotein complex aNOP56 subunit; Provisional

 Score = 45.7 bits (109), Expect = 1e-05
 Identities = 24/49 (48%), Positives = 36/49 (73%), Gaps = 1/49 (2%)

Query: 228 KKKKKKKKKE-KKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDEGRRR 275
           K++  K+ +E K+K  K  KKK+EEKK +K+KKKKK++KK KK + + R
Sbjct: 365 KEELNKRIEEIKEKYPKPPKKKREEKKPQKRKKKKKRKKKGKKRKKKGR 413

Length = 414

>gnl|CDD|202833 pfam03962, Mnd1, Mnd1 family

 Score = 44.5 bits (106), Expect = 1e-05
 Identities = 23/87 (26%), Positives = 52/87 (59%), Gaps = 2/87 (2%)

Query: 187 KRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKK 246
             K K + E+ +KE E+ +++  E + + +K KK +E+ +E+ +  ++ K+ +K+ K+ K
Sbjct: 64  LNKLKTRLEKLKKELEELKQRIAELQAQIEKLKKGREETEERTELLEELKQLEKELKKLK 123

Query: 247 KKKEEKKK--EKKKKKKKKEKKKKKDE 271
            + E+ +K   ++ +K K+E K  K+ 
Sbjct: 124 AELEKYEKNDPERIEKLKEETKVAKEA 150

This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair. Length = 188

>gnl|CDD|237035 PRK12280, rplW, 50S ribosomal protein L23; Reviewed

 Score = 44.0 bits (104), Expect = 1e-05
 Identities = 26/67 (38%), Positives = 42/67 (62%)

Query: 205 EEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKKKEKKKKKKKKE 264
            E+ ++++KE  KE ++KE  K KK+KK+KK++K  +K  KKK  +  K   KK  KK  
Sbjct: 92  PEESEKEQKEVSKETEEKEAIKAKKEKKEKKEKKVAEKLAKKKSTKTTKNTTKKATKKTT 151

Query: 265 KKKKKDE 271
            KK++ +
Sbjct: 152 TKKEEGK 158

Length = 158

>gnl|CDD|222581 pfam14181, YqfQ, YqfQ-like protein

 Score = 44.4 bits (105), Expect = 1e-05
 Identities = 24/56 (42%), Positives = 34/56 (60%)

Query: 193 KKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKK 248
             EEEE EEE  +E ++E   E K E K+K+K++  K K +K+K K + KK K  K
Sbjct: 95  DDEEEETEEESTDETEQEDPPETKTESKEKKKREVPKPKTEKEKPKTEPKKPKPSK 150

The YqfQ-like protein family includes the B. subtilis YqfQ protein, also known as VrrA, which is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 146 and 237 amino acids in length. There are two conserved sequence motifs: QYGP and PKLY. Length = 155

>gnl|CDD|222581 pfam14181, YqfQ, YqfQ-like protein

 Score = 44.4 bits (105), Expect = 1e-05
 Identities = 22/53 (41%), Positives = 32/53 (60%)

Query: 195 EEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKK 247
           E EE+  ++ E++   + K + KEKKK+E  K K +K+K K E KK K  K K
Sbjct: 100 ETEEESTDETEQEDPPETKTESKEKKKREVPKPKTEKEKPKTEPKKPKPSKPK 152

The YqfQ-like protein family includes the B. subtilis YqfQ protein, also known as VrrA, which is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 146 and 237 amino acids in length. There are two conserved sequence motifs: QYGP and PKLY. Length = 155

>gnl|CDD|177089 CHL00189, infB, translation initiation factor 2; Provisional

 Score = 46.4 bits (110), Expect = 1e-05
 Identities = 24/89 (26%), Positives = 39/89 (43%), Gaps = 1/89 (1%)

Query: 178 KERRKQRRRKRKRKRKK-EEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKK 236
           K+ +K + +++K+ +KK   ++  +   + K   K+           K K K +K KKK 
Sbjct: 70  KDSKKTKLKQKKKIKKKLHIDDDYDNFFDSKNNSKQFAGPLAISLMRKPKPKTEKLKKKI 129

Query: 237 EKKKKKKEKKKKKEEKKKEKKKKKKKKEK 265
              K   +KKKK    K E  K    K K
Sbjct: 130 TVNKSTNKKKKKVLSSKDELIKYDNNKPK 158

Length = 742

>gnl|CDD|240402 PTZ00399, PTZ00399, cysteinyl-tRNA-synthetase; Provisional

 Score = 45.8 bits (109), Expect = 1e-05
 Identities = 28/89 (31%), Positives = 48/89 (53%), Gaps = 21/89 (23%)

Query: 201 EEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKK-------KKKEKKKKK---- 249
           EE + EK++++  +++K  +K +K++EKKKK+ +K EK K       K++E K       
Sbjct: 551 EELQREKEEKEALKEQKRLRKLKKQEEKKKKELEKLEKAKIPPAEFFKRQEDKYSAFDET 610

Query: 250 ----------EEKKKEKKKKKKKKEKKKK 268
                     E  KKE+KK  K+ +K+ K
Sbjct: 611 GLPTHDADGEEISKKERKKLSKEYDKQAK 639

Length = 651

>gnl|CDD|219868 pfam08496, Peptidase_S49_N, Peptidase family S49 N-terminal

 Score = 43.7 bits (104), Expect = 1e-05
 Identities = 26/67 (38%), Positives = 39/67 (58%), Gaps = 1/67 (1%)

Query: 184 RRRKRKRKRKKEEEEKEEEKKEEKKK-EKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKK 242
            ++K+ +K + E  +  EE K+ K+  E     KKE K  EK ++K +K K K EKKK K
Sbjct: 32  AQKKKGKKGELEITDLNEEYKDLKESLEAALLDKKELKAWEKAEKKAEKAKAKAEKKKAK 91

Query: 243 KEKKKKK 249
           KE+ K +
Sbjct: 92  KEEPKPR 98

This domain is found to the N-terminus of bacterial signal peptidases of the S49 family (pfam01343). Length = 154

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 45.5 bits (107), Expect = 2e-05
 Identities = 39/103 (37%), Positives = 64/103 (62%), Gaps = 8/103 (7%)

Query: 180  RRKQRRRKRKRKRKKEEEEKEEEKK--------EEKKKEKKKEKKKEKKKKEKKKEKKKK 231
            ++ +  +K + K+K EE +K EE K        E KK E+ + ++  K  +E+KK K ++
Sbjct: 1552 KKAEELKKAEEKKKAEEAKKAEEDKNMALRKAEEAKKAEEARIEEVMKLYEEEKKMKAEE 1611

Query: 232  KKKKKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDEGRR 274
             KK +E K K +E KK +EEKKK ++ KKK+ E+KKK +E ++
Sbjct: 1612 AKKAEEAKIKAEELKKAEEEKKKVEQLKKKEAEEKKKAEELKK 1654

Length = 2084

>gnl|CDD|215214 PLN02381, PLN02381, valyl-tRNA synthetase

 Score = 45.3 bits (107), Expect = 2e-05
 Identities = 24/73 (32%), Positives = 42/73 (57%), Gaps = 1/73 (1%)

Query: 184 RRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEK-KKKEKKKEKKKKKKKKKEKKKKK 242
            R + + ++K   EE+ E KK++++K K+KE KK K  +KE K + + ++        KK
Sbjct: 2   SRTESEAEKKILTEEELERKKKKEEKAKEKELKKLKAAQKEAKAKLQAQQASDGTNVPKK 61

Query: 243 KEKKKKKEEKKKE 255
            EKK +K + + E
Sbjct: 62  SEKKSRKRDVEDE 74

Length = 1066

>gnl|CDD|217051 pfam02463, SMC_N, RecF/RecN/SMC N terminal domain

 Score = 45.7 bits (108), Expect = 2e-05
 Identities = 24/97 (24%), Positives = 63/97 (64%)

Query: 178 KERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKE 237
           KE  + +    K +R+K ++E++ ++ E++ K+ +KE KKEK++ E+ +++ K+ + K+E
Sbjct: 294 KEEEELKSELLKLERRKVDDEEKLKESEKELKKLEKELKKEKEEIEELEKELKELEIKRE 353

Query: 238 KKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDEGRR 274
            +++++E+ +K +EK ++ +++   K+K + +     
Sbjct: 354 AEEEEEEQLEKLQEKLEQLEEELLAKKKLESERLSSA 390

This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination. Length = 1162

>gnl|CDD|217051 pfam02463, SMC_N, RecF/RecN/SMC N terminal domain

 Score = 45.7 bits (108), Expect = 2e-05
 Identities = 19/100 (19%), Positives = 44/100 (44%)

Query: 172 GYKGGKKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKK 231
             +  KK   +           +E + +E + KE+ KK  +  + KEK + E++      
Sbjct: 172 KKERLKKLIEETENLAELIIDLEELKLQELKLKEQAKKALEYYQLKEKLELEEENLLYLD 231

Query: 232 KKKKKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDE 271
             K  E++    ++  + E+++ E  K++ +KE++     
Sbjct: 232 YLKLNEERIDLLQELLRDEQEEIESSKQELEKEEEILAQV 271

This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination. Length = 1162

>gnl|CDD|217051 pfam02463, SMC_N, RecF/RecN/SMC N terminal domain

 Score = 45.3 bits (107), Expect = 2e-05
 Identities = 26/95 (27%), Positives = 63/95 (66%)

Query: 177 KKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKK 236
            +E + +   + K   +K +E++EEE+K   KKE+++E+K E   KEK+  ++++K +K 
Sbjct: 728 VQEAQDKINEELKLLEQKIKEKEEEEEKSRLKKEEEEEEKSELSLKEKELAEEEEKTEKL 787

Query: 237 EKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDE 271
           + +++K+EK K +EE+ +  +++ K++ +  ++++
Sbjct: 788 KVEEEKEEKLKAQEEELRALEEELKEEAELLEEEQ 822

This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination. Length = 1162

>gnl|CDD|235640 PRK05901, PRK05901, RNA polymerase sigma factor; Provisional

 Score = 45.4 bits (108), Expect = 2e-05
 Identities = 20/94 (21%), Positives = 39/94 (41%)

Query: 177 KKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKK 236
           ++ ++K ++   K K K    ++E ++  E KK+  ++  +         +      +  
Sbjct: 14  EEAKKKLKKLAAKSKSKGFITKEEIKEALESKKKTPEQIDQVLIFLSGMVKDTDDATESD 73

Query: 237 EKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKD 270
             KKK K   K    K   KKK K + +  KK +
Sbjct: 74  IPKKKTKTAAKAAAAKAPAKKKLKDELDSSKKAE 107

Length = 509

>gnl|CDD|220252 pfam09468, RNase_H2-Ydr279, Ydr279p protein family (RNase H2 complex component)

 Score = 45.0 bits (107), Expect = 2e-05
 Identities = 20/71 (28%), Positives = 37/71 (52%)

Query: 177 KKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKK 236
            K       +   +  K+ +++K E +++ +  E + EKK++ K++ KKK+ K+ K  K 
Sbjct: 212 LKSLLIPEFKPLDKYLKESKKKKRETEEDVEAAESRAEKKRKSKEEIKKKKPKESKGVKA 271

Query: 237 EKKKKKKEKKK 247
            KK   K  KK
Sbjct: 272 LKKVVAKGMKK 282

RNases H are enzymes that specifically hydrolyse RNA when annealed to a complementary DNA and are present in all living organisms. In yeast RNase H2 is composed of a complex of three proteins (Rnh2Ap, Ydr279p and Ylr154p), this family represents the homologues of Ydr279p. It is not known whether non yeast proteins in this family fulfil the same function. Length = 287

>gnl|CDD|114011 pfam05262, Borrelia_P83, Borrelia P83/100 protein

 Score = 45.0 bits (106), Expect = 2e-05
 Identities = 26/88 (29%), Positives = 48/88 (54%), Gaps = 2/88 (2%)

Query: 186 RKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEK 245
           ++R   R+K++E K   K  +    K+ ++  E +K+E +K + + KK  +E  K K  K
Sbjct: 245 KQRDEVRQKQQEAKNLPKPADTSSPKEDKQVAENQKREIEKAQIEIKKNDEEALKAKDHK 304

Query: 246 KK--KKEEKKKEKKKKKKKKEKKKKKDE 271
               K+E K  EK+ + K+ E +KK++ 
Sbjct: 305 AFDLKQESKASEKEAEDKELEAQKKREP 332

This family consists of several Borrelia P83/P100 antigen proteins. Length = 489

>gnl|CDD|234750 PRK00409, PRK00409, recombination and DNA strand exchange inhibitor protein; Reviewed

 Score = 45.2 bits (108), Expect = 2e-05
 Identities = 32/119 (26%), Positives = 51/119 (42%), Gaps = 26/119 (21%)

Query: 177 KKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKK------ 230
           KKE  +  +  R+ ++      K  E  E +K+  K  +KKEKKKK++K+++++      
Sbjct: 583 KKEADEIIKELRQLQKGGYASVKAHELIEARKRLNKANEKKEKKKKKQKEKQEELKVGDE 642

Query: 231 -------------KKKKKKE-------KKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKK 269
                             KE        K K      +K +K K+KKKKK K  K K +
Sbjct: 643 VKYLSLGQKGEVLSIPDDKEAIVQAGIMKMKVPLSDLEKIQKPKKKKKKKPKTVKPKPR 701

Length = 782

>gnl|CDD|214661 smart00435, TOPEUc, DNA Topoisomerase I (eukaryota)

 Score = 45.0 bits (107), Expect = 2e-05
 Identities = 23/79 (29%), Positives = 46/79 (58%)

Query: 177 KKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKK 236
            K + K+ ++         + +++ + K E+  EK   + KEKKK++KK+EKKKK+ ++ 
Sbjct: 289 LKYQLKRLKKMILLFEMISDLKRKLKSKFERDNEKLDAEVKEKKKEKKKEEKKKKQIERL 348

Query: 237 EKKKKKKEKKKKKEEKKKE 255
           E++ +K E +   +E+ K 
Sbjct: 349 EERIEKLEVQATDKEENKT 367

DNA Topoisomerase I (eukaryota), DNA topoisomerase V, Vaccina virus topoisomerase, Variola virus topoisomerase, Shope fibroma virus topoisomeras. Length = 391

>gnl|CDD|237753 PRK14552, PRK14552, C/D box methylation guide ribonucleoprotein complex aNOP56 subunit; Provisional

 Score = 45.3 bits (108), Expect = 2e-05
 Identities = 21/50 (42%), Positives = 37/50 (74%)

Query: 222 KEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDE 271
           KE+  ++ ++ K+K  K  KKK ++KK +++KK+KK+KKK K++KKK  +
Sbjct: 365 KEELNKRIEEIKEKYPKPPKKKREEKKPQKRKKKKKRKKKGKKRKKKGRK 414

Length = 414

>gnl|CDD|237753 PRK14552, PRK14552, C/D box methylation guide ribonucleoprotein complex aNOP56 subunit; Provisional

 Score = 45.0 bits (107), Expect = 2e-05
 Identities = 23/52 (44%), Positives = 37/52 (71%)

Query: 218 EKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKK 269
           ++ K+E  K  ++ K+K  +  KKK+E+KK ++ KKK+K+KKK KK KKK +
Sbjct: 362 DELKEELNKRIEEIKEKYPKPPKKKREEKKPQKRKKKKKRKKKGKKRKKKGR 413

Length = 414

>gnl|CDD|233467 TIGR01554, major_cap_HK97, phage major capsid protein, HK97 family

 Score = 45.0 bits (107), Expect = 2e-05
 Identities = 15/86 (17%), Positives = 42/86 (48%)

Query: 190 RKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKK 249
           ++ ++   E  +E ++  + EK  E ++EK + +  KE+  K   + ++ ++  ++ + K
Sbjct: 2   KELREALAELAKELRKLTEDEKLAEAEEEKAEYDALKEEIDKLDAEIDRLEELLDELEAK 61

Query: 250 EEKKKEKKKKKKKKEKKKKKDEGRRR 275
                E    ++++E+ K +    R 
Sbjct: 62  PAASGEGGGGEEEEEEAKAEAAEFRA 87

This model family represents the major capsid protein component of the heads (capsids) of bacteriophage HK97, phi-105, P27, and related phage. This model represents one of several analogous families lacking detectable sequence similarity. The gene encoding this component is typically located in an operon encoding the small and large terminase subunits, the portal protein and the prohead or maturation protease [Mobile and extrachromosomal element functions, Prophage functions]. Length = 384

>gnl|CDD|214395 CHL00204, ycf1, Ycf1; Provisional

 Score = 45.1 bits (107), Expect = 2e-05
 Identities = 18/83 (21%), Positives = 40/83 (48%)

Query: 187  KRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKK 246
              +   KK  ++K+      +KK  + E + +++K+   + + +  K+KK   +     +
Sbjct: 1494 GNENVNKKINQKKKGFIPSNEKKSIEIENRNQEEKEPAGQGELESDKEKKGNLESVLSNQ 1553

Query: 247  KKKEEKKKEKKKKKKKKEKKKKK 269
            +K  E+   +   KK+K KK+ K
Sbjct: 1554 EKNIEEDYAESDIKKRKNKKQYK 1576

Length = 1832

>gnl|CDD|237258 PRK12903, secA, preprotein translocase subunit SecA; Reviewed

 Score = 45.4 bits (108), Expect = 2e-05
 Identities = 21/112 (18%), Positives = 42/112 (37%), Gaps = 12/112 (10%)

Query: 167 DNLEYGYKGGKKERRKQRRRKR--------KRKRKKEEEEKEEEKKEEKKKEKKKEKKKE 218
              E       +      R +         K  +++ + E  E ++ E++ +   E K E
Sbjct: 814 SEEERLKALRIQREEMLMRPEELELINEEQKNLKQEIKLELSEIQEAEEEIQNINENKNE 873

Query: 219 KKKKEKKKEKKKKKKKKKEKKKK----KKEKKKKKEEKKKEKKKKKKKKEKK 266
             + +   +K  K    K+   K      E K+ ++  KK+KK  +K  E+ 
Sbjct: 874 FVEFKNDPKKLNKLIIAKDVLIKLVISSDEIKQDEKTTKKKKKDLEKTDEEA 925

Length = 925

>gnl|CDD|215774 pfam00183, HSP90, Hsp90 protein

 Score = 45.5 bits (108), Expect = 2e-05
 Identities = 24/63 (38%), Positives = 43/63 (68%)

Query: 187 KRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKK 246
           K   K   +EEE+EE++++++++EK  +K++E  ++E+K+EKKKK KK KE   + +   
Sbjct: 29  KEVEKEVPDEEEEEEKEEKKEEEEKTTDKEEEVDEEEEKEEKKKKTKKVKETTTEWELLN 88

Query: 247 KKK 249
           K K
Sbjct: 89  KTK 91

Length = 529

>gnl|CDD|240246 PTZ00053, PTZ00053, methionine aminopeptidase 2; Provisional

 Score = 45.1 bits (107), Expect = 2e-05
 Identities = 22/85 (25%), Positives = 41/85 (48%), Gaps = 6/85 (7%)

Query: 191 KRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEK------KKEKKKKKKKKKEKKKKKKE 244
             +  E E +++K++ K+K  KK+ KK KK  +       +   + ++ + K+  KKKK+
Sbjct: 2   MNENGENEVKQQKQQNKQKGTKKKNKKSKKDVDDDDAFLAELISENQEAENKQNNKKKKK 61

Query: 245 KKKKKEEKKKEKKKKKKKKEKKKKK 269
           KKKKK++K   +             
Sbjct: 62  KKKKKKKKNLGEAYDLAYDLPVVWS 86

Length = 470

>gnl|CDD|240246 PTZ00053, PTZ00053, methionine aminopeptidase 2; Provisional

 Score = 45.1 bits (107), Expect = 2e-05
 Identities = 23/85 (27%), Positives = 40/85 (47%), Gaps = 7/85 (8%)

Query: 193 KKEEEEKEEEKKEEKKKEKKKEKKKEK-------KKKEKKKEKKKKKKKKKEKKKKKKEK 245
            + +++K++ K++  KK+ KK KK          +   + +E + K+  KK+KKKKKK+K
Sbjct: 8   NEVKQQKQQNKQKGTKKKNKKSKKDVDDDDAFLAELISENQEAENKQNNKKKKKKKKKKK 67

Query: 246 KKKKEEKKKEKKKKKKKKEKKKKKD 270
           KK   E                 +D
Sbjct: 68  KKNLGEAYDLAYDLPVVWSSAAFQD 92

Length = 470

>gnl|CDD|237035 PRK12280, rplW, 50S ribosomal protein L23; Reviewed

 Score = 43.6 bits (103), Expect = 2e-05
 Identities = 28/64 (43%), Positives = 40/64 (62%)

Query: 195 EEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKKK 254
            E+E++E  KE ++KE  K KK++K+KKEKK  +K  KKK  +  K   +K  KK   KK
Sbjct: 95  SEKEQKEVSKETEEKEAIKAKKEKKEKKEKKVAEKLAKKKSTKTTKNTTKKATKKTTTKK 154

Query: 255 EKKK 258
           E+ K
Sbjct: 155 EEGK 158

Length = 158

>gnl|CDD|237035 PRK12280, rplW, 50S ribosomal protein L23; Reviewed

 Score = 43.2 bits (102), Expect = 2e-05
 Identities = 27/67 (40%), Positives = 42/67 (62%)

Query: 200 EEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKKKEKKKK 259
            EE ++E+K+  K+ ++KE  K +K+K++KK+KK  ++  KKK  K  K   KK  KK  
Sbjct: 92  PEESEKEQKEVSKETEEKEAIKAKKEKKEKKEKKVAEKLAKKKSTKTTKNTTKKATKKTT 151

Query: 260 KKKKEKK 266
            KK+E K
Sbjct: 152 TKKEEGK 158

Length = 158

>gnl|CDD|177089 CHL00189, infB, translation initiation factor 2; Provisional

 Score = 45.6 bits (108), Expect = 2e-05
 Identities = 24/102 (23%), Positives = 42/102 (41%)

Query: 167 DNLEYGYKGGKKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKK 226
           D+L       K   +  ++ K+  K    ++ K+ + K++KK +KK     +       K
Sbjct: 41  DSLLNLDINKKLHEKLDKKNKKFNKTDDLKDSKKTKLKQKKKIKKKLHIDDDYDNFFDSK 100

Query: 227 EKKKKKKKKKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKK 268
              K+          +K K K ++ KKK    K   K+KKK 
Sbjct: 101 NNSKQFAGPLAISLMRKPKPKTEKLKKKITVNKSTNKKKKKV 142

Length = 742

>gnl|CDD|177089 CHL00189, infB, translation initiation factor 2; Provisional

 Score = 45.2 bits (107), Expect = 2e-05
 Identities = 28/93 (30%), Positives = 38/93 (40%), Gaps = 10/93 (10%)

Query: 189 KRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKK----------KEK 238
           K+ +K  + +  ++ K+ K K+KKK KKK     +       K   K            K
Sbjct: 58  KKNKKFNKTDDLKDSKKTKLKQKKKIKKKLHIDDDYDNFFDSKNNSKQFAGPLAISLMRK 117

Query: 239 KKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDE 271
            K K EK KKK    K   KKKKK    K +  
Sbjct: 118 PKPKTEKLKKKITVNKSTNKKKKKVLSSKDELI 150

Length = 742

>gnl|CDD|240402 PTZ00399, PTZ00399, cysteinyl-tRNA-synthetase; Provisional

 Score = 45.0 bits (107), Expect = 2e-05
 Identities = 24/64 (37%), Positives = 44/64 (68%)

Query: 208 KKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKK 267
           K + K+E ++EK++KE  KE+K+ +K KK+++KKKKE +K ++ K    +  K++++K  
Sbjct: 546 KLDDKEELQREKEEKEALKEQKRLRKLKKQEEKKKKELEKLEKAKIPPAEFFKRQEDKYS 605

Query: 268 KKDE 271
             DE
Sbjct: 606 AFDE 609

Length = 651

>gnl|CDD|178945 PRK00247, PRK00247, putative inner membrane protein translocase component YidC; Validated

 Score = 45.2 bits (107), Expect = 2e-05
 Identities = 21/91 (23%), Positives = 41/91 (45%), Gaps = 5/91 (5%)

Query: 177 KKERRKQRRRKRKRK--RKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKK 234
           KK      RR R R         E   E  E KK  +  EK + K +  KK+  +K++  
Sbjct: 301 KKAFLWTLRRNRLRMIITPWRAPELHAENAEIKK-TRTAEKNEAKAR--KKEIAQKRRAA 357

Query: 235 KKEKKKKKKEKKKKKEEKKKEKKKKKKKKEK 265
           ++E  ++ ++++     + + ++   K K+K
Sbjct: 358 EREINREARQERAAAMARARARRAAVKAKKK 388

Length = 429

>gnl|CDD|235322 PRK04950, PRK04950, ProP expression regulator; Provisional

 Score = 44.5 bits (106), Expect = 2e-05
 Identities = 12/60 (20%), Positives = 34/60 (56%)

Query: 209 KEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKK 268
           K K + ++ E++ K+++   +K+K  ++E+K K K  +KK++ + ++ + +        +
Sbjct: 107 KAKVQAQRAEQQAKKREAAGEKEKAPRRERKPKPKAPRKKRKPRAQKPEPQHTPVSDISE 166

Length = 213

>gnl|CDD|235322 PRK04950, PRK04950, ProP expression regulator; Provisional

 Score = 44.1 bits (105), Expect = 2e-05
 Identities = 13/73 (17%), Positives = 38/73 (52%)

Query: 190 RKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKK 249
           RK+ +E + K + ++ E++ +K++   +++K   ++++ K K  +KK K + +K + +  
Sbjct: 100 RKQLEEAKAKVQAQRAEQQAKKREAAGEKEKAPRRERKPKPKAPRKKRKPRAQKPEPQHT 159

Query: 250 EEKKKEKKKKKKK 262
                 +    + 
Sbjct: 160 PVSDISELTVGQA 172

Length = 213

>gnl|CDD|187751 cd09270, RNase_H2-B, Ribonuclease H2-B is a subunit of the eukaryotic RNase H complex which cleaves RNA-DNA hybrids

 Score = 44.2 bits (105), Expect = 2e-05
 Identities = 23/56 (41%), Positives = 33/56 (58%)

Query: 185 RRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKK 240
            +K +R +KKE + KE E   +KKK    E++K+KKKK+  K+KK KK      K 
Sbjct: 150 LKKVERLKKKELDIKEAEAARDKKKSNNAEEEKKKKKKKSAKKKKLKKVAAVGMKA 205

Ribonuclease H2B is one of the three proteins of eukaryotic RNase H2 complex that is required for nucleic acid binding and hydrolysis. RNase H is classified into two families, type I (prokaryotic RNase HI, eukaryotic RNase H1 and viral RNase H) and type II (prokaryotic RNase HII and HIII, and eukaryotic RNase H2/HII). RNase H endonucleolytically hydrolyzes an RNA strand when it is annealed to a complementary DNA strand in the presence of divalent cations, in DNA replication and repair. The enzyme can be found in bacteria, archaea, and eukaryotes. Most prokaryotic and eukaryotic genomes contain multiple RNase H genes. Despite a lack of evidence for homology from sequence comparisons, type I and type II RNase H share a common fold and similar steric configurations of the four acidic active-site residues, suggesting identical or very similar catalytic mechanisms. Eukaryotic RNase HII is active during replication and is believed to play a role in removal of Okazaki fragment primers and single ribonucleotides in DNA-DNA duplexes. Eukaryotic RNase HII is functional when it forms a complex with RNase H2B and RNase H2C proteins. It is speculated that the two accessory subunits are required for correct folding of the catalytic subunit of RNase HII. Mutations in the three subunits of human RNase HII cause neurological disorder. Length = 211

>gnl|CDD|222447 pfam13904, DUF4207, Domain of unknown function (DUF4207)

 Score = 44.3 bits (105), Expect = 2e-05
 Identities = 28/123 (22%), Positives = 72/123 (58%), Gaps = 23/123 (18%)

Query: 176 GKKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKK 235
            K+ +R+++ +K   +++K+E EKE E+ E +++  K++ ++  ++K ++  K++  K K
Sbjct: 95  AKQAQRQKKLQKLLEEKQKQEREKEREEAELRQRLAKEKYEEWCRQKAQQAAKQRTPKHK 154

Query: 236 K-----------------------EKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDEG 272
           K                       E KK+ +E + KK +++++K++++++K++KK+++E 
Sbjct: 155 KEAAESASSSLSGSAKPERNVSQEEAKKRLQEWELKKLKQQQQKREEERRKQRKKQQEEE 214

Query: 273 RRR 275
            R+
Sbjct: 215 ERK 217

This family is found in eukaryotes; it has several conserved tryptophan residues. The function is not known. Length = 261

>gnl|CDD|220383 pfam09756, DDRGK, DDRGK domain

 Score = 43.5 bits (103), Expect = 2e-05
 Identities = 28/84 (33%), Positives = 64/84 (76%), Gaps = 3/84 (3%)

Query: 177 KKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKK 236
           KK   K+R +  +++ ++++ E EEE++EE+   KK E+K+E ++KE+++ +++++KKK+
Sbjct: 1   KKIGAKKRAKLEEKQARRQQREAEEEEREER---KKLEEKREGERKEEEELEEEREKKKE 57

Query: 237 EKKKKKKEKKKKKEEKKKEKKKKK 260
           E+++K++E++ +KE+++ EK K  
Sbjct: 58  EEERKEREEQARKEQEEYEKLKSS 81

This is a family of proteins of approximately 300 residues, found in plants and vertebrates. They contain a highly conserved DDRGK motif. Length = 189

>gnl|CDD|219408 pfam07423, DUF1510, Protein of unknown function (DUF1510)

 Score = 44.0 bits (104), Expect = 2e-05
 Identities = 18/81 (22%), Positives = 48/81 (59%)

Query: 191 KRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKE 250
             +   +E+E +K ++++  + +E K+E+K+    ++K+ K   +KE ++ ++E +++ E
Sbjct: 41  SDQAAADEQEAKKSDDQETAEIEEVKEEEKEAANSEDKEDKGDAEKEDEESEEENEEEDE 100

Query: 251 EKKKEKKKKKKKKEKKKKKDE 271
           E   E +K+ ++K +   + E
Sbjct: 101 ESSDENEKETEEKTESNVEKE 121

This family consists of several hypothetical bacterial proteins of around 200 residues in length. The function of this family is unknown. Length = 214

>gnl|CDD|227446 COG5116, RPN2, 26S proteasome regulatory complex component [Posttranslational modification, protein turnover, chaperones]

 Score = 44.9 bits (106), Expect = 2e-05
 Identities = 16/57 (28%), Positives = 25/57 (43%)

Query: 207 KKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKKKEKKKKKKKK 263
             + K+K K+K    KE K E    + + +    K++E+K          KKKK  K
Sbjct: 794 AARAKQKPKEKGPNDKEIKIESPSVETEGERCTIKQREEKGIDAPAILNVKKKKPYK 850

Length = 926

>gnl|CDD|240388 PTZ00372, PTZ00372, endonuclease 4-like protein; Provisional

 Score = 44.7 bits (106), Expect = 3e-05
 Identities = 21/79 (26%), Positives = 37/79 (46%)

Query: 196 EEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKKKE 255
           ++ K +             K+      E++ +      KK +K+ K  E KKK E+KKK+
Sbjct: 17  QKSKLQPISYIYSNVLVLSKEILSTFSEEENKVATTSTKKDKKEDKNNESKKKSEKKKKK 76

Query: 256 KKKKKKKKEKKKKKDEGRR 274
           KK+KK+ K + + K   + 
Sbjct: 77  KKEKKEPKSEGETKLGFKT 95

Length = 413

>gnl|CDD|220648 pfam10243, MIP-T3, Microtubule-binding protein MIP-T3

 Score = 44.5 bits (105), Expect = 3e-05
 Identities = 25/92 (27%), Positives = 53/92 (57%)

Query: 174 KGGKKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKK 233
           K   KE+R  + +++++++K EE    EE+K+ ++   K   KK  KKK   K+K+  ++
Sbjct: 134 KEEAKEKRPPKEKEKEKEKKVEEPRDREEEKKRERVRAKSRPKKPPKKKPPNKKKEPPEE 193

Query: 234 KKKEKKKKKKEKKKKKEEKKKEKKKKKKKKEK 265
           +K+ +  ++  K K +E    E+++K++   K
Sbjct: 194 EKQRQAAREAVKGKPEEPDVNEEREKEEDDGK 225

This protein, which interacts with both microtubules and TRAF3 (tumour necrosis factor receptor-associated factor 3), is conserved from worms to humans. The N-terminal region is the microtubule binding domain and is well-conserved; the C-terminal 100 residues, also well-conserved, constitute the coiled-coil region which binds to TRAF3. The central region of the protein is rich in lysine and glutamic acid and carries KKE motifs which may also be necessary for tubulin-binding, but this region is the least well-conserved. Length = 506

>gnl|CDD|240271 PTZ00108, PTZ00108, DNA topoisomerase 2-like protein; Provisional

 Score = 45.0 bits (107), Expect = 3e-05
 Identities = 25/83 (30%), Positives = 43/83 (51%)

Query: 178  KERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKE 237
            +E  +++    +++  KE+  K + K +  K  K K KKKEKKKK+   +K KK      
Sbjct: 1138 EEALEEQEEVEEKEIAKEQRLKSKTKGKASKLRKPKLKKKEKKKKKSSADKSKKASVVGN 1197

Query: 238  KKKKKKEKKKKKEEKKKEKKKKK 260
             K+   ++K+K ++K   KK   
Sbjct: 1198 SKRVDSDEKRKLDDKPDNKKSNS 1220

Length = 1388

>gnl|CDD|235640 PRK05901, PRK05901, RNA polymerase sigma factor; Provisional

 Score = 45.0 bits (107), Expect = 3e-05
 Identities = 19/95 (20%), Positives = 36/95 (37%)

Query: 177 KKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKK 236
           +    ++ ++K K+   K + +    K+E K+  + K+K  E+  +         K    
Sbjct: 9   ELAAEEEAKKKLKKLAAKSKSKGFITKEEIKEALESKKKTPEQIDQVLIFLSGMVKDTDD 68

Query: 237 EKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDE 271
             +    +KK K   K    K   KKK K +    
Sbjct: 69  ATESDIPKKKTKTAAKAAAAKAPAKKKLKDELDSS 103

Length = 509

>gnl|CDD|235640 PRK05901, PRK05901, RNA polymerase sigma factor; Provisional

 Score = 44.6 bits (106), Expect = 3e-05
 Identities = 14/78 (17%), Positives = 28/78 (35%)

Query: 194 KEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKK 253
           K+ ++  E    +KK +   +    K   +KK + +    KK EKK    +       K 
Sbjct: 64  KDTDDATESDIPKKKTKTAAKAAAAKAPAKKKLKDELDSSKKAEKKNALDKDDDLNYVKD 123

Query: 254 KEKKKKKKKKEKKKKKDE 271
            +   +    +     D+
Sbjct: 124 IDVLNQADDDDDDDDDDD 141

Length = 509

>gnl|CDD|236944 PRK11642, PRK11642, exoribonuclease R; Provisional

 Score = 44.7 bits (106), Expect = 3e-05
 Identities = 20/84 (23%), Positives = 38/84 (45%), Gaps = 3/84 (3%)

Query: 181 RKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKK 240
           R   +  R++ +K +  +K  ++++  KK   +     + +K+ K +  KK  +   K K
Sbjct: 732 RNVGKTAREKAKKGDAGKKGGKRRQVGKKVNFEPDSAFRGEKKAKPKAAKKDAR---KAK 788

Query: 241 KKKEKKKKKEEKKKEKKKKKKKKE 264
           K   K +K     K K+  KKK  
Sbjct: 789 KPSAKTQKIAAATKAKRAAKKKVA 812

Length = 813

>gnl|CDD|172341 PRK13808, PRK13808, adenylate kinase; Provisional

 Score = 44.5 bits (105), Expect = 3e-05
 Identities = 27/96 (28%), Positives = 36/96 (37%)

Query: 174 KGGKKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKK 233
               K+  K    K   K+   + +   +K  +KK  K     K+  K   K  KK KK 
Sbjct: 196 AANAKKAAKTPAAKSGAKKASAKAKSAAKKVSKKKAAKTAVSAKKAAKTAAKAAKKAKKT 255

Query: 234 KKKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKK 269
            KK  KK  K  KK  ++  K   K  K   K  K 
Sbjct: 256 AKKALKKAAKAVKKAAKKAAKAAAKAAKGAAKATKG 291

Length = 333

>gnl|CDD|222581 pfam14181, YqfQ, YqfQ-like protein

 Score = 42.8 bits (101), Expect = 3e-05
 Identities = 24/61 (39%), Positives = 36/61 (59%)

Query: 194 KEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKK 253
              +++EEE +EE   E ++E   E K + K+K+K++  K K EK+K K E KK K  K 
Sbjct: 92  SSSDDEEEETEEESTDETEQEDPPETKTESKEKKKREVPKPKTEKEKPKTEPKKPKPSKP 151

Query: 254 K 254
           K
Sbjct: 152 K 152

The YqfQ-like protein family includes the B. subtilis YqfQ protein, also known as VrrA, which is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 146 and 237 amino acids in length. There are two conserved sequence motifs: QYGP and PKLY. Length = 155

>gnl|CDD|235322 PRK04950, PRK04950, ProP expression regulator; Provisional

 Score = 43.8 bits (104), Expect = 3e-05
 Identities = 19/77 (24%), Positives = 39/77 (50%), Gaps = 2/77 (2%)

Query: 192 RKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEE 251
           RK+ EE K   K + ++ E++ +K++   +KEK   +++K K K  +KK+K   +K + +
Sbjct: 100 RKQLEEAKA--KVQAQRAEQQAKKREAAGEKEKAPRRERKPKPKAPRKKRKPRAQKPEPQ 157

Query: 252 KKKEKKKKKKKKEKKKK 268
                   +    +  K
Sbjct: 158 HTPVSDISELTVGQAVK 174

Length = 213

>gnl|CDD|220383 pfam09756, DDRGK, DDRGK domain

 Score = 43.5 bits (103), Expect = 3e-05
 Identities = 22/73 (30%), Positives = 59/73 (80%)

Query: 199 KEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKKKEKKK 258
           K+   K+  K E+K+ ++++++ +E+++E++KK ++K+E ++K++E+ +++ EKKKE+++
Sbjct: 1   KKIGAKKRAKLEEKQARRQQREAEEEEREERKKLEEKREGERKEEEELEEEREKKKEEEE 60

Query: 259 KKKKKEKKKKKDE 271
           +K+++E+ +K+ E
Sbjct: 61  RKEREEQARKEQE 73

This is a family of proteins of approximately 300 residues, found in plants and vertebrates. They contain a highly conserved DDRGK motif. Length = 189

>gnl|CDD|220383 pfam09756, DDRGK, DDRGK domain

 Score = 43.1 bits (102), Expect = 3e-05
 Identities = 27/78 (34%), Positives = 61/78 (78%), Gaps = 1/78 (1%)

Query: 175 GGKKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEK-KKKEKKKEKKKKKK 233
           G KK  + + ++ R+++R+ EEEE+EE KK E+K+E ++++++E  +++EKKKE++++K+
Sbjct: 4   GAKKRAKLEEKQARRQQREAEEEEREERKKLEEKREGERKEEEELEEEREKKKEEEERKE 63

Query: 234 KKKEKKKKKKEKKKKKEE 251
           ++++ +K+++E +K K  
Sbjct: 64  REEQARKEQEEYEKLKSS 81

This is a family of proteins of approximately 300 residues, found in plants and vertebrates. They contain a highly conserved DDRGK motif. Length = 189

>gnl|CDD|219408 pfam07423, DUF1510, Protein of unknown function (DUF1510)

 Score = 43.6 bits (103), Expect = 3e-05
 Identities = 18/79 (22%), Positives = 46/79 (58%)

Query: 181 RKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKK 240
            +    +++ K+  ++E  E E+ +E++KE    + KE K   +K++++ +++ ++E ++
Sbjct: 42  DQAAADEQEAKKSDDQETAEIEEVKEEEKEAANSEDKEDKGDAEKEDEESEEENEEEDEE 101

Query: 241 KKKEKKKKKEEKKKEKKKK 259
              E +K+ EEK +   +K
Sbjct: 102 SSDENEKETEEKTESNVEK 120

This family consists of several hypothetical bacterial proteins of around 200 residues in length. The function of this family is unknown. Length = 214

>gnl|CDD|227446 COG5116, RPN2, 26S proteasome regulatory complex component [Posttranslational modification, protein turnover, chaperones]

 Score = 44.9 bits (106), Expect = 3e-05
 Identities = 16/59 (27%), Positives = 27/59 (45%)

Query: 187 KRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEK 245
           K   + K++ +EK    KE K +    E + E+   ++++EK          KKKK  K
Sbjct: 792 KAAARAKQKPKEKGPNDKEIKIESPSVETEGERCTIKQREEKGIDAPAILNVKKKKPYK 850

Length = 926

>gnl|CDD|200340 TIGR03927, T7SS_EssA_Firm, type VII secretion protein EssA

 Score = 42.7 bits (101), Expect = 3e-05
 Identities = 17/67 (25%), Positives = 33/67 (49%), Gaps = 1/67 (1%)

Query: 200 EEEKKEEKKKEKKKEKKKEKKKKEKKKEKKK-KKKKKKEKKKKKKEKKKKKEEKKKEKKK 258
            E+K  E   +  +E+ +  K+    +E+KK   +K KEK ++++ K +   E   E   
Sbjct: 31  YEKKDIEINTDYLQEETELDKELFTPEEQKKITFQKHKEKPEQEELKNQLFSENATENNT 90

Query: 259 KKKKKEK 265
            K  K++
Sbjct: 91  VKATKKQ 97

Members of this family are associated with type VII secretion of WXG100 family targets in the Firmicutes, but not in the Actinobacteria. This highly divergent protein family consists largely of a central region of highly polar low-complexity sequence containing occasional LF motifs in weak repeats about 17 residues in length, flanked by hydrophobic N- and C-terminal regions [Protein fate, Protein and peptide secretion and trafficking]. Length = 150

>gnl|CDD|217756 pfam03839, Sec62, Translocation protein Sec62

 Score = 43.6 bits (103), Expect = 3e-05
 Identities = 21/61 (34%), Positives = 31/61 (50%)

Query: 203 KKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKKKEKKKKKKK 262
            + EK K  K +   E   K   ++K  +K K   K +  +  KK   ++KKE+KKK KK
Sbjct: 16  LESEKYKANKDKGNPEIYNKINSQDKAIEKFKLLIKAQMAERVKKLHSQEKKEEKKKPKK 75

Query: 263 K 263
           K
Sbjct: 76  K 76

Length = 217

>gnl|CDD|217756 pfam03839, Sec62, Translocation protein Sec62

 Score = 43.6 bits (103), Expect = 3e-05
 Identities = 21/80 (26%), Positives = 37/80 (46%)

Query: 193 KKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEK 252
           K+     E EK +  K +   E   +   ++K  EK K   K +  ++ KK   ++K+E+
Sbjct: 10  KRVVRALESEKYKANKDKGNPEIYNKINSQDKAIEKFKLLIKAQMAERVKKLHSQEKKEE 69

Query: 253 KKEKKKKKKKKEKKKKKDEG 272
           KK+ KKKK   +    +   
Sbjct: 70  KKKPKKKKVPLQVNPAQLFV 89

Length = 217

>gnl|CDD|188306 TIGR03319, RNase_Y, ribonuclease Y

 Score = 44.5 bits (106), Expect = 3e-05
 Identities = 30/102 (29%), Positives = 54/102 (52%), Gaps = 11/102 (10%)

Query: 181 RKQRRRKRKRKRKKEEEEKE-EEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKK 239
           +K    +   KR  EE +KE E  K+E   E K+E  K + + E++ ++++ + ++ E++
Sbjct: 25  KKLGSAEELAKRIIEEAKKEAETLKKEALLEAKEEVHKLRAELERELKERRNELQRLERR 84

Query: 240 --------KKKKEKKKKKEEK--KKEKKKKKKKKEKKKKKDE 271
                    +K E   KKEE   KKEK+   K+K   +K++E
Sbjct: 85  LLQREETLDRKMESLDKKEENLEKKEKELSNKEKNLDEKEEE 126

Members of this family are RNase Y, an endoribonuclease. The member from Bacillus subtilis, YmdA, has been shown to be involved in turnover of yitJ riboswitch [Transcription, Degradation of RNA]. Length = 514

>gnl|CDD|218177 pfam04615, Utp14, Utp14 protein

 Score = 44.7 bits (106), Expect = 3e-05
 Identities = 32/105 (30%), Positives = 51/105 (48%), Gaps = 10/105 (9%)

Query: 177 KKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEK----------KK 226
           KKE + + + K++   ++E E++EE K E+   +  K  +K +K++E+          K 
Sbjct: 440 KKENKNEFKEKKESDEEEELEDEEEAKVEKVANKLLKRSEKAQKEEEEEELDEENPWLKT 499

Query: 227 EKKKKKKKKKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDE 271
                K  KK+  KKK   K  K   K  K   K KK+KKK+K  
Sbjct: 500 TSSVGKSAKKQDSKKKSSSKLDKAANKISKAAVKVKKKKKKEKSI 544

This protein is found to be part of a large ribonucleoprotein complex containing the U3 snoRNA. Depletion of the Utp proteins impedes production of the 18S rRNA, indicating that they are part of the active pre-rRNA processing complex. This large RNP complex has been termed the small subunit (SSU) processome. Length = 728

>gnl|CDD|236877 PRK11192, PRK11192, ATP-dependent RNA helicase SrmB; Provisional

 Score = 44.2 bits (105), Expect = 4e-05
 Identities = 16/61 (26%), Positives = 33/61 (54%)

Query: 178 KERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKE 237
            E R + +   ++K  K  ++   ++ E+K+KEK+K K K++ +  K   K++K     E
Sbjct: 374 DELRPKTKAPSEKKTGKPSKKVLAKRAEKKEKEKEKPKVKKRHRDTKNIGKRRKPSGTSE 433

Query: 238 K 238
           +
Sbjct: 434 E 434

Length = 434

>gnl|CDD|226894 COG4499, COG4499, Predicted membrane protein [Function unknown]

 Score = 44.4 bits (105), Expect = 4e-05
 Identities = 23/71 (32%), Positives = 44/71 (61%), Gaps = 3/71 (4%)

Query: 177 KKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKK 236
           ++E  K+  +K +   KK  E K+E    E+ + K KE   EK K+E+ ++K+K++  + 
Sbjct: 367 RQELLKEYNKKLQDYTKKLGEVKDETDASEEAEAKAKE---EKLKQEENEKKQKEQADED 423

Query: 237 EKKKKKKEKKK 247
           ++K++K E+KK
Sbjct: 424 KEKRQKDERKK 434

Length = 434

>gnl|CDD|240271 PTZ00108, PTZ00108, DNA topoisomerase 2-like protein; Provisional

 Score = 44.7 bits (106), Expect = 4e-05
 Identities = 22/104 (21%), Positives = 35/104 (33%), Gaps = 5/104 (4%)

Query: 177  KKERRKQRRRKRKRKRKKEEEEKEEEKK-----EEKKKEKKKEKKKEKKKKEKKKEKKKK 231
              +  +           KE + K   K+            K+   +     +     KKK
Sbjct: 1250 SSKSSEDNDEFSSDDLSKEGKPKNAPKRVSAVQYSPPPPSKRPDGESNGGSKPSSPTKKK 1309

Query: 232  KKKKKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDEGRRR 275
             KK+ E      +KKKK E+K   KKK K + ++       R  
Sbjct: 1310 VKKRLEGSLAALKKKKKSEKKTARKKKSKTRVKQASASQSSRLL 1353

Length = 1388

>gnl|CDD|214661 smart00435, TOPEUc, DNA Topoisomerase I (eukaryota)

 Score = 44.3 bits (105), Expect = 4e-05
 Identities = 22/86 (25%), Positives = 48/86 (55%)

Query: 181 RKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKK 240
           + Q + K  + + K  ++     +     ++K + K E+  ++   E K+KKK+KK+++K
Sbjct: 281 KLQEKIKALKYQLKRLKKMILLFEMISDLKRKLKSKFERDNEKLDAEVKEKKKEKKKEEK 340

Query: 241 KKKEKKKKKEEKKKEKKKKKKKKEKK 266
           KKK+ ++ +E  +K + +   K+E K
Sbjct: 341 KKKQIERLEERIEKLEVQATDKEENK 366

DNA Topoisomerase I (eukaryota), DNA topoisomerase V, Vaccina virus topoisomerase, Variola virus topoisomerase, Shope fibroma virus topoisomeras. Length = 391

>gnl|CDD|221952 pfam13166, AAA_13, AAA domain

 Score = 44.2 bits (105), Expect = 4e-05
 Identities = 26/78 (33%), Positives = 39/78 (50%), Gaps = 1/78 (1%)

Query: 195 EEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKK-KKKKEKKKKKKEKKKKKEEKK 253
           EE +KE +K EEK ++ + E +K++++ EK K K   K  KK  KK      +  K    
Sbjct: 98  EELKKELKKLEEKIEQLEAEIEKKEEELEKAKNKFLDKAWKKLAKKYDSNLSEALKGLNY 157

Query: 254 KEKKKKKKKKEKKKKKDE 271
           K+  K+K  KE K     
Sbjct: 158 KKNFKEKLLKELKSVILN 175

This family of domains contain a P-loop motif that is characteristic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins. This family includes the PrrC protein that is thought to be the active component of the anticodon nuclease. Length = 713

>gnl|CDD|237753 PRK14552, PRK14552, C/D box methylation guide ribonucleoprotein complex aNOP56 subunit; Provisional

 Score = 43.8 bits (104), Expect = 4e-05
 Identities = 22/46 (47%), Positives = 34/46 (73%)

Query: 192 RKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKE 237
            K+ EE KE+  K  KKK ++K+ +K KKKK++KK+ KK+KKK ++
Sbjct: 369 NKRIEEIKEKYPKPPKKKREEKKPQKRKKKKKRKKKGKKRKKKGRK 414

Length = 414

>gnl|CDD|130141 TIGR01069, mutS2, MutS2 family protein

 Score = 44.4 bits (105), Expect = 4e-05
 Identities = 26/92 (28%), Positives = 50/92 (54%), Gaps = 3/92 (3%)

Query: 183 QRRRKRKRKRKKEEEEKEEEKKE---EKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKK 239
             +   ++    E+  KE+EK +   E++ E+ KE+++ KK + +K+ ++  K  KKE +
Sbjct: 523 LEKELEQKNEHLEKLLKEQEKLKKELEQEMEELKERERNKKLELEKEAQEALKALKKEVE 582

Query: 240 KKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDE 271
              +E K+KK  K KE K  +   + K+ K +
Sbjct: 583 SIIRELKEKKIHKAKEIKSIEDLVKLKETKQK 614

Function of MutS2 is unknown. It should not be considered a DNA mismatch repair protein. It is likely a DNA mismatch binding protein of unknown cellular function [DNA metabolism, Other]. Length = 771

>gnl|CDD|220383 pfam09756, DDRGK, DDRGK domain

 Score = 42.8 bits (101), Expect = 4e-05
 Identities = 29/89 (32%), Positives = 65/89 (73%), Gaps = 2/89 (2%)

Query: 176 GKKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKK 235
            K   +K+ + + K+ R+++ E +EEE++E KK E+K+E   E+K++E+ +E+++KKK++
Sbjct: 1   KKIGAKKRAKLEEKQARRQQREAEEEEREERKKLEEKREG--ERKEEEELEEEREKKKEE 58

Query: 236 KEKKKKKKEKKKKKEEKKKEKKKKKKKKE 264
           +E+K+++++ +K++EE +K K     ++E
Sbjct: 59  EERKEREEQARKEQEEYEKLKSSFVVEEE 87

This is a family of proteins of approximately 300 residues, found in plants and vertebrates. They contain a highly conserved DDRGK motif. Length = 189

>gnl|CDD|218177 pfam04615, Utp14, Utp14 protein

 Score = 44.7 bits (106), Expect = 4e-05
 Identities = 27/91 (29%), Positives = 50/91 (54%)

Query: 179 ERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEK 238
            R+K+       + ++E E +EE  +EE ++  KK   + K   E  +++ + KK KKE 
Sbjct: 384 ARKKEENDAEIEELRRELEGEEESDEEENEEPSKKNVGRRKFGPENGEKEAESKKLKKEN 443

Query: 239 KKKKKEKKKKKEEKKKEKKKKKKKKEKKKKK 269
           K + KEKK+  EE++ E +++ K ++   K 
Sbjct: 444 KNEFKEKKESDEEEELEDEEEAKVEKVANKL 474

This protein is found to be part of a large ribonucleoprotein complex containing the U3 snoRNA. Depletion of the Utp proteins impedes production of the 18S rRNA, indicating that they are part of the active pre-rRNA processing complex. This large RNP complex has been termed the small subunit (SSU) processome. Length = 728

>gnl|CDD|219563 pfam07767, Nop53, Nop53 (60S ribosomal biogenesis)

 Score = 44.3 bits (105), Expect = 4e-05
 Identities = 25/73 (34%), Positives = 49/73 (67%)

Query: 177 KKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKK 236
            + +RK + ++ K KR+KE E + +E+K+ KKK  +  + KE  K+  +KEK + +KK++
Sbjct: 273 VRPKRKTKAQRNKEKRRKELEREAKEEKQLKKKLAQLARLKEIAKEVAQKEKARARKKEQ 332

Query: 237 EKKKKKKEKKKKK 249
            K++ +K+K K++
Sbjct: 333 RKERGEKKKLKRR 345

This nucleolar family of proteins are involved in 60S ribosomal biogenesis. They are specifically involved in the processing beyond the 27S stage of 25S rRNA maturation. This family contains sequences that bear similarity to the glioma tumour suppressor candidate region gene 2 protein (p60). This protein has been found to interact with herpes simplex type 1 regulatory proteins. Length = 387

>gnl|CDD|218188 pfam04641, Rtf2, Replication termination factor 2

 Score = 43.5 bits (103), Expect = 4e-05
 Identities = 21/76 (27%), Positives = 36/76 (47%)

Query: 194 KEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKK 253
           +EE E  + + EE++ +KKK+KKK+K KK        +         +      +  E K
Sbjct: 166 EEEVELLKARLEEERAKKKKKKKKKKTKKNNATGSSAEATVSSAVPTELSSGAGQVGEAK 225

Query: 254 KEKKKKKKKKEKKKKK 269
           K KKK+    + +K +
Sbjct: 226 KLKKKRSIAPDNEKSE 241

It is vital for effective cell-replication that replication is not stalled at any point by, for instance, damaged bases. Rtf2 stabilizes the replication fork stalled at the site-specific replication barrier RTS1 by preventing replication restart until completion of DNA synthesis by a converging replication fork initiated at a flanking origin. The RTS1 element terminates replication forks that are moving in the cen2-distal direction while allowing forks moving in the cen2-proximal direction to pass through the region. Rtf2 contains a C2HC2 motif related to the C3HC4 RING-finger motif, and would appear to fold up, creating a RING finger-like structure but forming only one functional Zn2+ ion-binding site. Length = 254

>gnl|CDD|215214 PLN02381, PLN02381, valyl-tRNA synthetase

 Score = 44.1 bits (104), Expect = 5e-05
 Identities = 23/78 (29%), Positives = 42/78 (53%), Gaps = 2/78 (2%)

Query: 174 KGGKKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKK 233
              + E  K+   + + +RKK++EEK +EK  E KK K  +K+ + K + ++        
Sbjct: 2   SRTESEAEKKILTEEELERKKKKEEKAKEK--ELKKLKAAQKEAKAKLQAQQASDGTNVP 59

Query: 234 KKKEKKKKKKEKKKKKEE 251
           KK EKK +K++ + +  E
Sbjct: 60  KKSEKKSRKRDVEDENPE 77

Length = 1066

>gnl|CDD|217051 pfam02463, SMC_N, RecF/RecN/SMC N terminal domain

 Score = 44.2 bits (104), Expect = 5e-05
 Identities = 21/97 (21%), Positives = 47/97 (48%)

Query: 175 GGKKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKK 234
            G +E+RK++ R +K   + E   +     EE K ++ K K++ KK  E  + K+K + +
Sbjct: 164 AGSREKRKKKERLKKLIEETENLAELIIDLEELKLQELKLKEQAKKALEYYQLKEKLELE 223

Query: 235 KKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDE 271
           ++        K  ++     ++  + +++E +  K E
Sbjct: 224 EENLLYLDYLKLNEERIDLLQELLRDEQEEIESSKQE 260

This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination. Length = 1162

>gnl|CDD|217051 pfam02463, SMC_N, RecF/RecN/SMC N terminal domain

 Score = 44.2 bits (104), Expect = 5e-05
 Identities = 17/93 (18%), Positives = 45/93 (48%)

Query: 177 KKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKK 236
            +        K +  + KE+ +K  E  + K+K + +E+        K  E++    ++ 
Sbjct: 187 AELIIDLEELKLQELKLKEQAKKALEYYQLKEKLELEEENLLYLDYLKLNEERIDLLQEL 246

Query: 237 EKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKK 269
            + ++++ +  K+E +K+E+   +  KE K+++
Sbjct: 247 LRDEQEEIESSKQELEKEEEILAQVLKENKEEE 279

This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination. Length = 1162

>gnl|CDD|217051 pfam02463, SMC_N, RecF/RecN/SMC N terminal domain

 Score = 44.2 bits (104), Expect = 5e-05
 Identities = 26/95 (27%), Positives = 63/95 (66%)

Query: 177 KKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKK 236
           K+++ ++   K   K ++E + +  + +  K  +++K K+ EK+ K+ +KE KK+K++ +
Sbjct: 280 KEKKLQEEELKLLAKEEEELKSELLKLERRKVDDEEKLKESEKELKKLEKELKKEKEEIE 339

Query: 237 EKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDE 271
           E +K+ KE + K+E +++E+++ +K +EK ++ +E
Sbjct: 340 ELEKELKELEIKREAEEEEEEQLEKLQEKLEQLEE 374

This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination. Length = 1162

>gnl|CDD|221952 pfam13166, AAA_13, AAA domain

 Score = 44.2 bits (105), Expect = 5e-05
 Identities = 20/70 (28%), Positives = 37/70 (52%)

Query: 206 EKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKKKEKKKKKKKKEK 265
           E+  E + + ++ KK+ +K +EK ++ + + EKK+++ EK K K   K  KK  KK    
Sbjct: 88  EENIEIEAQIEELKKELKKLEEKIEQLEAEIEKKEEELEKAKNKFLDKAWKKLAKKYDSN 147

Query: 266 KKKKDEGRRR 275
             +  +G   
Sbjct: 148 LSEALKGLNY 157

This family of domains contain a P-loop motif that is characteristic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins. This family includes the PrrC protein that is thought to be the active component of the anticodon nuclease. Length = 713

>gnl|CDD|221952 pfam13166, AAA_13, AAA domain

 Score = 43.8 bits (104), Expect = 5e-05
 Identities = 22/75 (29%), Positives = 38/75 (50%), Gaps = 2/75 (2%)

Query: 201 EEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKKKEKKKKK 260
           EE  E   + + +E KKE KK E+K E+ + + +KKE++ +K + K   +  KK  KK  
Sbjct: 88  EENIE--IEAQIEELKKELKKLEEKIEQLEAEIEKKEEELEKAKNKFLDKAWKKLAKKYD 145

Query: 261 KKKEKKKKKDEGRRR 275
               +  K    ++ 
Sbjct: 146 SNLSEALKGLNYKKN 160

This family of domains contain a P-loop motif that is characteristic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins. This family includes the PrrC protein that is thought to be the active component of the anticodon nuclease. Length = 713

>gnl|CDD|214395 CHL00204, ycf1, Ycf1; Provisional

 Score = 44.3 bits (105), Expect = 5e-05
 Identities = 19/92 (20%), Positives = 42/92 (45%), Gaps = 3/92 (3%)

Query: 180  RRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKK 239
              +   +K  +K+K      E++  E + + +++++   + + E  KEKK   +     +
Sbjct: 1494 GNENVNKKINQKKKGFIPSNEKKSIEIENRNQEEKEPAGQGELESDKEKKGNLESVLSNQ 1553

Query: 240  KKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDE 271
            +K  E+      +   KK+K KK+ K   + E
Sbjct: 1554 EKNIEED---YAESDIKKRKNKKQYKSNTEAE 1582

Length = 1832

>gnl|CDD|219408 pfam07423, DUF1510, Protein of unknown function (DUF1510)

 Score = 43.2 bits (102), Expect = 5e-05
 Identities = 19/74 (25%), Positives = 43/74 (58%)

Query: 182 KQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKK 241
           +Q  +K   +   E EE +EE+KE    E K++K   +K+ E+ +E+ +++ ++   + +
Sbjct: 48  EQEAKKSDDQETAEIEEVKEEEKEAANSEDKEDKGDAEKEDEESEEENEEEDEESSDENE 107

Query: 242 KKEKKKKKEEKKKE 255
           K+ ++K +   +KE
Sbjct: 108 KETEEKTESNVEKE 121

This family consists of several hypothetical bacterial proteins of around 200 residues in length. The function of this family is unknown. Length = 214

>gnl|CDD|227446 COG5116, RPN2, 26S proteasome regulatory complex component [Posttranslational modification, protein turnover, chaperones]

 Score = 44.2 bits (104), Expect = 5e-05
 Identities = 17/61 (27%), Positives = 28/61 (45%), Gaps = 2/61 (3%)

Query: 181 RKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKK 240
           +   R K+K K K   +  +E K E    E + E+   K+++EK  +       KK+K  
Sbjct: 792 KAAARAKQKPKEKGPND--KEIKIESPSVETEGERCTIKQREEKGIDAPAILNVKKKKPY 849

Query: 241 K 241
           K
Sbjct: 850 K 850

Length = 926

>gnl|CDD|227446 COG5116, RPN2, 26S proteasome regulatory complex component [Posttranslational modification, protein turnover, chaperones]

 Score = 44.2 bits (104), Expect = 5e-05
 Identities = 21/77 (27%), Positives = 32/77 (41%)

Query: 195 EEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKKK 254
           EEEE E  +  E+   K   K          K   + K+K KEK    KE K +    + 
Sbjct: 761 EEEEFEYPRMYEEASGKSVRKVNTAVLSTTIKAAARAKQKPKEKGPNDKEIKIESPSVET 820

Query: 255 EKKKKKKKKEKKKKKDE 271
           E ++   K+ ++K  D 
Sbjct: 821 EGERCTIKQREEKGIDA 837

Length = 926

>gnl|CDD|234767 PRK00448, polC, DNA polymerase III PolC; Validated

 Score = 44.1 bits (105), Expect = 5e-05
 Identities = 21/66 (31%), Positives = 38/66 (57%)

Query: 194 KEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKK 253
           K + E ++ K+E +K E +KE++ EK  KE  +  KK + +KK++ K    K+   +  K
Sbjct: 160 KIDFEIDDSKEELEKFEAQKEEEDEKLAKEALEAMKKLEAEKKKQSKNFDPKEGPVQIGK 219

Query: 254 KEKKKK 259
           K  K++
Sbjct: 220 KIDKEE 225

Length = 1437

>gnl|CDD|221733 pfam12720, DUF3807, Protein of unknown function (DUF3807)

 Score = 42.4 bits (100), Expect = 5e-05
 Identities = 15/70 (21%), Positives = 32/70 (45%)

Query: 188 RKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKK 247
           R+R+ K+E E +EE + +          +    +KE +++   +K+K    K++K  K  
Sbjct: 67  RERELKEEAEAEEEGEVDASPDAGAVAGESSADRKEAEQQGAAQKRKSCRDKERKSAKDP 126

Query: 248 KKEEKKKEKK 257
           +   +    K
Sbjct: 127 RGGTQDVVDK 136

This is a family of conserved fungal proteins of unknown function. Length = 169

>gnl|CDD|217051 pfam02463, SMC_N, RecF/RecN/SMC N terminal domain

 Score = 44.2 bits (104), Expect = 6e-05
 Identities = 30/109 (27%), Positives = 65/109 (59%), Gaps = 1/109 (0%)

Query: 168 NLEYGYKGGKKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKK-KKEKKK 226
             E      ++E  K    K +R++  +EE+ +E +KE KK EK+ +K+KE+  + EK+ 
Sbjct: 286 EEELKLLAKEEEELKSELLKLERRKVDDEEKLKESEKELKKLEKELKKEKEEIEELEKEL 345

Query: 227 EKKKKKKKKKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDEGRRR 275
           ++ + K++ +E+++++ EK ++K E+ +E+   KKK E ++     + +
Sbjct: 346 KELEIKREAEEEEEEQLEKLQEKLEQLEEELLAKKKLESERLSSAAKLK 394

This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination. Length = 1162

>gnl|CDD|240271 PTZ00108, PTZ00108, DNA topoisomerase 2-like protein; Provisional

 Score = 43.9 bits (104), Expect = 6e-05
 Identities = 28/98 (28%), Positives = 55/98 (56%)

Query: 178  KERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKE 237
            KE+ ++   + ++K K+ E+ K    K+   ++  K ++  ++++E ++++  K+++ K 
Sbjct: 1101 KEKVEKLNAELEKKEKELEKLKNTTPKDMWLEDLDKFEEALEEQEEVEEKEIAKEQRLKS 1160

Query: 238  KKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDEGRRR 275
            K K K  K +K + KKKEKKKKK   +K KK       
Sbjct: 1161 KTKGKASKLRKPKLKKKEKKKKKSSADKSKKASVVGNS 1198

Length = 1388

>gnl|CDD|215774 pfam00183, HSP90, Hsp90 protein

 Score = 43.6 bits (103), Expect = 6e-05
 Identities = 22/64 (34%), Positives = 46/64 (71%)

Query: 195 EEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKKK 254
           E+E ++E   EE+++EK+++K++E+K  +K++E  ++++K+++KKK KK K+   E +  
Sbjct: 28  EKEVEKEVPDEEEEEEKEEKKEEEEKTTDKEEEVDEEEEKEEKKKKTKKVKETTTEWELL 87

Query: 255 EKKK 258
            K K
Sbjct: 88  NKTK 91

Length = 529

>gnl|CDD|236545 PRK09510, tolA, cell envelope integrity inner membrane protein TolA; Provisional

 Score = 43.6 bits (103), Expect = 6e-05
 Identities = 25/85 (29%), Positives = 36/85 (42%)

Query: 191 KRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKE 250
           K+K E E  ++   E KKK + +   K   + +KK E + KKK   E KKK   + K   
Sbjct: 168 KKKAEAEAAKKAAAEAKKKAEAEAAAKAAAEAKKKAEAEAKKKAAAEAKKKAAAEAKAAA 227

Query: 251 EKKKEKKKKKKKKEKKKKKDEGRRR 275
            K   + K   +K    K  E    
Sbjct: 228 AKAAAEAKAAAEKAAAAKAAEKAAA 252

Length = 387

>gnl|CDD|240246 PTZ00053, PTZ00053, methionine aminopeptidase 2; Provisional

 Score = 43.9 bits (104), Expect = 6e-05
 Identities = 20/79 (25%), Positives = 42/79 (53%)

Query: 194 KEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKK 253
           +  E + +++K++ K++  K+K K+ KK     +    +   + ++ + K+  KKK++KK
Sbjct: 4   ENGENEVKQQKQQNKQKGTKKKNKKSKKDVDDDDAFLAELISENQEAENKQNNKKKKKKK 63

Query: 254 KEKKKKKKKKEKKKKKDEG 272
           K+KKKK   +      D  
Sbjct: 64  KKKKKKNLGEAYDLAYDLP 82

Length = 470

>gnl|CDD|240246 PTZ00053, PTZ00053, methionine aminopeptidase 2; Provisional

 Score = 43.5 bits (103), Expect = 6e-05
 Identities = 23/76 (30%), Positives = 41/76 (53%)

Query: 195 EEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKKK 254
              E  E + +++K++ K++  K+K KK KK          +   + ++ + K+  +KKK
Sbjct: 1   AMNENGENEVKQQKQQNKQKGTKKKNKKSKKDVDDDDAFLAELISENQEAENKQNNKKKK 60

Query: 255 EKKKKKKKKEKKKKKD 270
           +KKKKKKKK   +  D
Sbjct: 61  KKKKKKKKKNLGEAYD 76

Length = 470

>gnl|CDD|221275 pfam11861, DUF3381, Domain of unknown function (DUF3381)

 Score = 41.9 bits (99), Expect = 6e-05
 Identities = 19/62 (30%), Positives = 41/62 (66%)

Query: 181 RKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKK 240
           RK+ R+     +K++EEE+EEE + E+  E+++  +  +K+  K K +K+++ ++K+K+ 
Sbjct: 87  RKKVRKLLGLDKKEKEEEEEEEVEVEELDEEEQIDELLEKELAKLKREKRRENERKQKEI 146

Query: 241 KK 242
            K
Sbjct: 147 LK 148

This domain is functionally uncharacterized. This domain is found in eukaryotes. This presumed domain is typically between 156 to 174 amino acids in length. This domain is found associated with pfam07780, pfam01728. Length = 154

>gnl|CDD|218737 pfam05764, YL1, YL1 nuclear protein

 Score = 43.1 bits (102), Expect = 6e-05
 Identities = 25/81 (30%), Positives = 43/81 (53%)

Query: 195 EEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKKK 254
           + E+ E E  +E++ EK+ ++++  KKK++ K K  K+  KK+KKK     K  K    +
Sbjct: 60  DSEDDEPESDDEEEGEKELQREERLKKKKRVKTKAYKEPTKKKKKKDPTAAKSPKAAAPR 119

Query: 255 EKKKKKKKKEKKKKKDEGRRR 275
            KKK ++        D  RR+
Sbjct: 120 PKKKSERISWAPTLLDSPRRK 140

The proteins in this family are designated YL1. These proteins have been shown to be DNA-binding and may be a transcription factor. Length = 238

>gnl|CDD|220648 pfam10243, MIP-T3, Microtubule-binding protein MIP-T3

 Score = 43.3 bits (102), Expect = 7e-05
 Identities = 28/85 (32%), Positives = 55/85 (64%)

Query: 191 KRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKE 250
           K   +E  K  EK   K    K +  KE K +  K+E+K+K++ K+EKKKKK++ K++ +
Sbjct: 70  KLSSDEAVKRVEKGGSKGPAAKTKPAKEPKNESGKEEEKEKEQVKEEKKKKKEKPKEEPK 129

Query: 251 EKKKEKKKKKKKKEKKKKKDEGRRR 275
           ++K +++ K+K+  K+K+K++ ++ 
Sbjct: 130 DRKPKEEAKEKRPPKEKEKEKEKKV 154

This protein, which interacts with both microtubules and TRAF3 (tumour necrosis factor receptor-associated factor 3), is conserved from worms to humans. The N-terminal region is the microtubule binding domain and is well-conserved; the C-terminal 100 residues, also well-conserved, constitute the coiled-coil region which binds to TRAF3. The central region of the protein is rich in lysine and glutamic acid and carries KKE motifs which may also be necessary for tubulin-binding, but this region is the least well-conserved. Length = 506

>gnl|CDD|191187 pfam05087, Rota_VP2, Rotavirus VP2 protein

 Score = 43.8 bits (103), Expect = 7e-05
 Identities = 25/95 (26%), Positives = 47/95 (49%), Gaps = 8/95 (8%)

Query: 177 KKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKE--------KKKEKKKKEKKKEK 228
           ++E       + + K  +++++K   + +EK  +KK+E          KE+  +E  K  
Sbjct: 6   RREANINNNDRMQEKDDEKQDQKNRMELKEKVLDKKEEVVTDNVDSPVKEQSSQENLKIA 65

Query: 229 KKKKKKKKEKKKKKKEKKKKKEEKKKEKKKKKKKK 263
            + KK  KE+ K+  E  K KEE +KE + +  +K
Sbjct: 66  DEVKKSTKEESKQLLEVLKTKEEHQKEIQYEILQK 100

Rotavirus particles consist of three concentric proteinaceous capsid layers. The innermost capsid (core) is made of VP2. The genomic RNA and the two minor proteins VP1 and VP3 are encapsidated within this layer. The N-terminus of rotavirus VP2 is necessary for the encapsidation of VP1 and VP3. Length = 887

>gnl|CDD|217051 pfam02463, SMC_N, RecF/RecN/SMC N terminal domain

 Score = 43.8 bits (103), Expect = 7e-05
 Identities = 25/98 (25%), Positives = 62/98 (63%)

Query: 178 KERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKE 237
            +  K+ + + K K+ +EEE K   K+EE+ K +  + ++ K   E+K ++ +K+ KK E
Sbjct: 269 AQVLKENKEEEKEKKLQEEELKLLAKEEEELKSELLKLERRKVDDEEKLKESEKELKKLE 328

Query: 238 KKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDEGRRR 275
           K+ KK++++ ++ EK+ ++ + K++ E+++++   + +
Sbjct: 329 KELKKEKEEIEELEKELKELEIKREAEEEEEEQLEKLQ 366

This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination. Length = 1162

>gnl|CDD|220252 pfam09468, RNase_H2-Ydr279, Ydr279p protein family (RNase H2 complex component)

 Score = 43.1 bits (102), Expect = 7e-05
 Identities = 18/62 (29%), Positives = 34/62 (54%)

Query: 188 RKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKK 247
           +   +  +E +K++ + EE  +  +   +K++K KE+ K+KK K+ K  +  KK   K  
Sbjct: 221 KPLDKYLKESKKKKRETEEDVEAAESRAEKKRKSKEEIKKKKPKESKGVKALKKVVAKGM 280

Query: 248 KK 249
           KK
Sbjct: 281 KK 282

RNases H are enzymes that specifically hydrolyse RNA when annealed to a complementary DNA and are present in all living organisms. In yeast RNase H2 is composed of a complex of three proteins (Rnh2Ap, Ydr279p and Ylr154p), this family represents the homologues of Ydr279p. It is not known whether non yeast proteins in this family fulfil the same function. Length = 287

>gnl|CDD|237753 PRK14552, PRK14552, C/D box methylation guide ribonucleoprotein complex aNOP56 subunit; Provisional

 Score = 43.4 bits (103), Expect = 7e-05
 Identities = 22/50 (44%), Positives = 38/50 (76%)

Query: 225 KKEKKKKKKKKKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDEGRR 274
           K+E  K+ ++ KEK  K  +KK+++++ +K KKKKK+KK+ KK+K +GR+
Sbjct: 365 KEELNKRIEEIKEKYPKPPKKKREEKKPQKRKKKKKRKKKGKKRKKKGRK 414

Length = 414

>gnl|CDD|237753 PRK14552, PRK14552, C/D box methylation guide ribonucleoprotein complex aNOP56 subunit; Provisional

 Score = 43.4 bits (103), Expect = 7e-05
 Identities = 24/53 (45%), Positives = 40/53 (75%)

Query: 200 EEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEK 252
           +E K+E  K+ ++ ++K  K  K+K++EKK +K+KKK+K+KKK +K+KKK  K
Sbjct: 362 DELKEELNKRIEEIKEKYPKPPKKKREEKKPQKRKKKKKRKKKGKKRKKKGRK 414

Length = 414

>gnl|CDD|235322 PRK04950, PRK04950, ProP expression regulator; Provisional

 Score = 42.6 bits (101), Expect = 7e-05
 Identities = 20/75 (26%), Positives = 42/75 (56%)

Query: 197 EEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKKKEK 256
            E EEE  E  +K+ ++ K K + ++ +++ KK++   +KEK  +++ K K K  +KK K
Sbjct: 89  GELEEEHVEHARKQLEEAKAKVQAQRAEQQAKKREAAGEKEKAPRRERKPKPKAPRKKRK 148

Query: 257 KKKKKKKEKKKKKDE 271
            + +K + +     +
Sbjct: 149 PRAQKPEPQHTPVSD 163

Length = 213

>gnl|CDD|234017 TIGR02794, tolA_full, TolA protein

 Score = 42.9 bits (101), Expect = 8e-05
 Identities = 27/97 (27%), Positives = 46/97 (47%), Gaps = 6/97 (6%)

Query: 179 ERRKQRRRKRKRKRKKEEEEKEEE---KKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKK 235
           E + ++  + K K + E E+K +E   K+ E++ + K   + +KK  E KK+ + + K K
Sbjct: 123 EAKAKQAAEAKAKAEAEAEKKAKEEAKKQAEEEAKAKAAAEAKKKAAEAKKKAEAEAKAK 182

Query: 236 KEKKKKKKE---KKKKKEEKKKEKKKKKKKKEKKKKK 269
            E K K K    K K +  K K   +   K E +   
Sbjct: 183 AEAKAKAKAEEAKAKAEAAKAKAAAEAAAKAEAEAAA 219

TolA couples the inner membrane complex of itself with TolQ and TolR to the outer membrane complex of TolB and OprL (also called Pal). Most of the length of the protein consists of low-complexity sequence that may differ in both length and composition from one species to another, complicating efforts to discriminate TolA (the most divergent gene in the tol-pal system) from paralogs such as TonB. Selection of members of the seed alignment and criteria for setting scoring cutoffs are based largely conserved operon struction. //The Tol-Pal complex is required for maintaining outer membrane integrity. Also involved in transport (uptake) of colicins and filamentous DNA, and implicated in pathogenesis. Transport is energized by the proton motive force. TolA is an inner membrane protein that interacts with periplasmic TolB and with outer membrane porins ompC, phoE and lamB [Transport and binding proteins, Other, Cellular processes, Pathogenesis]. Length = 346

>gnl|CDD|220252 pfam09468, RNase_H2-Ydr279, Ydr279p protein family (RNase H2 complex component)

 Score = 42.7 bits (101), Expect = 8e-05
 Identities = 22/67 (32%), Positives = 37/67 (55%)

Query: 176 GKKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKK 235
              E +   +  ++ K+KK E E++ E  E + ++K+K K++ KKKK K+ +  K  KK 
Sbjct: 216 LIPEFKPLDKYLKESKKKKRETEEDVEAAESRAEKKRKSKEEIKKKKPKESKGVKALKKV 275

Query: 236 KEKKKKK 242
             K  KK
Sbjct: 276 VAKGMKK 282

RNases H are enzymes that specifically hydrolyse RNA when annealed to a complementary DNA and are present in all living organisms. In yeast RNase H2 is composed of a complex of three proteins (Rnh2Ap, Ydr279p and Ylr154p), this family represents the homologues of Ydr279p. It is not known whether non yeast proteins in this family fulfil the same function. Length = 287

>gnl|CDD|214395 CHL00204, ycf1, Ycf1; Provisional

 Score = 43.6 bits (103), Expect = 8e-05
 Identities = 20/88 (22%), Positives = 43/88 (48%), Gaps = 1/88 (1%)

Query: 182  KQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKK 241
             Q+++      +K+  E E   +EEK+   + E + +K+KK   +     ++K  E+   
Sbjct: 1503 NQKKKGFIPSNEKKSIEIENRNQEEKEPAGQGELESDKEKKGNLESVLSNQEKNIEEDYA 1562

Query: 242  KKEKKKKKEEKKKEKKKKKKKKEKKKKK 269
            + + KK+K  KK+ K   + + +   K+
Sbjct: 1563 ESDIKKRKN-KKQYKSNTEAELDFFLKR 1589

Length = 1832

>gnl|CDD|215774 pfam00183, HSP90, Hsp90 protein

 Score = 43.2 bits (102), Expect = 8e-05
 Identities = 23/58 (39%), Positives = 44/58 (75%)

Query: 214 EKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDE 271
           EK+ EK+  ++++E++K++KK++E+K   KE++  +EE+K+EKKKK KK ++   + E
Sbjct: 28  EKEVEKEVPDEEEEEEKEEKKEEEEKTTDKEEEVDEEEEKEEKKKKTKKVKETTTEWE 85

Length = 529

>gnl|CDD|177089 CHL00189, infB, translation initiation factor 2; Provisional

 Score = 43.7 bits (103), Expect = 8e-05
 Identities = 22/93 (23%), Positives = 41/93 (44%)

Query: 177 KKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKK 236
           KK   K  ++ +K  +  + ++ ++ K ++KKK KKK    +        +   K+    
Sbjct: 50  KKLHEKLDKKNKKFNKTDDLKDSKKTKLKQKKKIKKKLHIDDDYDNFFDSKNNSKQFAGP 109

Query: 237 EKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKK 269
                 ++ K K E+ KK+    K   +KKKK 
Sbjct: 110 LAISLMRKPKPKTEKLKKKITVNKSTNKKKKKV 142

Length = 742

>gnl|CDD|200340 TIGR03927, T7SS_EssA_Firm, type VII secretion protein EssA

 Score = 41.6 bits (98), Expect = 8e-05
 Identities = 16/68 (23%), Positives = 34/68 (50%)

Query: 195 EEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKKK 254
             E+K+ E   +  +E+ +  K+    +E+KK   +K K+K E+++ K +   +   +  
Sbjct: 30  RYEKKDIEINTDYLQEETELDKELFTPEEQKKITFQKHKEKPEQEELKNQLFSENATENN 89

Query: 255 EKKKKKKK 262
             K  KK+
Sbjct: 90  TVKATKKQ 97

Members of this family are associated with type VII secretion of WXG100 family targets in the Firmicutes, but not in the Actinobacteria. This highly divergent protein family consists largely of a central region of highly polar low-complexity sequence containing occasional LF motifs in weak repeats about 17 residues in length, flanked by hydrophobic N- and C-terminal regions [Protein fate, Protein and peptide secretion and trafficking]. Length = 150

>gnl|CDD|234767 PRK00448, polC, DNA polymerase III PolC; Validated

 Score = 43.7 bits (104), Expect = 8e-05
 Identities = 21/94 (22%), Positives = 46/94 (48%), Gaps = 6/94 (6%)

Query: 176 GKKERRKQRRRKRKRKRKK------EEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKK 229
            + ER   +++   +  K+         + + E  + K++ +K E +KE++ ++  KE  
Sbjct: 132 NEIERDHLKKKHLPKLIKQYEKFGFGILKIDFEIDDSKEELEKFEAQKEEEDEKLAKEAL 191

Query: 230 KKKKKKKEKKKKKKEKKKKKEEKKKEKKKKKKKK 263
           +  KK + +KKK+ +    KE   +  KK  K++
Sbjct: 192 EAMKKLEAEKKKQSKNFDPKEGPVQIGKKIDKEE 225

Length = 1437

>gnl|CDD|215774 pfam00183, HSP90, Hsp90 protein

 Score = 43.2 bits (102), Expect = 9e-05
 Identities = 25/64 (39%), Positives = 46/64 (71%)

Query: 196 EEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKKKE 255
           E+E E+E  +E+++E+K+EKK+E++K   K+E+  ++++K+EKKKK K+ K+   E +  
Sbjct: 28  EKEVEKEVPDEEEEEEKEEKKEEEEKTTDKEEEVDEEEEKEEKKKKTKKVKETTTEWELL 87

Query: 256 KKKK 259
            K K
Sbjct: 88  NKTK 91

Length = 529

>gnl|CDD|235322 PRK04950, PRK04950, ProP expression regulator; Provisional

 Score = 42.2 bits (100), Expect = 9e-05
 Identities = 16/70 (22%), Positives = 35/70 (50%)

Query: 178 KERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKE 237
           K + + +R +++ K+++   EKE+  + E+K + K  +KK K + +K + +        E
Sbjct: 107 KAKVQAQRAEQQAKKREAAGEKEKAPRRERKPKPKAPRKKRKPRAQKPEPQHTPVSDISE 166

Query: 238 KKKKKKEKKK 247
               +  K K
Sbjct: 167 LTVGQAVKVK 176

Length = 213

>gnl|CDD|150884 pfam10278, Med19, Mediator of RNA pol II transcription subunit 19

 Score = 41.7 bits (98), Expect = 9e-05
 Identities = 25/59 (42%), Positives = 38/59 (64%)

Query: 184 RRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKK 242
           ++ K K K+ + ++   EE   + +  K  EKK +KKK E  KE+KKKKK+KK+KKK+ 
Sbjct: 111 KKHKHKHKKHRTQDPLPEETPSDSEGLKGHEKKHKKKKHEDDKERKKKKKEKKKKKKRH 169

Med19 represents a family of conserved proteins which are members of the multi-protein co-activator Mediator complex. Mediator is required for activation of RNA polymerase II transcription by DNA binding transactivators. Length = 178

>gnl|CDD|222160 pfam13476, AAA_23, AAA domain

 Score = 42.2 bits (99), Expect = 9e-05
 Identities = 23/64 (35%), Positives = 43/64 (67%)

Query: 201 EEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKKKEKKKKK 260
            +++ E+ K K+KEKK+  ++ EK+ E+ + +K   EK  ++KEKKK+ EE K+E ++  
Sbjct: 141 GQERLEELKFKRKEKKERLEELEKELEELEDEKDLLEKLLEEKEKKKELEELKEELEELL 200

Query: 261 KKKE 264
           ++ E
Sbjct: 201 EELE 204

Length = 204

>gnl|CDD|234017 TIGR02794, tolA_full, TolA protein

 Score = 42.9 bits (101), Expect = 1e-04
 Identities = 24/95 (25%), Positives = 45/95 (47%)

Query: 177 KKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKK 236
           K E   +++ K + K++ EEE K +   E KKK  + +KK E + K K + K K K ++ 
Sbjct: 135 KAEAEAEKKAKEEAKKQAEEEAKAKAAAEAKKKAAEAKKKAEAEAKAKAEAKAKAKAEEA 194

Query: 237 EKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDE 271
           + K +  + K   E   K + +       + ++  
Sbjct: 195 KAKAEAAKAKAAAEAAAKAEAEAAAAAAAEAERKA 229

TolA couples the inner membrane complex of itself with TolQ and TolR to the outer membrane complex of TolB and OprL (also called Pal). Most of the length of the protein consists of low-complexity sequence that may differ in both length and composition from one species to another, complicating efforts to discriminate TolA (the most divergent gene in the tol-pal system) from paralogs such as TonB. Selection of members of the seed alignment and criteria for setting scoring cutoffs are based largely conserved operon struction. //The Tol-Pal complex is required for maintaining outer membrane integrity. Also involved in transport (uptake) of colicins and filamentous DNA, and implicated in pathogenesis. Transport is energized by the proton motive force. TolA is an inner membrane protein that interacts with periplasmic TolB and with outer membrane porins ompC, phoE and lamB [Transport and binding proteins, Other, Cellular processes, Pathogenesis]. Length = 346

>gnl|CDD|217051 pfam02463, SMC_N, RecF/RecN/SMC N terminal domain

 Score = 43.0 bits (101), Expect = 1e-04
 Identities = 27/102 (26%), Positives = 62/102 (60%), Gaps = 7/102 (6%)

Query: 177 KKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKK 236
           +++ R ++  + + K +   +EKE  ++EEK ++ K E++KE+K K +++E +  +++ K
Sbjct: 753 EEKSRLKKEEEEEEKSELSLKEKELAEEEEKTEKLKVEEEKEEKLKAQEEELRALEEELK 812

Query: 237 EKKKKKKE-------KKKKKEEKKKEKKKKKKKKEKKKKKDE 271
           E+ +  +E       ++K KEE+ +E   + K+++K +K  E
Sbjct: 813 EEAELLEEEQLLIEQEEKIKEEELEELALELKEEQKLEKLAE 854

This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination. Length = 1162

>gnl|CDD|217051 pfam02463, SMC_N, RecF/RecN/SMC N terminal domain

 Score = 42.6 bits (100), Expect = 1e-04
 Identities = 25/94 (26%), Positives = 62/94 (65%)

Query: 182 KQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKK 241
           ++ ++ ++ + K   +E+EE K E  K E++K   +EK K+ +K+ KK +K+ KKEK++ 
Sbjct: 279 EKEKKLQEEELKLLAKEEEELKSELLKLERRKVDDEEKLKESEKELKKLEKELKKEKEEI 338

Query: 242 KKEKKKKKEEKKKEKKKKKKKKEKKKKKDEGRRR 275
           ++ +K+ KE + K + +++++++ +K +++  + 
Sbjct: 339 EELEKELKELEIKREAEEEEEEQLEKLQEKLEQL 372

This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination. Length = 1162

>gnl|CDD|240271 PTZ00108, PTZ00108, DNA topoisomerase 2-like protein; Provisional

 Score = 43.1 bits (102), Expect = 1e-04
 Identities = 23/99 (23%), Positives = 48/99 (48%)

Query: 177  KKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKK 236
            + E ++  + +R + + K +  K  + K +KK++KKK+   +K KK       K+    +
Sbjct: 1146 EVEEKEIAKEQRLKSKTKGKASKLRKPKLKKKEKKKKKSSADKSKKASVVGNSKRVDSDE 1205

Query: 237  EKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDEGRRR 275
            ++K   K   KK      +++  +++K K KK    R +
Sbjct: 1206 KRKLDDKPDNKKSNSSGSDQEDDEEQKTKPKKSSVKRLK 1244

Length = 1388

>gnl|CDD|240271 PTZ00108, PTZ00108, DNA topoisomerase 2-like protein; Provisional

 Score = 43.1 bits (102), Expect = 1e-04
 Identities = 22/109 (20%), Positives = 39/109 (35%)

Query: 167  DNLEYGYKGGKKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKK 226
            +N     +   +       ++ K K   +     +       K    E     K     K
Sbjct: 1248 NNSSKSSEDNDEFSSDDLSKEGKPKNAPKRVSAVQYSPPPPSKRPDGESNGGSKPSSPTK 1307

Query: 227  EKKKKKKKKKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDEGRRR 275
            +K KK+ +      KKK+K +KK  +KK+ K + K+    +     RR 
Sbjct: 1308 KKVKKRLEGSLAALKKKKKSEKKTARKKKSKTRVKQASASQSSRLLRRP 1356

Length = 1388

>gnl|CDD|235640 PRK05901, PRK05901, RNA polymerase sigma factor; Provisional

 Score = 42.7 bits (101), Expect = 1e-04
 Identities = 14/76 (18%), Positives = 25/76 (32%)

Query: 197 EEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKKKEK 256
           E    +KK +   +    K   KKK + + +  KK +KK    K       K  +   + 
Sbjct: 71  ESDIPKKKTKTAAKAAAAKAPAKKKLKDELDSSKKAEKKNALDKDDDLNYVKDIDVLNQA 130

Query: 257 KKKKKKKEKKKKKDEG 272
                  +     D+ 
Sbjct: 131 DDDDDDDDDDDLDDDD 146

Length = 509

>gnl|CDD|221641 pfam12569, NARP1, NMDA receptor-regulated protein 1

 Score = 43.0 bits (102), Expect = 1e-04
 Identities = 16/47 (34%), Positives = 29/47 (61%)

Query: 187 KRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKK 233
           +RK+ RKK+ + +++ +KEE +K   K+K +   KK K  + + KK 
Sbjct: 410 ERKKLRKKQRKAEKKAEKEEAEKAAAKKKAEAAAKKAKGPDGETKKV 456

This domain family is found in eukaryotes, and is approximately 40 amino acids in length. The family is found in association with pfam07719, pfam00515. There is a single completely conserved residue L that may be functionally important. NARP1 is the mammalian homologue of a yeast N-terminal acetyltransferase that regulates entry into the G(0) phase of the cell cycle. Length = 516

>gnl|CDD|221641 pfam12569, NARP1, NMDA receptor-regulated protein 1

 Score = 42.6 bits (101), Expect = 1e-04
 Identities = 18/46 (39%), Positives = 28/46 (60%)

Query: 186 RKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKK 231
           RK+ RK++++ E+K E+++ EK   KKK +   KK K    E KK 
Sbjct: 411 RKKLRKKQRKAEKKAEKEEAEKAAAKKKAEAAAKKAKGPDGETKKV 456

This domain family is found in eukaryotes, and is approximately 40 amino acids in length. The family is found in association with pfam07719, pfam00515. There is a single completely conserved residue L that may be functionally important. NARP1 is the mammalian homologue of a yeast N-terminal acetyltransferase that regulates entry into the G(0) phase of the cell cycle. Length = 516

>gnl|CDD|214395 CHL00204, ycf1, Ycf1; Provisional

 Score = 43.2 bits (102), Expect = 1e-04
 Identities = 19/82 (23%), Positives = 39/82 (47%), Gaps = 2/82 (2%)

Query: 177  KKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKK 236
            KK  +K++      ++K  E E   ++++E   + + E  KEKK   +     ++K  ++
Sbjct: 1500 KKINQKKKGFIPSNEKKSIEIENRNQEEKEPAGQGELESDKEKKGNLESVLSNQEKNIEE 1559

Query: 237  E--KKKKKKEKKKKKEEKKKEK 256
            +  +   KK K KK+ +   E 
Sbjct: 1560 DYAESDIKKRKNKKQYKSNTEA 1581

Length = 1832

>gnl|CDD|236545 PRK09510, tolA, cell envelope integrity inner membrane protein TolA; Provisional

 Score = 42.5 bits (100), Expect = 1e-04
 Identities = 25/94 (26%), Positives = 41/94 (43%)

Query: 177 KKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKK 236
           K +   + +R     +K   E K++ + E  KK   + KKK + +   K   + KKK + 
Sbjct: 146 KAKAEAEAKRAAAAAKKAAAEAKKKAEAEAAKKAAAEAKKKAEAEAAAKAAAEAKKKAEA 205

Query: 237 EKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKD 270
           E KKK   + KKK   + +    K   E K   +
Sbjct: 206 EAKKKAAAEAKKKAAAEAKAAAAKAAAEAKAAAE 239

Length = 387

>gnl|CDD|222581 pfam14181, YqfQ, YqfQ-like protein

 Score = 41.3 bits (97), Expect = 1e-04
 Identities = 23/72 (31%), Positives = 39/72 (54%), Gaps = 8/72 (11%)

Query: 190 RKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKK 249
           R+    ++E+EE ++E   + ++++  + K +         K+KKK+E  K K EK+K K
Sbjct: 89  RELSSSDDEEEETEEESTDETEQEDPPETKTES--------KEKKKREVPKPKTEKEKPK 140

Query: 250 EEKKKEKKKKKK 261
            E KK K  K K
Sbjct: 141 TEPKKPKPSKPK 152

The YqfQ-like protein family includes the B. subtilis YqfQ protein, also known as VrrA, which is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 146 and 237 amino acids in length. There are two conserved sequence motifs: QYGP and PKLY. Length = 155

>gnl|CDD|240402 PTZ00399, PTZ00399, cysteinyl-tRNA-synthetase; Provisional

 Score = 43.1 bits (102), Expect = 1e-04
 Identities = 26/98 (26%), Positives = 52/98 (53%), Gaps = 14/98 (14%)

Query: 177 KKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEK-KKKEKK---------- 225
           ++E+ ++   K +++ +K ++++E++KKE +K EK K    E  K++E K          
Sbjct: 554 QREKEEKEALKEQKRLRKLKKQEEKKKKELEKLEKAKIPPAEFFKRQEDKYSAFDETGLP 613

Query: 226 -KEKKKKKKKKKEKKK--KKKEKKKKKEEKKKEKKKKK 260
             +   ++  KKE+KK  K+ +K+ K  E+   K  K 
Sbjct: 614 THDADGEEISKKERKKLSKEYDKQAKLHEEYLAKGGKS 651

Length = 651

>gnl|CDD|219868 pfam08496, Peptidase_S49_N, Peptidase family S49 N-terminal

 Score = 41.4 bits (98), Expect = 1e-04
 Identities = 26/65 (40%), Positives = 35/65 (53%), Gaps = 8/65 (12%)

Query: 207 KKKEKKK--------EKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKKKEKKK 258
           KKK KK         E+ K+ K+  +     KK+ K  EK +KK EK K K EKKK KK+
Sbjct: 34  KKKGKKGELEITDLNEEYKDLKESLEAALLDKKELKAWEKAEKKAEKAKAKAEKKKAKKE 93

Query: 259 KKKKK 263
           + K +
Sbjct: 94  EPKPR 98

This domain is found to the N-terminus of bacterial signal peptidases of the S49 family (pfam01343). Length = 154

>gnl|CDD|219408 pfam07423, DUF1510, Protein of unknown function (DUF1510)

 Score = 42.0 bits (99), Expect = 1e-04
 Identities = 14/72 (19%), Positives = 42/72 (58%)

Query: 201 EEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKKKEKKKKK 260
            ++    ++E KK   +E  + E+ KE++K+    ++K+ K   +K+ +E +++ +++ +
Sbjct: 41  SDQAAADEQEAKKSDDQETAEIEEVKEEEKEAANSEDKEDKGDAEKEDEESEEENEEEDE 100

Query: 261 KKKEKKKKKDEG 272
           +  ++ +K+ E 
Sbjct: 101 ESSDENEKETEE 112

This family consists of several hypothetical bacterial proteins of around 200 residues in length. The function of this family is unknown. Length = 214

>gnl|CDD|219408 pfam07423, DUF1510, Protein of unknown function (DUF1510)

 Score = 41.6 bits (98), Expect = 1e-04
 Identities = 15/76 (19%), Positives = 45/76 (59%)

Query: 193 KKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEK 252
              ++   +E++ +K  +++  + +E K++EK+    + K+ K + +K+ +E +++ EE+
Sbjct: 39  SPSDQAAADEQEAKKSDDQETAEIEEVKEEEKEAANSEDKEDKGDAEKEDEESEEENEEE 98

Query: 253 KKEKKKKKKKKEKKKK 268
            +E   + +K+ ++K 
Sbjct: 99  DEESSDENEKETEEKT 114

This family consists of several hypothetical bacterial proteins of around 200 residues in length. The function of this family is unknown. Length = 214

>gnl|CDD|217756 pfam03839, Sec62, Translocation protein Sec62

 Score = 41.7 bits (98), Expect = 1e-04
 Identities = 21/62 (33%), Positives = 32/62 (51%)

Query: 178 KERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKE 237
            E  K +  K K   +   +   ++K  EK K   K +  E+ KK   +EKK++KKK K+
Sbjct: 16  LESEKYKANKDKGNPEIYNKINSQDKAIEKFKLLIKAQMAERVKKLHSQEKKEEKKKPKK 75

Query: 238 KK 239
           KK
Sbjct: 76  KK 77

Length = 217

>gnl|CDD|219563 pfam07767, Nop53, Nop53 (60S ribosomal biogenesis)

 Score = 42.8 bits (101), Expect = 1e-04
 Identities = 25/78 (32%), Positives = 50/78 (64%)

Query: 177 KKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKK 236
              +  + +RK K +R KE+  KE E++ +++K+ KK+  +  + KE  KE  +K+K + 
Sbjct: 268 PINKPVRPKRKTKAQRNKEKRRKELEREAKEEKQLKKKLAQLARLKEIAKEVAQKEKARA 327

Query: 237 EKKKKKKEKKKKKEEKKK 254
            KK+++KE+ +KK+ K++
Sbjct: 328 RKKEQRKERGEKKKLKRR 345

This nucleolar family of proteins are involved in 60S ribosomal biogenesis. They are specifically involved in the processing beyond the 27S stage of 25S rRNA maturation. This family contains sequences that bear similarity to the glioma tumour suppressor candidate region gene 2 protein (p60). This protein has been found to interact with herpes simplex type 1 regulatory proteins. Length = 387

>gnl|CDD|218734 pfam05758, Ycf1, Ycf1

 Score = 43.1 bits (102), Expect = 1e-04
 Identities = 17/70 (24%), Positives = 35/70 (50%)

Query: 187 KRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKK 246
           K K   + EE E+E + + E   E K  K++++   E+      ++K+  +K +   + +
Sbjct: 225 KLKETSETEEREEETDVEIETTSETKGTKQEQEGSTEEDPSLFSEEKEDPDKTEDLDKLE 284

Query: 247 KKKEEKKKEK 256
             KE+K +E 
Sbjct: 285 ILKEKKDEEL 294

The chloroplast genomes of most higher plants contain two giant open reading frames designated ycf1 and ycf2. Although the function of Ycf1 is unknown, it is known to be an essential gene. Length = 832

>gnl|CDD|218734 pfam05758, Ycf1, Ycf1

 Score = 42.7 bits (101), Expect = 1e-04
 Identities = 23/77 (29%), Positives = 36/77 (46%), Gaps = 2/77 (2%)

Query: 189 KRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKK 248
           K K   E EE+EEE   E   E   E K  K+++E   E+      ++++   K E   K
Sbjct: 225 KLKETSETEEREEETDVE--IETTSETKGTKQEQEGSTEEDPSLFSEEKEDPDKTEDLDK 282

Query: 249 KEEKKKEKKKKKKKKEK 265
            E  K++K ++    EK
Sbjct: 283 LEILKEKKDEELFWFEK 299

The chloroplast genomes of most higher plants contain two giant open reading frames designated ycf1 and ycf2. Although the function of Ycf1 is unknown, it is known to be an essential gene. Length = 832

>gnl|CDD|236048 PRK07561, PRK07561, DNA topoisomerase I subunit omega; Validated

 Score = 42.9 bits (102), Expect = 1e-04
 Identities = 9/45 (20%), Positives = 17/45 (37%)

Query: 204 KEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKK 248
             EK ++ +       K    KK   K  +K K++    ++  K 
Sbjct: 814 LAEKPEKLRYLADAPAKDPAGKKAAVKFSRKTKQQYVASEKDGKA 858

Length = 859

>gnl|CDD|222636 pfam14265, DUF4355, Domain of unknown function (DUF4355)

 Score = 40.3 bits (95), Expect = 1e-04
 Identities = 22/76 (28%), Positives = 44/76 (57%)

Query: 195 EEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKKK 254
           E EE++    +E  K   KEK K +KK+E+KK + +K  K   ++K + E +K ++E ++
Sbjct: 1   EPEEEKTFTDKEVDKAIAKEKAKWEKKQEEKKSEAEKLAKMSAEEKAEYELEKLEKELEE 60

Query: 255 EKKKKKKKKEKKKKKD 270
            + +  +++ K + K 
Sbjct: 61  LEAELARRELKAEAKK 76

This family of proteins is found in bacteria and viruses. Proteins in this family are typically between 180 and 214 amino acids in length. Length = 125

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 42.4 bits (99), Expect = 2e-04
 Identities = 31/102 (30%), Positives = 61/102 (59%)

Query: 170  EYGYKGGKKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKK 229
            E   K  + ++  + ++K    +K EE +K +E K+ ++ +K  E KK ++KK+  + KK
Sbjct: 1494 EAKKKADEAKKAAEAKKKADEAKKAEEAKKADEAKKAEEAKKADEAKKAEEKKKADELKK 1553

Query: 230  KKKKKKKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDE 271
             ++ KK E+KKK +E KK +E+K    +K ++ K+ ++ + E
Sbjct: 1554 AEELKKAEEKKKAEEAKKAEEDKNMALRKAEEAKKAEEARIE 1595

Length = 2084

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 42.1 bits (98), Expect = 2e-04
 Identities = 39/105 (37%), Positives = 62/105 (59%), Gaps = 9/105 (8%)

Query: 178  KERRKQRRRKRKRKRKKEEEEK---EEEKKEEKKKEKKKEKKKEKKKKE---KKKEKKKK 231
            K++ ++ ++K    +K  E +K   E +K EE KK  + +K +E KK +   K +EKKK 
Sbjct: 1489 KKKAEEAKKKADEAKKAAEAKKKADEAKKAEEAKKADEAKKAEEAKKADEAKKAEEKKKA 1548

Query: 232  KKKKKEKKKKKKEKKKKKEEKKKEKKKKK---KKKEKKKKKDEGR 273
             + KK ++ KK E+KKK EE KK ++ K    +K E+ KK +E R
Sbjct: 1549 DELKKAEELKKAEEKKKAEEAKKAEEDKNMALRKAEEAKKAEEAR 1593

Length = 2084

>gnl|CDD|219746 pfam08208, RNA_polI_A34, DNA-directed RNA polymerase I subunit RPA34

 Score = 41.2 bits (97), Expect = 2e-04
 Identities = 25/74 (33%), Positives = 46/74 (62%)

Query: 201 EEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKKKEKKKKK 260
                  +   + E  +++   + +KE + ++++KKEKKKKK+ KK+KKE+K K++K  +
Sbjct: 120 APDGPPSELGSESETSEKETTAKVEKEAEVEEEEKKEKKKKKEVKKEKKEKKDKKEKMVE 179

Query: 261 KKKEKKKKKDEGRR 274
            K  KKKKK + ++
Sbjct: 180 PKGSKKKKKKKKKK 193

5. This is a family of proteins conserved from yeasts to human. Subunit A34.5 of RNA polymerase I is a non-essential subunit which is thought to help Pol I overcome topological constraints imposed on ribosomal DNA during the process of transcription. Length = 193

>gnl|CDD|217051 pfam02463, SMC_N, RecF/RecN/SMC N terminal domain

 Score = 42.3 bits (99), Expect = 2e-04
 Identities = 21/103 (20%), Positives = 50/103 (48%)

Query: 169 LEYGYKGGKKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEK 228
                K  KKER K+   + +   +   + +E + +E K KE+ K+  +  + KEK + +
Sbjct: 164 AGSREKRKKKERLKKLIEETENLAELIIDLEELKLQELKLKEQAKKALEYYQLKEKLELE 223

Query: 229 KKKKKKKKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDE 271
           ++        K  ++     +E  + E+++ +  K++ +K++E
Sbjct: 224 EENLLYLDYLKLNEERIDLLQELLRDEQEEIESSKQELEKEEE 266

This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination. Length = 1162

>gnl|CDD|217051 pfam02463, SMC_N, RecF/RecN/SMC N terminal domain

 Score = 42.3 bits (99), Expect = 2e-04
 Identities = 30/100 (30%), Positives = 61/100 (61%), Gaps = 1/100 (1%)

Query: 177 KKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEK-KKEKKKKEKKKEKKKKKKKK 235
           K +  ++  +K +++ KKE+EE EE +KE K+ E K+E  ++E+++ EK +EK ++ +++
Sbjct: 316 KLKESEKELKKLEKELKKEKEEIEELEKELKELEIKREAEEEEEEQLEKLQEKLEQLEEE 375

Query: 236 KEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDEGRRR 275
              KKK + ++     K KE++ + K +E+K+ K      
Sbjct: 376 LLAKKKLESERLSSAAKLKEEELELKNEEEKEAKLLLELS 415

This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination. Length = 1162

>gnl|CDD|217051 pfam02463, SMC_N, RecF/RecN/SMC N terminal domain

 Score = 42.3 bits (99), Expect = 2e-04
 Identities = 25/94 (26%), Positives = 61/94 (64%)

Query: 177 KKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKK 236
            K   + +  ++K K K+EEEEK   KKEE+++EK +   KEK+  E++++ +K K +++
Sbjct: 733 DKINEELKLLEQKIKEKEEEEEKSRLKKEEEEEEKSELSLKEKELAEEEEKTEKLKVEEE 792

Query: 237 EKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKD 270
           +++K K ++++ +  +++ K++ +  +E++   +
Sbjct: 793 KEEKLKAQEEELRALEEELKEEAELLEEEQLLIE 826

This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination. Length = 1162

>gnl|CDD|217051 pfam02463, SMC_N, RecF/RecN/SMC N terminal domain

 Score = 42.3 bits (99), Expect = 2e-04
 Identities = 27/94 (28%), Positives = 63/94 (67%)

Query: 177 KKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKK 236
           KK + ++ +   K + + + E  + E+++   +EK KE +KE KK EK+ +K+K++ ++ 
Sbjct: 282 KKLQEEELKLLAKEEEELKSELLKLERRKVDDEEKLKESEKELKKLEKELKKEKEEIEEL 341

Query: 237 EKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKD 270
           EK+ K+ E K++ EE+++E+ +K ++K ++ +++
Sbjct: 342 EKELKELEIKREAEEEEEEQLEKLQEKLEQLEEE 375

This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination. Length = 1162

>gnl|CDD|221641 pfam12569, NARP1, NMDA receptor-regulated protein 1

 Score = 42.6 bits (101), Expect = 2e-04
 Identities = 15/49 (30%), Positives = 29/49 (59%)

Query: 177 KKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKK 225
             ER+K R+++RK ++K E+EE E+   ++K +   K+ K    + +K 
Sbjct: 408 PAERKKLRKKQRKAEKKAEKEEAEKAAAKKKAEAAAKKAKGPDGETKKV 456

This domain family is found in eukaryotes, and is approximately 40 amino acids in length. The family is found in association with pfam07719, pfam00515. There is a single completely conserved residue L that may be functionally important. NARP1 is the mammalian homologue of a yeast N-terminal acetyltransferase that regulates entry into the G(0) phase of the cell cycle. Length = 516

>gnl|CDD|223880 COG0810, TonB, Periplasmic protein TonB, links inner and outer membranes [Cell envelope biogenesis, outer membrane]

 Score = 41.3 bits (97), Expect = 2e-04
 Identities = 16/75 (21%), Positives = 32/75 (42%)

Query: 196 EEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKKKE 255
                   K  +   ++ + + E  +++ K   + +   +    K K++ K +K+ KK +
Sbjct: 39  LAVFLLAAKVLEAPTEEPQPEPEPPEEQPKPPTEPETPPEPTPPKPKEKPKPEKKPKKPK 98

Query: 256 KKKKKKKKEKKKKKD 270
            K K K K K K K 
Sbjct: 99  PKPKPKPKPKPKVKP 113

Length = 244

>gnl|CDD|214661 smart00435, TOPEUc, DNA Topoisomerase I (eukaryota)

 Score = 42.0 bits (99), Expect = 2e-04
 Identities = 26/83 (31%), Positives = 51/83 (61%), Gaps = 1/83 (1%)

Query: 177 KKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKK 236
           +K +  + + KR +K     E   + K++ K K ++  +K + + KEKKKEKKK++KKKK
Sbjct: 284 EKIKALKYQLKRLKKMILLFEMISDLKRKLKSKFERDNEKLDAEVKEKKKEKKKEEKKKK 343

Query: 237 E-KKKKKKEKKKKKEEKKKEKKK 258
           + ++ +++ +K + +   KE+ K
Sbjct: 344 QIERLEERIEKLEVQATDKEENK 366

DNA Topoisomerase I (eukaryota), DNA topoisomerase V, Vaccina virus topoisomerase, Variola virus topoisomerase, Shope fibroma virus topoisomeras. Length = 391

>gnl|CDD|221952 pfam13166, AAA_13, AAA domain

 Score = 41.9 bits (99), Expect = 2e-04
 Identities = 21/90 (23%), Positives = 43/90 (47%)

Query: 176 GKKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKK 235
           G++    + + +  +K  K+ EEK E+ + E +K++++ +K + K  +K  +K  KK   
Sbjct: 87  GEENIEIEAQIEELKKELKKLEEKIEQLEAEIEKKEEELEKAKNKFLDKAWKKLAKKYDS 146

Query: 236 KEKKKKKKEKKKKKEEKKKEKKKKKKKKEK 265
              +  K    KK  ++K  K+ K      
Sbjct: 147 NLSEALKGLNYKKNFKEKLLKELKSVILNA 176

This family of domains contain a P-loop motif that is characteristic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins. This family includes the PrrC protein that is thought to be the active component of the anticodon nuclease. Length = 713

>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]

 Score = 42.8 bits (101), Expect = 2e-04
 Identities = 18/93 (19%), Positives = 49/93 (52%), Gaps = 1/93 (1%)

Query: 180 RRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKK-EKKKKKKKKKEK 238
             K+   + + +     E  EE + E ++ E++ E+ KEK +  K++ E+++   ++ E+
Sbjct: 292 ELKEEIEELEGEISLLRERLEELENELEELEERLEELKEKIEALKEELEERETLLEELEQ 351

Query: 239 KKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDE 271
              + E+ K++ E+K     ++ ++  +  ++E
Sbjct: 352 LLAELEEAKEELEEKLSALLEELEELFEALREE 384

Length = 1163

>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]

 Score = 42.4 bits (100), Expect = 2e-04
 Identities = 19/98 (19%), Positives = 51/98 (52%)

Query: 177 KKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKK 236
           ++E  + +    + K + EE E E     E+ +E + E ++ +++ E+ KEK +  K++ 
Sbjct: 280 REELEELQEELLELKEEIEELEGEISLLRERLEELENELEELEERLEELKEKIEALKEEL 339

Query: 237 EKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDEGRR 274
           E+++   E+ ++   + +E K++ ++K     ++    
Sbjct: 340 EERETLLEELEQLLAELEEAKEELEEKLSALLEELEEL 377

Length = 1163

>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]

 Score = 42.4 bits (100), Expect = 2e-04
 Identities = 18/108 (16%), Positives = 60/108 (55%), Gaps = 2/108 (1%)

Query: 169 LEYGYKGGKKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEK 228
           LE      K +  ++   + + +  + EEE EE ++E ++ EK+ E+ K + ++ +++ +
Sbjct: 225 LELALLLAKLKELRKELEELEEELSRLEEELEELQEELEEAEKEIEELKSELEELREELE 284

Query: 229 KKKKK--KKKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDEGRR 274
           + +++  + KE+ ++ + +     E+ +E + + ++ E++ ++ + + 
Sbjct: 285 ELQEELLELKEEIEELEGEISLLRERLEELENELEELEERLEELKEKI 332

Length = 1163

>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]

 Score = 42.4 bits (100), Expect = 2e-04
 Identities = 15/103 (14%), Positives = 51/103 (49%), Gaps = 4/103 (3%)

Query: 177 KKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKK 236
           ++    + + +  ++  +E E   EE ++   + ++ +++ E+K     +E ++  +  +
Sbjct: 323 ERLEELKEKIEALKEELEERETLLEELEQLLAELEEAKEELEEKLSALLEELEELFEALR 382

Query: 237 EK----KKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDEGRRR 275
           E+    + +  E + + EE K+E +  +++ E+  ++ E  + 
Sbjct: 383 EELAELEAELAEIRNELEELKREIESLEERLERLSERLEDLKE 425

Length = 1163

>gnl|CDD|236545 PRK09510, tolA, cell envelope integrity inner membrane protein TolA; Provisional

 Score = 42.1 bits (99), Expect = 2e-04
 Identities = 24/97 (24%), Positives = 40/97 (41%), Gaps = 3/97 (3%)

Query: 177 KKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKK---EKKKEKKKEKKKKEKKKEKKKKKK 233
           K     +++ + +  +K   E K++ + E   K   E KK+ + E KKK   + KKK   
Sbjct: 162 KAAAEAKKKAEAEAAKKAAAEAKKKAEAEAAAKAAAEAKKKAEAEAKKKAAAEAKKKAAA 221

Query: 234 KKKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKD 270
           + K    K   + K   EK    K  +K    K   +
Sbjct: 222 EAKAAAAKAAAEAKAAAEKAAAAKAAEKAAAAKAAAE 258

Length = 387

>gnl|CDD|237035 PRK12280, rplW, 50S ribosomal protein L23; Reviewed

 Score = 40.9 bits (96), Expect = 2e-04
 Identities = 23/66 (34%), Positives = 42/66 (63%)

Query: 195 EEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKKK 254
           EE EKE+++  ++ +EK+  K K++KK++K+K+  +K  KKK  K  K   KK  ++   
Sbjct: 93  EESEKEQKEVSKETEEKEAIKAKKEKKEKKEKKVAEKLAKKKSTKTTKNTTKKATKKTTT 152

Query: 255 EKKKKK 260
           +K++ K
Sbjct: 153 KKEEGK 158

Length = 158

>gnl|CDD|222581 pfam14181, YqfQ, YqfQ-like protein

 Score = 40.5 bits (95), Expect = 2e-04
 Identities = 20/63 (31%), Positives = 36/63 (57%)

Query: 206 EKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKKKEKKKKKKKKEK 265
           E      +E++ E++  ++ +++   + K + K+KKK+E  K K EK+K K + KK K  
Sbjct: 90  ELSSSDDEEEETEEESTDETEQEDPPETKTESKEKKKREVPKPKTEKEKPKTEPKKPKPS 149

Query: 266 KKK 268
           K K
Sbjct: 150 KPK 152

The YqfQ-like protein family includes the B. subtilis YqfQ protein, also known as VrrA, which is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 146 and 237 amino acids in length. There are two conserved sequence motifs: QYGP and PKLY. Length = 155

>gnl|CDD|177089 CHL00189, infB, translation initiation factor 2; Provisional

 Score = 42.1 bits (99), Expect = 2e-04
 Identities = 24/86 (27%), Positives = 39/86 (45%), Gaps = 1/86 (1%)

Query: 177 KKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEK-KKKKKKK 235
           KK + KQ+++ +K+    ++ +   + K   K+          +K + K EK KKK    
Sbjct: 73  KKTKLKQKKKIKKKLHIDDDYDNFFDSKNNSKQFAGPLAISLMRKPKPKTEKLKKKITVN 132

Query: 236 KEKKKKKKEKKKKKEEKKKEKKKKKK 261
           K   KKKK+    K+E  K    K K
Sbjct: 133 KSTNKKKKKVLSSKDELIKYDNNKPK 158

Length = 742

>gnl|CDD|219868 pfam08496, Peptidase_S49_N, Peptidase family S49 N-terminal

 Score = 41.0 bits (97), Expect = 2e-04
 Identities = 25/66 (37%), Positives = 35/66 (53%), Gaps = 9/66 (13%)

Query: 211 KKKEKKKE-------KKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKKKEKKKKKKKK 263
           KKK KK E       ++ K+ K+  +     KKE K    EK +KK EK K K +KKK K
Sbjct: 34  KKKGKKGELEITDLNEEYKDLKESLEAALLDKKELKAW--EKAEKKAEKAKAKAEKKKAK 91

Query: 264 EKKKKK 269
           +++ K 
Sbjct: 92  KEEPKP 97

This domain is found to the N-terminus of bacterial signal peptidases of the S49 family (pfam01343). Length = 154

>gnl|CDD|219868 pfam08496, Peptidase_S49_N, Peptidase family S49 N-terminal

 Score = 40.6 bits (96), Expect = 2e-04
 Identities = 21/66 (31%), Positives = 37/66 (56%)

Query: 189 KRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKK 248
            +K+K ++ E E     E+ K+ K+  +     K++ K  +K +KK ++ K K ++KK K
Sbjct: 32  AQKKKGKKGELEITDLNEEYKDLKESLEAALLDKKELKAWEKAEKKAEKAKAKAEKKKAK 91

Query: 249 KEEKKK 254
           KEE K 
Sbjct: 92  KEEPKP 97

This domain is found to the N-terminus of bacterial signal peptidases of the S49 family (pfam01343). Length = 154

>gnl|CDD|219408 pfam07423, DUF1510, Protein of unknown function (DUF1510)

 Score = 41.3 bits (97), Expect = 2e-04
 Identities = 14/80 (17%), Positives = 48/80 (60%)

Query: 187 KRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKK 246
             +    ++E +K ++++  + +E K+E+K+    ++K+ +   +K+ ++ +++ ++E +
Sbjct: 41  SDQAAADEQEAKKSDDQETAEIEEVKEEEKEAANSEDKEDKGDAEKEDEESEEENEEEDE 100

Query: 247 KKKEEKKKEKKKKKKKKEKK 266
           +  +E +KE ++K +   +K
Sbjct: 101 ESSDENEKETEEKTESNVEK 120

This family consists of several hypothetical bacterial proteins of around 200 residues in length. The function of this family is unknown. Length = 214

>gnl|CDD|188306 TIGR03319, RNase_Y, ribonuclease Y

 Score = 42.2 bits (100), Expect = 2e-04
 Identities = 22/94 (23%), Positives = 54/94 (57%), Gaps = 2/94 (2%)

Query: 178 KERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKE 237
           +  +K+   + K +  K   E E E KE + + ++ E++    ++E+  ++K +   KKE
Sbjct: 46  ETLKKEALLEAKEEVHKLRAELERELKERRNELQRLERR--LLQREETLDRKMESLDKKE 103

Query: 238 KKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDE 271
           +  +KKEK+   +EK  ++K+++ ++   ++++E
Sbjct: 104 ENLEKKEKELSNKEKNLDEKEEELEELIAEQREE 137

Members of this family are RNase Y, an endoribonuclease. The member from Bacillus subtilis, YmdA, has been shown to be involved in turnover of yitJ riboswitch [Transcription, Degradation of RNA]. Length = 514

>gnl|CDD|188306 TIGR03319, RNase_Y, ribonuclease Y

 Score = 41.8 bits (99), Expect = 2e-04
 Identities = 24/92 (26%), Positives = 55/92 (59%), Gaps = 3/92 (3%)

Query: 177 KKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEK-KKKEKKKEKKKKKKKK 235
           KKE   + + +  + R + E E +E + E ++ E++  +++E   +K +  +KK++  +K
Sbjct: 49  KKEALLEAKEEVHKLRAELERELKERRNELQRLERRLLQREETLDRKMESLDKKEENLEK 108

Query: 236 KEKKKKKKEK--KKKKEEKKKEKKKKKKKKEK 265
           KEK+   KEK   +K+EE ++   +++++ E+
Sbjct: 109 KEKELSNKEKNLDEKEEELEELIAEQREELER 140

Members of this family are RNase Y, an endoribonuclease. The member from Bacillus subtilis, YmdA, has been shown to be involved in turnover of yitJ riboswitch [Transcription, Degradation of RNA]. Length = 514

>gnl|CDD|218177 pfam04615, Utp14, Utp14 protein

 Score = 42.4 bits (100), Expect = 2e-04
 Identities = 23/95 (24%), Positives = 52/95 (54%)

Query: 177 KKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKK 236
             E  + RR     +   EEE +E  KK   +++   E  +++ + +K K++ K + K+K
Sbjct: 391 DAEIEELRRELEGEEESDEEENEEPSKKNVGRRKFGPENGEKEAESKKLKKENKNEFKEK 450

Query: 237 EKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDE 271
           ++  +++E + ++E K ++   K  K+ +K +K+E
Sbjct: 451 KESDEEEELEDEEEAKVEKVANKLLKRSEKAQKEE 485

This protein is found to be part of a large ribonucleoprotein complex containing the U3 snoRNA. Depletion of the Utp proteins impedes production of the 18S rRNA, indicating that they are part of the active pre-rRNA processing complex. This large RNP complex has been termed the small subunit (SSU) processome. Length = 728

>gnl|CDD|150884 pfam10278, Med19, Mediator of RNA pol II transcription subunit 19

 Score = 41.0 bits (96), Expect = 2e-04
 Identities = 24/62 (38%), Positives = 38/62 (61%)

Query: 208 KKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKK 267
             +  K+K K K KK + ++   ++     +  K  EKK KK++ + +K++KKKKKEKKK
Sbjct: 105 HIQPPKKKHKHKHKKHRTQDPLPEETPSDSEGLKGHEKKHKKKKHEDDKERKKKKKEKKK 164

Query: 268 KK 269
           KK
Sbjct: 165 KK 166

Med19 represents a family of conserved proteins which are members of the multi-protein co-activator Mediator complex. Mediator is required for activation of RNA polymerase II transcription by DNA binding transactivators. Length = 178

>gnl|CDD|218734 pfam05758, Ycf1, Ycf1

 Score = 42.7 bits (101), Expect = 2e-04
 Identities = 21/75 (28%), Positives = 37/75 (49%), Gaps = 3/75 (4%)

Query: 192 RKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEE 251
            KK +E  E E++EE   E   E +   + K  K+E++   ++      ++KE   K E+
Sbjct: 223 TKKLKETSETEEREE---ETDVEIETTSETKGTKQEQEGSTEEDPSLFSEEKEDPDKTED 279

Query: 252 KKKEKKKKKKKKEKK 266
             K +  K+KK E+ 
Sbjct: 280 LDKLEILKEKKDEEL 294

The chloroplast genomes of most higher plants contain two giant open reading frames designated ycf1 and ycf2. Although the function of Ycf1 is unknown, it is known to be an essential gene. Length = 832

>gnl|CDD|236048 PRK07561, PRK07561, DNA topoisomerase I subunit omega; Validated

 Score = 42.5 bits (101), Expect = 2e-04
 Identities = 11/45 (24%), Positives = 18/45 (40%)

Query: 209 KEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKK 253
             +K EK +       K    KK   K  +K K++    +K+ K 
Sbjct: 814 LAEKPEKLRYLADAPAKDPAGKKAAVKFSRKTKQQYVASEKDGKA 858

Length = 859

>gnl|CDD|236048 PRK07561, PRK07561, DNA topoisomerase I subunit omega; Validated

 Score = 42.1 bits (100), Expect = 2e-04
 Identities = 13/56 (23%), Positives = 20/56 (35%)

Query: 205 EEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKKKEKKKKK 260
                E+  E   EK +K +       K    +K   K  +K K++    EK  K 
Sbjct: 803 RAPTVEEALELLAEKPEKLRYLADAPAKDPAGKKAAVKFSRKTKQQYVASEKDGKA 858

Length = 859

>gnl|CDD|236048 PRK07561, PRK07561, DNA topoisomerase I subunit omega; Validated

 Score = 42.1 bits (100), Expect = 2e-04
 Identities = 9/42 (21%), Positives = 16/42 (38%)

Query: 221 KKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKKKEKKKKKKK 262
           K EK +       K    KK   +  +K +++    +K  K 
Sbjct: 817 KPEKLRYLADAPAKDPAGKKAAVKFSRKTKQQYVASEKDGKA 858

Length = 859

>gnl|CDD|236978 PRK11778, PRK11778, putative inner membrane peptidase; Provisional

 Score = 42.1 bits (100), Expect = 2e-04
 Identities = 21/62 (33%), Positives = 34/62 (54%), Gaps = 1/62 (1%)

Query: 209 KEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKK-KEEKKKEKKKKKKKKEKKK 267
            ++KK +K E +     ++ K+ K++ K     KKE K   K +KKKEK++ K  K K K
Sbjct: 30  AQRKKSQKGELEVTNLNEQYKEMKEELKAALLDKKELKAWHKAQKKKEKQEAKAAKAKSK 89

Query: 268 KK 269
            +
Sbjct: 90  PR 91

Length = 330

>gnl|CDD|236978 PRK11778, PRK11778, putative inner membrane peptidase; Provisional

 Score = 42.1 bits (100), Expect = 2e-04
 Identities = 20/62 (32%), Positives = 34/62 (54%), Gaps = 5/62 (8%)

Query: 186 RKRKRKRKKEEE-----EKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKK 240
            +RK+ +K E E     E+ +E KEE K     +K+ +   K +KK++K++ K  K K K
Sbjct: 30  AQRKKSQKGELEVTNLNEQYKEMKEELKAALLDKKELKAWHKAQKKKEKQEAKAAKAKSK 89

Query: 241 KK 242
            +
Sbjct: 90  PR 91

Length = 330

>gnl|CDD|220371 pfam09736, Bud13, Pre-mRNA-splicing factor of RES complex

 Score = 40.4 bits (95), Expect = 2e-04
 Identities = 23/74 (31%), Positives = 50/74 (67%)

Query: 191 KRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKE 250
           +    EE++EE+++E+++KE+K+EK+KE  K   +KE+++K+ ++ EK K K   +   +
Sbjct: 10  RIIDIEEKREEKEREKEEKERKEEKEKEWGKGLVQKEEREKRLEELEKAKNKPLARYADD 69

Query: 251 EKKKEKKKKKKKKE 264
           E   E+ K++++ +
Sbjct: 70  EDYDEELKEQERWD 83

This entry is characterized by proteins with alternating conserved and low-complexity regions. Bud13 together with Snu17p and a newly identified factor, Pml1p/Ylr016c, form a novel trimeric complex. called The RES complex, pre-mRNA retention and splicing complex. Subunits of this complex are not essential for viability of yeasts but they are required for efficient splicing in vitro and in vivo. Furthermore, inactivation of this complex causes pre-mRNA leakage from the nucleus. Bud13 contains a unique, phylogenetically conserved C-terminal region of unknown function. Length = 141

>gnl|CDD|235971 PRK07219, PRK07219, DNA topoisomerase I; Validated

 Score = 42.3 bits (100), Expect = 2e-04
 Identities = 12/77 (15%), Positives = 24/77 (31%)

Query: 187 KRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKK 246
           + K     E       K    +K+KK+++ K + +  K    K  +K K    +   +  
Sbjct: 745 RVKGGFGDELGCCNNPKCNYTEKQKKEKESKSELEALKGVGAKTAEKLKDAGVETVTDLT 804

Query: 247 KKKEEKKKEKKKKKKKK 263
               +    K       
Sbjct: 805 AADPDAVAAKVDGVSAD 821

Length = 822

>gnl|CDD|235971 PRK07219, PRK07219, DNA topoisomerase I; Validated

 Score = 42.3 bits (100), Expect = 2e-04
 Identities = 12/58 (20%), Positives = 19/58 (32%)

Query: 189 KRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKK 246
             K+KKE+E K E +  +    K  EK K+   +               K       +
Sbjct: 765 TEKQKKEKESKSELEALKGVGAKTAEKLKDAGVETVTDLTAADPDAVAAKVDGVSADR 822

Length = 822

>gnl|CDD|206039 pfam13868, Trichoplein, Tumour suppressor, Mitostatin

 Score = 41.8 bits (99), Expect = 2e-04
 Identities = 24/102 (23%), Positives = 69/102 (67%), Gaps = 12/102 (11%)

Query: 178 KERRKQRRRKRKRKRK------------KEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKK 225
           +ER K+R+ + + + +            +EE+E E ++K EK+K+ ++E  +  +++ ++
Sbjct: 81  EEREKRRQEEYEERLQEREQMDEIIERIQEEDEAEAQEKREKQKKLREEIDEFNEERIER 140

Query: 226 KEKKKKKKKKKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKK 267
           KE++K++++++E K  + +++K + E+++E +++++K+EK++
Sbjct: 141 KEEEKEREREEELKILEYQREKAEREEEREAERRERKEEKER 182

Trichoplein or mitostatin, was first defined as a meiosis-specific nuclear structural protein. It has since been linked with mitochondrial movement. It is associated with the mitochondrial outer membrane, and over-expression leads to reduction in mitochondrial motility whereas lack of it enhances mitochondrial movement. The activity appears to be mediated through binding the mitochondria to the actin intermediate filaments (IFs). Length = 349

>gnl|CDD|224212 COG1293, COG1293, Predicted RNA-binding protein homologous to eukaryotic snRNP [Transcription]

 Score = 42.0 bits (99), Expect = 2e-04
 Identities = 28/110 (25%), Positives = 46/110 (41%), Gaps = 11/110 (10%)

Query: 174 KGGKKERRKQRR------RKRKRKRKKEEEEKEEEKKEEKKKEKKKE----KKKEKKKKE 223
           + G K  R          +    K K   E  +   K+ KK +  K     +  E K+  
Sbjct: 334 EEGLKSVRLADFYGNEEIKIELDKSKTPSENAQRYFKKYKKLKGAKVNLDRQLSELKEAI 393

Query: 224 KKKEKKKKKKKKKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDEGR 273
              E  K   +K E KK  +E +++  E+    K KKKK++KK+  ++ R
Sbjct: 394 AYYESAKTALEKAEGKKAIEEIREELIEEG-LLKSKKKKRKKKEWFEKFR 442

Length = 564

>gnl|CDD|226138 COG3611, DnaB, Replication initiation/membrane attachment protein [DNA replication, recombination, and repair]

 Score = 42.0 bits (99), Expect = 2e-04
 Identities = 22/75 (29%), Positives = 38/75 (50%), Gaps = 2/75 (2%)

Query: 189 KRKRKKEEEE--KEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKK 246
            RK+ K   E  KE  K++E    KK+    ++K+   K    + KK   ++++ K E  
Sbjct: 343 ARKKVKTAYEAIKENRKRKELALAKKQSSTTKRKENLPKWSNPEYKKTTSQEEQAKLEFI 402

Query: 247 KKKEEKKKEKKKKKK 261
           K +E K+ E  K+K+
Sbjct: 403 KLEELKRLENGKQKR 417

Length = 417

>gnl|CDD|227519 COG5192, BMS1, GTP-binding protein required for 40S ribosome biogenesis [Translation, ribosomal structure and biogenesis]

 Score = 42.4 bits (99), Expect = 2e-04
 Identities = 18/60 (30%), Positives = 38/60 (63%)

Query: 182  KQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKK 241
            K R  K + K ++E+E  E  ++ ++++  KKEK++E++ ++   +  K+  KK+ KKK+
Sbjct: 1018 KDRIVKERIKDQEEKERMESLQRAKEEEIGKKEKEREQRIRKTIHDNYKEMAKKRLKKKR 1077

Length = 1077

>gnl|CDD|227492 COG5163, NOP7, Protein required for biogenesis of the 60S ribosomal subunit [Translation, ribosomal structure and biogenesis]

 Score = 42.0 bits (98), Expect = 2e-04
 Identities = 27/66 (40%), Positives = 39/66 (59%), Gaps = 2/66 (3%)

Query: 183 QRRRKRKRKRKKEEEEKEEEKKEEKKKEKK--KEKKKEKKKKEKKKEKKKKKKKKKEKKK 240
            + + +KRK  +EEEEK+ +      K+KK  K+ K    KKE++ E  KKKKK+  K+K
Sbjct: 526 NKSKNKKRKVDEEEEEKKLKMIMMSNKQKKLYKKMKYSNAKKEEQAENLKKKKKQIAKQK 585

Query: 241 KKKEKK 246
           K   KK
Sbjct: 586 KLDSKK 591

Length = 591

>gnl|CDD|225606 COG3064, TolA, Membrane protein involved in colicin uptake [Cell envelope biogenesis, outer membrane]

 Score = 41.9 bits (98), Expect = 2e-04
 Identities = 24/95 (25%), Positives = 42/95 (44%)

Query: 177 KKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKK 236
           K     +++ +   K  +E + K E    +KK E + +   EK K E + + K +KK + 
Sbjct: 164 KAAAEAKKKAEEAAKAAEEAKAKAEAAAAKKKAEAEAKAAAEKAKAEAEAKAKAEKKAEA 223

Query: 237 EKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDE 271
             ++K   +KKK   K K  K     K  ++K   
Sbjct: 224 AAEEKAAAEKKKAAAKAKADKAAAAAKAAERKAAA 258

Length = 387

>gnl|CDD|227352 COG5019, CDC3, Septin family protein [Cell division and chromosome partitioning / Cytoskeleton]

 Score = 41.5 bits (98), Expect = 2e-04
 Identities = 23/91 (25%), Positives = 50/91 (54%), Gaps = 1/91 (1%)

Query: 173 YKGGKKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKK 232
           Y+  + E+    +   +   K+  E +  E++ E KK K  EK +EK+K+ ++ E+   +
Sbjct: 284 YENYRTEKLSGLKNSGEPSLKEIHEARLNEEERELKK-KFTEKIREKEKRLEELEQNLIE 342

Query: 233 KKKKEKKKKKKEKKKKKEEKKKEKKKKKKKK 263
           ++K+   K ++ +KK ++ +K+ +K K  K 
Sbjct: 343 ERKELNSKLEEIQKKLEDLEKRLEKLKSNKS 373

Length = 373

>gnl|CDD|217927 pfam04147, Nop14, Nop14-like family

 Score = 41.9 bits (99), Expect = 2e-04
 Identities = 22/96 (22%), Positives = 49/96 (51%), Gaps = 8/96 (8%)

Query: 182 KQRRRKRKRKRKKEEEEKEEEKKEEKKKE-------KKKEKKKEKKKKEKKKEKKKKKKK 234
           K +  K +R++ KEE+E   E+ ++  K+        K   K     +EK  E  ++ ++
Sbjct: 185 KSKFYKAERQKAKEEDEDLREELDDDFKDLMSLLRTVKPPPKPPMTPEEKDDEYDQRVRE 244

Query: 235 -KKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKK 269
              +++ +  ++ K +EE  KE+ ++ KK E ++ +
Sbjct: 245 LTFDRRAQPTDRTKTEEELAKEEAERLKKLEAERLR 280

Emg1 and Nop14 are novel proteins whose interaction is required for the maturation of the 18S rRNA and for 40S ribosome production. Length = 809

>gnl|CDD|184900 PRK14907, rplD, 50S ribosomal protein L4; Provisional

 Score = 41.5 bits (97), Expect = 2e-04
 Identities = 26/77 (33%), Positives = 36/77 (46%)

Query: 193 KKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEK 252
           KK  ++K  E+K+   K+    K+  K KK  K    K  KK  + KK K  K   K+  
Sbjct: 5   KKTTKKKTTEEKKPAAKKATTSKETAKTKKTAKTTSTKAAKKAAKVKKTKSVKTTTKKVT 64

Query: 253 KKEKKKKKKKKEKKKKK 269
            K +K +  KKE   KK
Sbjct: 65  VKFEKTESVKKESVAKK 81

Length = 295

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 42.1 bits (98), Expect = 3e-04
 Identities = 30/101 (29%), Positives = 61/101 (60%)

Query: 174  KGGKKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKK 233
            K   + ++ + ++K    +K EE +K EEKK+ ++ +K +E K    +K ++ +K ++ +
Sbjct: 1534 KKADEAKKAEEKKKADELKKAEELKKAEEKKKAEEAKKAEEDKNMALRKAEEAKKAEEAR 1593

Query: 234  KKKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDEGRR 274
             ++  K  ++EKK K EE KK ++ K K +E KK ++E ++
Sbjct: 1594 IEEVMKLYEEEKKMKAEEAKKAEEAKIKAEELKKAEEEKKK 1634

Length = 2084

>gnl|CDD|220648 pfam10243, MIP-T3, Microtubule-binding protein MIP-T3

 Score = 41.4 bits (97), Expect = 3e-04
 Identities = 24/81 (29%), Positives = 48/81 (59%)

Query: 194 KEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKK 253
           + +   +E  K  +K   K    K K  KE K E  K+++K+KE+ K++K+KKK+K +++
Sbjct: 68  ESKLSSDEAVKRVEKGGSKGPAAKTKPAKEPKNESGKEEEKEKEQVKEEKKKKKEKPKEE 127

Query: 254 KEKKKKKKKKEKKKKKDEGRR 274
            + +K K++ ++K+   E  +
Sbjct: 128 PKDRKPKEEAKEKRPPKEKEK 148

This protein, which interacts with both microtubules and TRAF3 (tumour necrosis factor receptor-associated factor 3), is conserved from worms to humans. The N-terminal region is the microtubule binding domain and is well-conserved; the C-terminal 100 residues, also well-conserved, constitute the coiled-coil region which binds to TRAF3. The central region of the protein is rich in lysine and glutamic acid and carries KKE motifs which may also be necessary for tubulin-binding, but this region is the least well-conserved. Length = 506

>gnl|CDD|237177 PRK12704, PRK12704, phosphodiesterase; Provisional

 Score = 41.7 bits (99), Expect = 3e-04
 Identities = 27/115 (23%), Positives = 61/115 (53%), Gaps = 29/115 (25%)

Query: 178 KERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKE 237
           +ERR + ++  KR  +KEE    + +  EK++E+ ++K+KE ++K+++ EKK+++ ++  
Sbjct: 78  RERRNELQKLEKRLLQKEENLDRKLELLEKREEELEKKEKELEQKQQELEKKEEELEELI 137

Query: 238 KKKKKK--------------------EKK---------KKKEEKKKEKKKKKKKK 263
           +++ ++                    E++         K+ EE+ KE+  KK K+
Sbjct: 138 EEQLQELERISGLTAEEAKEILLEKVEEEARHEAAVLIKEIEEEAKEEADKKAKE 192

Length = 520

>gnl|CDD|217051 pfam02463, SMC_N, RecF/RecN/SMC N terminal domain

 Score = 41.9 bits (98), Expect = 3e-04
 Identities = 21/95 (22%), Positives = 48/95 (50%)

Query: 177 KKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKK 236
            + + K    +         +  EE     ++  + ++++ E  K+E +KE++   +  K
Sbjct: 214 YQLKEKLELEEENLLYLDYLKLNEERIDLLQELLRDEQEEIESSKQELEKEEEILAQVLK 273

Query: 237 EKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDE 271
           E K+++KEKK ++EE K   K++++ K +  K + 
Sbjct: 274 ENKEEEKEKKLQEEELKLLAKEEEELKSELLKLER 308

This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination. Length = 1162

>gnl|CDD|217051 pfam02463, SMC_N, RecF/RecN/SMC N terminal domain

 Score = 41.9 bits (98), Expect = 3e-04
 Identities = 23/93 (24%), Positives = 57/93 (61%)

Query: 177 KKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKK 236
             E + +   K  +K +KE ++++EE +E +K+ K+ E K+E +++E+++ +K ++K ++
Sbjct: 312 DDEEKLKESEKELKKLEKELKKEKEEIEELEKELKELEIKREAEEEEEEQLEKLQEKLEQ 371

Query: 237 EKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKK 269
            +++   +KK + E      K K+++ E K ++
Sbjct: 372 LEEELLAKKKLESERLSSAAKLKEEELELKNEE 404

This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination. Length = 1162

>gnl|CDD|215521 PLN02967, PLN02967, kinase

 Score = 41.6 bits (97), Expect = 3e-04
 Identities = 22/99 (22%), Positives = 42/99 (42%), Gaps = 8/99 (8%)

Query: 166 GDNLEYGYKGGKKERRKQRRRKRKRKRKKEEEEKEE-------EKKEEKKKEKKKEKKKE 218
            +  E G    KK  R   +R  K+   +  E  EE       E     K+ KK  ++  
Sbjct: 60  EEPDENGAVSKKKPTRS-VKRATKKTVVEISEPLEEGSELVVNEDAALDKESKKTPRRTR 118

Query: 219 KKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKKKEKK 257
           +K      + +++K +KK +K++K +K  +  E +  + 
Sbjct: 119 RKAAAASSDVEEEKTEKKVRKRRKVKKMDEDVEDQGSES 157

Length = 581

>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]

 Score = 42.0 bits (99), Expect = 3e-04
 Identities = 21/89 (23%), Positives = 57/89 (64%)

Query: 181 RKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKK 240
           R ++  +   +  +E EEK +E +EE ++ +K+ ++ +++ +E + EK++ + + KE ++
Sbjct: 825 RLEQEIEELEEEIEELEEKLDELEEELEELEKELEELKEELEELEAEKEELEDELKELEE 884

Query: 241 KKKEKKKKKEEKKKEKKKKKKKKEKKKKK 269
           +K+E +++  E + E  + K++ EK +++
Sbjct: 885 EKEELEEELRELESELAELKEEIEKLRER 913

Length = 1163

>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]

 Score = 41.6 bits (98), Expect = 3e-04
 Identities = 18/95 (18%), Positives = 56/95 (58%)

Query: 181 RKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKK 240
            K +  +++ +  +EE  + EE+ EE ++E ++ +K+ ++ K + +E +++ ++ +E+  
Sbjct: 232 AKLKELRKELEELEEELSRLEEELEELQEELEEAEKEIEELKSELEELREELEELQEELL 291

Query: 241 KKKEKKKKKEEKKKEKKKKKKKKEKKKKKDEGRRR 275
           + KE+ ++ E +    +++ ++ E + ++ E R  
Sbjct: 292 ELKEEIEELEGEISLLRERLEELENELEELEERLE 326

Length = 1163

>gnl|CDD|130141 TIGR01069, mutS2, MutS2 family protein

 Score = 41.7 bits (98), Expect = 3e-04
 Identities = 27/109 (24%), Positives = 47/109 (43%), Gaps = 8/109 (7%)

Query: 169 LEYGYKGGKKERRKQRRRKRKRKRKKEEE--------EKEEEKKEEKKKEKKKEKKKEKK 220
            E   K  ++E  + + R+R +K + E+E        +KE E    + KEKK  K KE K
Sbjct: 541 QEKLKKELEQEMEELKERERNKKLELEKEAQEALKALKKEVESIIRELKEKKIHKAKEIK 600

Query: 221 KKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKK 269
             E   + K+ K+K  +K    +  K   + + +   +K K  +     
Sbjct: 601 SIEDLVKLKETKQKIPQKPTNFQADKIGDKVRIRYFGQKGKIVQILGGN 649

Function of MutS2 is unknown. It should not be considered a DNA mismatch repair protein. It is likely a DNA mismatch binding protein of unknown cellular function [DNA metabolism, Other]. Length = 771

>gnl|CDD|236545 PRK09510, tolA, cell envelope integrity inner membrane protein TolA; Provisional

 Score = 41.7 bits (98), Expect = 3e-04
 Identities = 21/84 (25%), Positives = 36/84 (42%)

Query: 191 KRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKE 250
            +KK E E  ++   E KK+ + E   +   + KKK + + KKK   + KKK   + K  
Sbjct: 167 AKKKAEAEAAKKAAAEAKKKAEAEAAAKAAAEAKKKAEAEAKKKAAAEAKKKAAAEAKAA 226

Query: 251 EKKKEKKKKKKKKEKKKKKDEGRR 274
             K   + K   ++    K   + 
Sbjct: 227 AAKAAAEAKAAAEKAAAAKAAEKA 250

Length = 387

>gnl|CDD|236545 PRK09510, tolA, cell envelope integrity inner membrane protein TolA; Provisional

 Score = 41.3 bits (97), Expect = 3e-04
 Identities = 22/90 (24%), Positives = 38/90 (42%)

Query: 186 RKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEK 245
           +K   + KK+ E +  +K   + K+K + +   K   E KK+ + + KKK   + KKK  
Sbjct: 161 KKAAAEAKKKAEAEAAKKAAAEAKKKAEAEAAAKAAAEAKKKAEAEAKKKAAAEAKKKAA 220

Query: 246 KKKKEEKKKEKKKKKKKKEKKKKKDEGRRR 275
            + K    K   + K   EK        + 
Sbjct: 221 AEAKAAAAKAAAEAKAAAEKAAAAKAAEKA 250

Length = 387

>gnl|CDD|236048 PRK07561, PRK07561, DNA topoisomerase I subunit omega; Validated

 Score = 41.7 bits (99), Expect = 3e-04
 Identities = 10/43 (23%), Positives = 18/43 (41%)

Query: 227 EKKKKKKKKKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKK 269
           EK +K +   +   K    KK   +  ++ K++    EK  K 
Sbjct: 816 EKPEKLRYLADAPAKDPAGKKAAVKFSRKTKQQYVASEKDGKA 858

Length = 859

>gnl|CDD|236048 PRK07561, PRK07561, DNA topoisomerase I subunit omega; Validated

 Score = 41.7 bits (99), Expect = 3e-04
 Identities = 10/45 (22%), Positives = 16/45 (35%)

Query: 222 KEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKK 266
             +K EK +       K    K+   K   K K++    +K  K 
Sbjct: 814 LAEKPEKLRYLADAPAKDPAGKKAAVKFSRKTKQQYVASEKDGKA 858

Length = 859

>gnl|CDD|235971 PRK07219, PRK07219, DNA topoisomerase I; Validated

 Score = 41.9 bits (99), Expect = 3e-04
 Identities = 13/78 (16%), Positives = 24/78 (30%), Gaps = 7/78 (8%)

Query: 189 KRKRKKEEEEK-------EEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKK 241
           + K    +E            +K++K+KE K E +  K    K  EK K    +      
Sbjct: 745 RVKGGFGDELGCCNNPKCNYTEKQKKEKESKSELEALKGVGAKTAEKLKDAGVETVTDLT 804

Query: 242 KKEKKKKKEEKKKEKKKK 259
             +      +       +
Sbjct: 805 AADPDAVAAKVDGVSADR 822

Length = 822

>gnl|CDD|227492 COG5163, NOP7, Protein required for biogenesis of the 60S ribosomal subunit [Translation, ribosomal structure and biogenesis]

 Score = 41.6 bits (97), Expect = 3e-04
 Identities = 29/69 (42%), Positives = 41/69 (59%), Gaps = 4/69 (5%)

Query: 206 EKKKEKKKEKKKEKKKKEKKKEKKKKK----KKKKEKKKKKKEKKKKKEEKKKEKKKKKK 261
           E  K+  K K K++K  E+++EKK K      K+K+  KK K    KKEE+ +  KKKKK
Sbjct: 520 EADKDVNKSKNKKRKVDEEEEEKKLKMIMMSNKQKKLYKKMKYSNAKKEEQAENLKKKKK 579

Query: 262 KKEKKKKKD 270
           +  K+KK D
Sbjct: 580 QIAKQKKLD 588

Length = 591

>gnl|CDD|225606 COG3064, TolA, Membrane protein involved in colicin uptake [Cell envelope biogenesis, outer membrane]

 Score = 41.5 bits (97), Expect = 3e-04
 Identities = 28/93 (30%), Positives = 47/93 (50%)

Query: 177 KKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKK 236
           +K++ +Q R+    ++KK E  K +   E  K +   E KK+ ++  K  E+ K K +  
Sbjct: 131 QKQQEEQARKAAAEQKKKAEAAKAKAAAEAAKLKAAAEAKKKAEEAAKAAEEAKAKAEAA 190

Query: 237 EKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKK 269
             KKK + + K   EK K + + K K EKK + 
Sbjct: 191 AAKKKAEAEAKAAAEKAKAEAEAKAKAEKKAEA 223

Length = 387

>gnl|CDD|225606 COG3064, TolA, Membrane protein involved in colicin uptake [Cell envelope biogenesis, outer membrane]

 Score = 41.1 bits (96), Expect = 3e-04
 Identities = 27/100 (27%), Positives = 46/100 (46%)

Query: 174 KGGKKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKK 233
           K  +  + K      K K   E ++K EE  +  ++ K K +    KKK + + K   +K
Sbjct: 147 KKAEAAKAKAAAEAAKLKAAAEAKKKAEEAAKAAEEAKAKAEAAAAKKKAEAEAKAAAEK 206

Query: 234 KKKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDEGR 273
            K E + K K +KK +   +++   +KKK   K K D+  
Sbjct: 207 AKAEAEAKAKAEKKAEAAAEEKAAAEKKKAAAKAKADKAA 246

Length = 387

>gnl|CDD|235175 PRK03918, PRK03918, chromosome segregation protein; Provisional

 Score = 42.0 bits (99), Expect = 3e-04
 Identities = 30/104 (28%), Positives = 59/104 (56%), Gaps = 1/104 (0%)

Query: 173 YKGGKKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEK-KKKEKKKEKKKK 231
            +  K+  R +       +R KE EEKEE  +E KKK K+ EK+ E+ +++ +  E+ K 
Sbjct: 310 REIEKRLSRLEEEINGIEERIKELEEKEERLEELKKKLKELEKRLEELEERHELYEEAKA 369

Query: 232 KKKKKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDEGRRR 275
           KK++ E+ KK+      ++ +K+ ++ +K K+E +++  +   R
Sbjct: 370 KKEELERLKKRLTGLTPEKLEKELEELEKAKEEIEEEISKITAR 413

Length = 880

>gnl|CDD|235175 PRK03918, PRK03918, chromosome segregation protein; Provisional

 Score = 41.6 bits (98), Expect = 3e-04
 Identities = 25/98 (25%), Positives = 58/98 (59%), Gaps = 1/98 (1%)

Query: 178 KERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKE 237
            E  + R    K +++ +E E+ +E+ EE +KE +  +  ++K +EK +E +++ ++ K+
Sbjct: 214 SELPELREELEKLEKEVKELEELKEEIEELEKELESLEGSKRKLEEKIRELEERIEELKK 273

Query: 238 KKKKKKEKKKKKEE-KKKEKKKKKKKKEKKKKKDEGRR 274
           + ++ +EK K+ +E K+K ++  K  +  ++  DE R 
Sbjct: 274 EIEELEEKVKELKELKEKAEEYIKLSEFYEEYLDELRE 311

Length = 880

>gnl|CDD|225324 COG2604, COG2604, Uncharacterized protein conserved in bacteria [Function unknown]

 Score = 42.0 bits (99), Expect = 3e-04
 Identities = 20/73 (27%), Positives = 29/73 (39%), Gaps = 1/73 (1%)

Query: 199 KEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKKKEKKK 258
            E   KE  +K   K+K K   K        ++K   K  +K KK     K E + +  K
Sbjct: 440 IELPFKEVCEKLLDKDKNKPFIKLILLSNNSQEKAVLKLLQKIKKNNDFIK-EFETDALK 498

Query: 259 KKKKKEKKKKKDE 271
            ++  EK   K E
Sbjct: 499 LQEILEKVDSKSE 511

Length = 594

>gnl|CDD|219124 pfam06658, DUF1168, Protein of unknown function (DUF1168)

 Score = 39.6 bits (93), Expect = 3e-04
 Identities = 32/96 (33%), Positives = 64/96 (66%)

Query: 178 KERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKE 237
           +E  +      K K++ E+EE +++++E+K+K+++K  KK  K+++KK++KKKKKK KK 
Sbjct: 47  REYERLELMDEKWKKETEDEEFQQKREEKKRKDEEKTAKKRAKRQKKKQKKKKKKKAKKG 106

Query: 238 KKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDEGR 273
            KK++KE  K  EE   E+++ ++ K+++  +   +
Sbjct: 107 NKKEEKEGSKSSEESSDEEEEGEEDKQEEPVEIMEK 142

This family consists of several hypothetical eukaryotic proteins of unknown function. Length = 142

>gnl|CDD|224415 COG1498, SIK1, Protein implicated in ribosomal biogenesis, Nop56p homolog [Translation, ribosomal structure and biogenesis]

 Score = 41.2 bits (97), Expect = 3e-04
 Identities = 13/61 (21%), Positives = 34/61 (55%)

Query: 201 EEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKKKEKKKKK 260
            E      +E+ +++ ++ K+K  K   K K ++ K+++  +  +KKK+++ K E++  +
Sbjct: 335 GEPDGISLREELEKRIEKLKEKPPKPPTKAKPERDKKERPGRYRRKKKEKKAKSERRGLQ 394

Query: 261 K 261
            
Sbjct: 395 N 395

Length = 395

>gnl|CDD|215214 PLN02381, PLN02381, valyl-tRNA synthetase

 Score = 41.4 bits (97), Expect = 4e-04
 Identities = 20/65 (30%), Positives = 38/65 (58%)

Query: 210 EKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKK 269
           E + EKK   +++ ++K+KK++K K+KE KK K  +K+ K + + ++        KK +K
Sbjct: 5   ESEAEKKILTEEELERKKKKEEKAKEKELKKLKAAQKEAKAKLQAQQASDGTNVPKKSEK 64

Query: 270 DEGRR 274
              +R
Sbjct: 65  KSRKR 69

Length = 1066

>gnl|CDD|233467 TIGR01554, major_cap_HK97, phage major capsid protein, HK97 family

 Score = 40.8 bits (96), Expect = 4e-04
 Identities = 13/90 (14%), Positives = 39/90 (43%)

Query: 186 RKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEK 245
           ++ +    +  +E  +  ++EK  E ++EK +    KE+  +   +  + +E   + + K
Sbjct: 2   KELREALAELAKELRKLTEDEKLAEAEEEKAEYDALKEEIDKLDAEIDRLEELLDELEAK 61

Query: 246 KKKKEEKKKEKKKKKKKKEKKKKKDEGRRR 275
                E    ++++++ K +  +     R 
Sbjct: 62  PAASGEGGGGEEEEEEAKAEAAEFRAYLRG 91

This model family represents the major capsid protein component of the heads (capsids) of bacteriophage HK97, phi-105, P27, and related phage. This model represents one of several analogous families lacking detectable sequence similarity. The gene encoding this component is typically located in an operon encoding the small and large terminase subunits, the portal protein and the prohead or maturation protease [Mobile and extrachromosomal element functions, Prophage functions]. Length = 384

>gnl|CDD|236944 PRK11642, PRK11642, exoribonuclease R; Provisional

 Score = 41.3 bits (97), Expect = 4e-04
 Identities = 22/85 (25%), Positives = 38/85 (44%), Gaps = 6/85 (7%)

Query: 179 ERRKQRRRKRKRKR-KKEEEEKEEEKKEEKKKEKKKE-----KKKEKKKKEKKKEKKKKK 232
           ER  +   K  R++ KK +  K+  K+ +  K+   E     + ++K K +  K+  +K 
Sbjct: 728 ERAPRNVGKTAREKAKKGDAGKKGGKRRQVGKKVNFEPDSAFRGEKKAKPKAAKKDARKA 787

Query: 233 KKKKEKKKKKKEKKKKKEEKKKEKK 257
           KK   K +K     K K   KK+  
Sbjct: 788 KKPSAKTQKIAAATKAKRAAKKKVA 812

Length = 813

>gnl|CDD|172341 PRK13808, PRK13808, adenylate kinase; Provisional

 Score = 41.0 bits (96), Expect = 4e-04
 Identities = 26/102 (25%), Positives = 40/102 (39%)

Query: 174 KGGKKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKK 233
           K     ++  +++  K     ++  K   K  +K K+  K+  K+  K  KK  KK  K 
Sbjct: 218 KAKSAAKKVSKKKAAKTAVSAKKAAKTAAKAAKKAKKTAKKALKKAAKAVKKAAKKAAKA 277

Query: 234 KKKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDEGRRR 275
             K  K   K  K K + KKK  KK     + K      +R 
Sbjct: 278 AAKAAKGAAKATKGKAKAKKKAGKKAAAGSKAKATAKAPKRG 319

Length = 333

>gnl|CDD|240246 PTZ00053, PTZ00053, methionine aminopeptidase 2; Provisional

 Score = 40.9 bits (96), Expect = 4e-04
 Identities = 23/76 (30%), Positives = 39/76 (51%)

Query: 200 EEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKKKEKKKK 259
              +  E + +++K++ K+K  K+K K+ KK          +   + ++ E K+  KKKK
Sbjct: 1   AMNENGENEVKQQKQQNKQKGTKKKNKKSKKDVDDDDAFLAELISENQEAENKQNNKKKK 60

Query: 260 KKKKEKKKKKDEGRRR 275
           KKKK+KKKK       
Sbjct: 61  KKKKKKKKKNLGEAYD 76

Length = 470

>gnl|CDD|235322 PRK04950, PRK04950, ProP expression regulator; Provisional

 Score = 40.3 bits (95), Expect = 4e-04
 Identities = 15/69 (21%), Positives = 35/69 (50%), Gaps = 1/69 (1%)

Query: 204 KEEKKKEKKKEKKKEKKKKEKKKEKKKK-KKKKKEKKKKKKEKKKKKEEKKKEKKKKKKK 262
           +E K K + +  +++ KK+E   EK+K  ++++K K K  ++K+K + +K + +      
Sbjct: 104 EEAKAKVQAQRAEQQAKKREAAGEKEKAPRRERKPKPKAPRKKRKPRAQKPEPQHTPVSD 163

Query: 263 KEKKKKKDE 271
             +      
Sbjct: 164 ISELTVGQA 172

Length = 213

>gnl|CDD|219408 pfam07423, DUF1510, Protein of unknown function (DUF1510)

 Score = 40.5 bits (95), Expect = 4e-04
 Identities = 14/74 (18%), Positives = 43/74 (58%)

Query: 199 KEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKKKEKKK 258
             ++   ++++ KK + ++  + +E K+E+K+    + ++ K   EK+ ++ E++ E++ 
Sbjct: 40  PSDQAAADEQEAKKSDDQETAEIEEVKEEEKEAANSEDKEDKGDAEKEDEESEEENEEED 99

Query: 259 KKKKKEKKKKKDEG 272
           ++   E +K+ +E 
Sbjct: 100 EESSDENEKETEEK 113

This family consists of several hypothetical bacterial proteins of around 200 residues in length. The function of this family is unknown. Length = 214

>gnl|CDD|234767 PRK00448, polC, DNA polymerase III PolC; Validated

 Score = 41.4 bits (98), Expect = 4e-04
 Identities = 22/90 (24%), Positives = 45/90 (50%)

Query: 182 KQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKK 241
           +   +K+   +  ++ EK      +   E    K++ +K + +K+E+ +K  K+  +  K
Sbjct: 136 RDHLKKKHLPKLIKQYEKFGFGILKIDFEIDDSKEELEKFEAQKEEEDEKLAKEALEAMK 195

Query: 242 KKEKKKKKEEKKKEKKKKKKKKEKKKKKDE 271
           K E +KKK+ K  + K+   +  KK  K+E
Sbjct: 196 KLEAEKKKQSKNFDPKEGPVQIGKKIDKEE 225

Length = 1437

>gnl|CDD|150884 pfam10278, Med19, Mediator of RNA pol II transcription subunit 19

 Score = 39.8 bits (93), Expect = 4e-04
 Identities = 24/65 (36%), Positives = 39/65 (60%)

Query: 187 KRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKK 246
           K+K K K ++   ++   EE   + +  K  EKK K+KK E  K++KKKK++KKKKK++ 
Sbjct: 110 KKKHKHKHKKHRTQDPLPEETPSDSEGLKGHEKKHKKKKHEDDKERKKKKKEKKKKKKRH 169

Query: 247 KKKEE 251
             +  
Sbjct: 170 SPEHP 174

Med19 represents a family of conserved proteins which are members of the multi-protein co-activator Mediator complex. Mediator is required for activation of RNA polymerase II transcription by DNA binding transactivators. Length = 178

>gnl|CDD|227519 COG5192, BMS1, GTP-binding protein required for 40S ribosome biogenesis [Translation, ribosomal structure and biogenesis]

 Score = 41.3 bits (96), Expect = 4e-04
 Identities = 23/85 (27%), Positives = 47/85 (55%), Gaps = 3/85 (3%)

Query: 182  KQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKK---KKEK 238
             +R      +R +     E  +K E K    KE+ K++++KE+ +  ++ K++   KKEK
Sbjct: 992  DKRSIAVVSRRIELPVPPECREKHEIKDRIVKERIKDQEEKERMESLQRAKEEEIGKKEK 1051

Query: 239  KKKKKEKKKKKEEKKKEKKKKKKKK 263
            +++++ +K   +  K+  KK+ KKK
Sbjct: 1052 EREQRIRKTIHDNYKEMAKKRLKKK 1076

Length = 1077

>gnl|CDD|115057 pfam06375, BLVR, Bovine leukaemia virus receptor (BLVR)

 Score = 41.2 bits (96), Expect = 4e-04
 Identities = 32/118 (27%), Positives = 56/118 (47%), Gaps = 16/118 (13%)

Query: 174 KGGKKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKK----------------K 217
           K  +K       +K K+ +KKE++EKE+E+ ++KKKE +  K                 +
Sbjct: 185 KSPEKGDVPAVEKKSKKPKKKEKKEKEKERDKDKKKEVEGFKSLLLALDDSPASAASVAE 244

Query: 218 EKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDEGRRR 275
             +              + ++ K  + ++ KK  K K+KK++K+K+EKKKKK     R
Sbjct: 245 ADEASLANTVSGTAPDSEPDEPKDAEAEETKKSPKHKKKKQRKEKEEKKKKKKHHHHR 302

This family consists of several bovine specific leukaemia virus receptors which are thought to function as transmembrane proteins, although their exact function is unknown. Length = 561

>gnl|CDD|220684 pfam10310, DUF2413, Protein of unknown function (DUF2413)

 Score = 41.3 bits (97), Expect = 4e-04
 Identities = 20/105 (19%), Positives = 40/105 (38%)

Query: 167 DNLEYGYKGGKKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKK 226
           D+L       KK ++    +      +   E  +E ++ EK K  KK K+  +    +  
Sbjct: 6   DSLPDEKAPTKKPKKGDASKDSTEDDEDILEFLDELEQSEKAKPPKKPKEASRPGTPRNP 65

Query: 227 EKKKKKKKKKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDE 271
           +K  K  +      ++K  K +K  +       K K    + ++E
Sbjct: 66  KKSSKPTESSAASSEEKPAKPRKSAESTRSSHPKSKAPSTESEEE 110

This is a family of proteins conserved in fungi. The function is not known. Length = 436

>gnl|CDD|223496 COG0419, SbcC, ATPase involved in DNA repair [DNA replication, recombination, and repair]

 Score = 41.3 bits (97), Expect = 4e-04
 Identities = 17/108 (15%), Positives = 57/108 (52%)

Query: 168 NLEYGYKGGKKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKE 227
            LE   K  +  +   +  K K +  + +  +  E  E+  +  ++E K+ KK +E ++E
Sbjct: 165 GLEKYEKLSELLKEVIKEAKAKIEELEGQLSELLEDIEDLLEALEEELKELKKLEEIQEE 224

Query: 228 KKKKKKKKKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDEGRRR 275
           +++++ +++ +  +++  + ++E+++ E+ K +  + +  + +  + R
Sbjct: 225 QEEEELEQEIEALEERLAELEEEKERLEELKARLLEIESLELEALKIR 272

Length = 908

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 41.3 bits (96), Expect = 5e-04
 Identities = 32/94 (34%), Positives = 64/94 (68%)

Query: 177  KKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKK 236
            KKE  ++++ +  +K ++E + K EE K+E +++KKK ++ +K ++EKKK    KK+++K
Sbjct: 1709 KKEAEEKKKAEELKKAEEENKIKAEEAKKEAEEDKKKAEEAKKDEEEKKKIAHLKKEEEK 1768

Query: 237  EKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKD 270
            + ++ +KEK+   EE+  E+ +K++ +  KK KD
Sbjct: 1769 KAEEIRKEKEAVIEEELDEEDEKRRMEVDKKIKD 1802

Length = 2084

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 41.3 bits (96), Expect = 5e-04
 Identities = 32/106 (30%), Positives = 63/106 (59%), Gaps = 4/106 (3%)

Query: 174  KGGKKERRKQRRRKRKRKRKKEEEEKEEEKKE----EKKKEKKKEKKKEKKKKEKKKEKK 229
            K  ++ ++    +K +  +K +E +K EEKK+    +K +E KK ++K+K ++ KK E+ 
Sbjct: 1516 KKAEEAKKADEAKKAEEAKKADEAKKAEEKKKADELKKAEELKKAEEKKKAEEAKKAEED 1575

Query: 230  KKKKKKKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDEGRRR 275
            K    +K ++ KK E+ + +E  K  +++KK K E+ KK +E + +
Sbjct: 1576 KNMALRKAEEAKKAEEARIEEVMKLYEEEKKMKAEEAKKAEEAKIK 1621

Length = 2084

>gnl|CDD|172341 PRK13808, PRK13808, adenylate kinase; Provisional

 Score = 40.6 bits (95), Expect = 5e-04
 Identities = 26/100 (26%), Positives = 40/100 (40%)

Query: 176 GKKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKK 235
           G    +K  +    +   K+   K +   ++  K+K  +     KK  K   K  KK KK
Sbjct: 195 GAANAKKAAKTPAAKSGAKKASAKAKSAAKKVSKKKAAKTAVSAKKAAKTAAKAAKKAKK 254

Query: 236 KEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDEGRRR 275
             KK  KK  K  K+  KK  K   K  +   K  +G+ +
Sbjct: 255 TAKKALKKAAKAVKKAAKKAAKAAAKAAKGAAKATKGKAK 294

Length = 333

>gnl|CDD|236545 PRK09510, tolA, cell envelope integrity inner membrane protein TolA; Provisional

 Score = 40.6 bits (95), Expect = 5e-04
 Identities = 20/89 (22%), Positives = 57/89 (64%)

Query: 181 RKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKK 240
           R+Q+++K  ++ +++ ++KE+++ EE ++++  E+++ K+ ++++   +++KK+ +E  K
Sbjct: 66  RQQQQQKSAKRAEEQRKKKEQQQAEELQQKQAAEQERLKQLEKERLAAQEQKKQAEEAAK 125

Query: 241 KKKEKKKKKEEKKKEKKKKKKKKEKKKKK 269
           +   K+K+ EE   +     K K + + K
Sbjct: 126 QAALKQKQAEEAAAKAAAAAKAKAEAEAK 154

Length = 387

>gnl|CDD|187751 cd09270, RNase_H2-B, Ribonuclease H2-B is a subunit of the eukaryotic RNase H complex which cleaves RNA-DNA hybrids

 Score = 40.0 bits (94), Expect = 5e-04
 Identities = 23/55 (41%), Positives = 34/55 (61%)

Query: 207 KKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKKKEKKKKKK 261
           KK E+ K+K+ + K+ E  ++KKK    ++EKKKKKK+  KKK+ KK      K 
Sbjct: 151 KKVERLKKKELDIKEAEAARDKKKSNNAEEEKKKKKKKSAKKKKLKKVAAVGMKA 205

Ribonuclease H2B is one of the three proteins of eukaryotic RNase H2 complex that is required for nucleic acid binding and hydrolysis. RNase H is classified into two families, type I (prokaryotic RNase HI, eukaryotic RNase H1 and viral RNase H) and type II (prokaryotic RNase HII and HIII, and eukaryotic RNase H2/HII). RNase H endonucleolytically hydrolyzes an RNA strand when it is annealed to a complementary DNA strand in the presence of divalent cations, in DNA replication and repair. The enzyme can be found in bacteria, archaea, and eukaryotes. Most prokaryotic and eukaryotic genomes contain multiple RNase H genes. Despite a lack of evidence for homology from sequence comparisons, type I and type II RNase H share a common fold and similar steric configurations of the four acidic active-site residues, suggesting identical or very similar catalytic mechanisms. Eukaryotic RNase HII is active during replication and is believed to play a role in removal of Okazaki fragment primers and single ribonucleotides in DNA-DNA duplexes. Eukaryotic RNase HII is functional when it forms a complex with RNase H2B and RNase H2C proteins. It is speculated that the two accessory subunits are required for correct folding of the catalytic subunit of RNase HII. Mutations in the three subunits of human RNase HII cause neurological disorder. Length = 211

>gnl|CDD|218188 pfam04641, Rtf2, Replication termination factor 2

 Score = 40.0 bits (94), Expect = 5e-04
 Identities = 20/77 (25%), Positives = 35/77 (45%), Gaps = 1/77 (1%)

Query: 195 EEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKKK 254
           EEE +  + + E+++ KKK+KKK+KK K K        +         +      +  + 
Sbjct: 166 EEEVELLKARLEEERAKKKKKKKKKKTK-KNNATGSSAEATVSSAVPTELSSGAGQVGEA 224

Query: 255 EKKKKKKKKEKKKKKDE 271
           +K KKK+      +K E
Sbjct: 225 KKLKKKRSIAPDNEKSE 241

It is vital for effective cell-replication that replication is not stalled at any point by, for instance, damaged bases. Rtf2 stabilizes the replication fork stalled at the site-specific replication barrier RTS1 by preventing replication restart until completion of DNA synthesis by a converging replication fork initiated at a flanking origin. The RTS1 element terminates replication forks that are moving in the cen2-distal direction while allowing forks moving in the cen2-proximal direction to pass through the region. Rtf2 contains a C2HC2 motif related to the C3HC4 RING-finger motif, and would appear to fold up, creating a RING finger-like structure but forming only one functional Zn2+ ion-binding site. Length = 254

>gnl|CDD|227519 COG5192, BMS1, GTP-binding protein required for 40S ribosome biogenesis [Translation, ribosomal structure and biogenesis]

 Score = 40.9 bits (95), Expect = 5e-04
 Identities = 20/86 (23%), Positives = 48/86 (55%)

Query: 184  RRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKK 243
             +R      ++ E     E +E+ + + +  K++ K ++EK++ +  ++ K++E  KK+K
Sbjct: 992  DKRSIAVVSRRIELPVPPECREKHEIKDRIVKERIKDQEEKERMESLQRAKEEEIGKKEK 1051

Query: 244  EKKKKKEEKKKEKKKKKKKKEKKKKK 269
            E++++  +   +  K+  KK  KKK+
Sbjct: 1052 EREQRIRKTIHDNYKEMAKKRLKKKR 1077

Length = 1077

>gnl|CDD|235175 PRK03918, PRK03918, chromosome segregation protein; Provisional

 Score = 40.8 bits (96), Expect = 5e-04
 Identities = 29/97 (29%), Positives = 55/97 (56%)

Query: 173 YKGGKKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKK 232
           Y    +E  K+  R  +     EE  KE E+KEE+ +E KK+ K+ +K+ E+ +E+ +  
Sbjct: 305 YLDELREIEKRLSRLEEEINGIEERIKELEEKEERLEELKKKLKELEKRLEELEERHELY 364

Query: 233 KKKKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKK 269
           ++ K KK++ +  KK+      EK +K+ ++ +K K+
Sbjct: 365 EEAKAKKEELERLKKRLTGLTPEKLEKELEELEKAKE 401

Length = 880

>gnl|CDD|235175 PRK03918, PRK03918, chromosome segregation protein; Provisional

 Score = 40.8 bits (96), Expect = 5e-04
 Identities = 25/96 (26%), Positives = 58/96 (60%)

Query: 178 KERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKE 237
           KE+ ++  +  +   +  +E +E EK+  + +E+    ++  K+ E+K+E+ ++ KKK +
Sbjct: 289 KEKAEEYIKLSEFYEEYLDELREIEKRLSRLEEEINGIEERIKELEEKEERLEELKKKLK 348

Query: 238 KKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDEGR 273
           + +K+ E+ +++ E  +E K KK++ E+ KK+  G 
Sbjct: 349 ELEKRLEELEERHELYEEAKAKKEELERLKKRLTGL 384

Length = 880

>gnl|CDD|218585 pfam05424, Duffy_binding, Duffy binding domain

 Score = 40.4 bits (95), Expect = 5e-04
 Identities = 29/77 (37%), Positives = 43/77 (55%)

Query: 190 RKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKK 249
           R+RKK+ E+ +++ KE+K  +   +K  + K   KK +K    KKK+  K+KKK KK KK
Sbjct: 199 RERKKKLEKLKKKCKEKKCNKYCSKKCTKCKNACKKYKKWIDNKKKEWDKQKKKYKKYKK 258

Query: 250 EEKKKEKKKKKKKKEKK 266
              KK     K K  K+
Sbjct: 259 RNNKKNYSDIKDKYAKE 275

This domain is found in Plasmodium Duffy binding proteins. Plasmodium vivax and Plasmodium knowlesi merozoites invade human erythrocytes that express Duffy blood group surface determinants. The Duffy receptor family is localised in micronemes, an organelle found in all organisms of the phylum Apicomplexa. Length = 276

>gnl|CDD|149343 pfam08229, SHR3_chaperone, ER membrane protein SH3

 Score = 40.0 bits (94), Expect = 5e-04
 Identities = 12/37 (32%), Positives = 21/37 (56%)

Query: 196 EEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKK 232
           ++ K  E+   ++ E     K+E+  + +KKE KKKK
Sbjct: 160 KDAKLLEEFAAEEAEAAAAAKEEESAEGEKKESKKKK 196

This family of proteins are membrane localised chaperones that are required for correct plasma membrane localisation of amino acid permeases (AAPs). SH3 prevents AAPs proteins from aggregating and assists in their correct folding. In the absence of SH3, AAPs are retained in the ER. Length = 196

>gnl|CDD|233757 TIGR02168, SMC_prok_B, chromosome segregation protein SMC, common bacterial type

 Score = 41.2 bits (97), Expect = 5e-04
 Identities = 20/82 (24%), Positives = 48/82 (58%), Gaps = 3/82 (3%)

Query: 177 KKERRKQRRRKRKRKRKKEEEEKEEE-KKEEKKKEKKKEKKKEKKKK--EKKKEKKKKKK 233
           + E++KQ  R+R    +++ EE E + ++ E K ++  E+  E ++K  E K+E +  + 
Sbjct: 299 RLEQQKQILRERLANLERQLEELEAQLEELESKLDELAEELAELEEKLEELKEELESLEA 358

Query: 234 KKKEKKKKKKEKKKKKEEKKKE 255
           + +E + + +E + + EE +++
Sbjct: 359 ELEELEAELEELESRLEELEEQ 380

SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]. Length = 1179

>gnl|CDD|224114 COG1193, COG1193, Mismatch repair ATPase (MutS family) [DNA replication, recombination, and repair]

 Score = 40.8 bits (96), Expect = 5e-04
 Identities = 26/113 (23%), Positives = 39/113 (34%), Gaps = 19/113 (16%)

Query: 175 GGKKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKK 234
           G +KE  ++   K +  RK+ EEE EE +K   + E         K    + + +     
Sbjct: 500 GEEKELLEELIEKLEEVRKELEEELEEVEKLLDEVELLTGANSGGKTSLLELKAQIVVLA 559

Query: 235 KKE-------------------KKKKKKEKKKKKEEKKKEKKKKKKKKEKKKK 268
                                 KKKK        E   K+KK K   + KK+K
Sbjct: 560 HMGLPVPAEEAKVEAVDEVKFLKKKKGILDAGAFESTLKDKKNKVLPEAKKRK 612

Length = 753

>gnl|CDD|221937 pfam13148, DUF3987, Protein of unknown function (DUF3987)

 Score = 40.7 bits (96), Expect = 5e-04
 Identities = 19/60 (31%), Positives = 37/60 (61%)

Query: 197 EEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKKKEK 256
           EE EEE +EE ++E K+ + +++  + +KK  +KK KK  +K K ++   ++  E + E+
Sbjct: 64  EEIEEELREEYEEELKEYEAEKEIWEAEKKGLEKKAKKAIKKGKDEEALAEELLELEAEE 123

A family of uncharacterized proteins found by clustering human gut metagenomic sequences. Length = 379

>gnl|CDD|223599 COG0525, ValS, Valyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]

 Score = 41.1 bits (97), Expect = 5e-04
 Identities = 18/80 (22%), Positives = 32/80 (40%), Gaps = 2/80 (2%)

Query: 191 KRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKK--KKKKEKKKK 248
           +   E        +         +   E  + EK+ EK +K+  + EKK   +    K  
Sbjct: 788 EPPVEVTAVVGGAELFLPLAGLIDLAAELARLEKELEKLEKEIDRIEKKLSNEGFVAKAP 847

Query: 249 KEEKKKEKKKKKKKKEKKKK 268
           +E  +KEK+K  + + K  K
Sbjct: 848 EEVVEKEKEKLAEYQVKLAK 867

Length = 877

>gnl|CDD|220648 pfam10243, MIP-T3, Microtubule-binding protein MIP-T3

 Score = 40.6 bits (95), Expect = 6e-04
 Identities = 26/102 (25%), Positives = 55/102 (53%), Gaps = 3/102 (2%)

Query: 177 KKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEK---KKEKKKEKKKKEKKKEKKKKKK 233
           K++R  + + K K K+ +E  ++EEEKK E+ + K   KK  KK+   K+K+  +++K++
Sbjct: 138 KEKRPPKEKEKEKEKKVEEPRDREEEKKRERVRAKSRPKKPPKKKPPNKKKEPPEEEKQR 197

Query: 234 KKKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDEGRRR 275
           +   +  K K ++    E++++++   K +E      E    
Sbjct: 198 QAAREAVKGKPEEPDVNEEREKEEDDGKDRETTTSPMEEDES 239

This protein, which interacts with both microtubules and TRAF3 (tumour necrosis factor receptor-associated factor 3), is conserved from worms to humans. The N-terminal region is the microtubule binding domain and is well-conserved; the C-terminal 100 residues, also well-conserved, constitute the coiled-coil region which binds to TRAF3. The central region of the protein is rich in lysine and glutamic acid and carries KKE motifs which may also be necessary for tubulin-binding, but this region is the least well-conserved. Length = 506

>gnl|CDD|217051 pfam02463, SMC_N, RecF/RecN/SMC N terminal domain

 Score = 41.1 bits (96), Expect = 6e-04
 Identities = 14/95 (14%), Positives = 48/95 (50%)

Query: 177 KKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKK 236
           + E   +     +  + +E + KE+ KK  +  + K++ + E++        K  +++  
Sbjct: 182 ETENLAELIIDLEELKLQELKLKEQAKKALEYYQLKEKLELEEENLLYLDYLKLNEERID 241

Query: 237 EKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDE 271
             ++  ++++++ E  K+E +K+++   +  K+++
Sbjct: 242 LLQELLRDEQEEIESSKQELEKEEEILAQVLKENK 276

This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination. Length = 1162

>gnl|CDD|221641 pfam12569, NARP1, NMDA receptor-regulated protein 1

 Score = 40.7 bits (96), Expect = 6e-04
 Identities = 19/50 (38%), Positives = 27/50 (54%), Gaps = 1/50 (2%)

Query: 178 KERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKE 227
              RK+ R+K+++  KK E+E E EK   KKK +   KK +    E KK 
Sbjct: 408 PAERKKLRKKQRKAEKKAEKE-EAEKAAAKKKAEAAAKKAKGPDGETKKV 456

This domain family is found in eukaryotes, and is approximately 40 amino acids in length. The family is found in association with pfam07719, pfam00515. There is a single completely conserved residue L that may be functionally important. NARP1 is the mammalian homologue of a yeast N-terminal acetyltransferase that regulates entry into the G(0) phase of the cell cycle. Length = 516

>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]

 Score = 40.9 bits (96), Expect = 6e-04
 Identities = 23/91 (25%), Positives = 54/91 (59%), Gaps = 5/91 (5%)

Query: 184 RRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKK---- 239
           + RK + +RK E  E+  E+ E+  +E +K+ +K +++ EK +  ++ K + +E +    
Sbjct: 171 KERKEEAERKLERTEENLERLEDLLEELEKQLEKLERQAEKAERYQELKAELRELELALL 230

Query: 240 -KKKKEKKKKKEEKKKEKKKKKKKKEKKKKK 269
             K KE +K+ EE ++E  + +++ E+ +++
Sbjct: 231 LAKLKELRKELEELEEELSRLEEELEELQEE 261

Length = 1163

>gnl|CDD|237753 PRK14552, PRK14552, C/D box methylation guide ribonucleoprotein complex aNOP56 subunit; Provisional

 Score = 40.3 bits (95), Expect = 6e-04
 Identities = 21/46 (45%), Positives = 36/46 (78%)

Query: 190 RKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKK 235
            KR +E +EK  +  ++K++EKK +K+K+KKK++KK +K+KKK +K
Sbjct: 369 NKRIEEIKEKYPKPPKKKREEKKPQKRKKKKKRKKKGKKRKKKGRK 414

Length = 414

>gnl|CDD|240402 PTZ00399, PTZ00399, cysteinyl-tRNA-synthetase; Provisional

 Score = 40.8 bits (96), Expect = 6e-04
 Identities = 22/58 (37%), Positives = 39/58 (67%), Gaps = 3/58 (5%)

Query: 201 EEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKKKEKKK 258
           E+K +     K  +K++ +++KE+K+     K++K+ +K KK+E+KKKKE +K EK K
Sbjct: 536 EDKPDGPSVWKLDDKEELQREKEEKEA---LKEQKRLRKLKKQEEKKKKELEKLEKAK 590

Length = 651

>gnl|CDD|178945 PRK00247, PRK00247, putative inner membrane protein translocase component YidC; Validated

 Score = 40.6 bits (95), Expect = 6e-04
 Identities = 15/97 (15%), Positives = 41/97 (42%), Gaps = 20/97 (20%)

Query: 191 KRKKEEEEKEEEKKEEKKKEKKK-------------------EKKKEKKKKEKKKEKKKK 231
           +++ +  EK++EKK      ++                    E KK +   EK + K +K
Sbjct: 289 EQRAQYREKQKEKKAFLWTLRRNRLRMIITPWRAPELHAENAEIKKTRTA-EKNEAKARK 347

Query: 232 KKKKKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKK 268
           K+  ++++  ++E  ++  +++     + + +    K
Sbjct: 348 KEIAQKRRAAEREINREARQERAAAMARARARRAAVK 384

Length = 429

>gnl|CDD|217756 pfam03839, Sec62, Translocation protein Sec62

 Score = 39.8 bits (93), Expect = 6e-04
 Identities = 22/68 (32%), Positives = 34/68 (50%)

Query: 191 KRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKE 250
           KR     E E+ K  + K   +   K   + K  +K K   K +  E+ KK   ++KK+E
Sbjct: 10  KRVVRALESEKYKANKDKGNPEIYNKINSQDKAIEKFKLLIKAQMAERVKKLHSQEKKEE 69

Query: 251 EKKKEKKK 258
           +KK +KKK
Sbjct: 70  KKKPKKKK 77

Length = 217

>gnl|CDD|218188 pfam04641, Rtf2, Replication termination factor 2

 Score = 40.0 bits (94), Expect = 6e-04
 Identities = 19/83 (22%), Positives = 35/83 (42%)

Query: 189 KRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKK 248
            + R +EE  K+++KK++KK +K        +         +      +  + KK KKK+
Sbjct: 172 LKARLEEERAKKKKKKKKKKTKKNNATGSSAEATVSSAVPTELSSGAGQVGEAKKLKKKR 231

Query: 249 KEEKKKEKKKKKKKKEKKKKKDE 271
                 EK +  K      KK++
Sbjct: 232 SIAPDNEKSEVYKSLFTSHKKEK 254

It is vital for effective cell-replication that replication is not stalled at any point by, for instance, damaged bases. Rtf2 stabilizes the replication fork stalled at the site-specific replication barrier RTS1 by preventing replication restart until completion of DNA synthesis by a converging replication fork initiated at a flanking origin. The RTS1 element terminates replication forks that are moving in the cen2-distal direction while allowing forks moving in the cen2-proximal direction to pass through the region. Rtf2 contains a C2HC2 motif related to the C3HC4 RING-finger motif, and would appear to fold up, creating a RING finger-like structure but forming only one functional Zn2+ ion-binding site. Length = 254

>gnl|CDD|227352 COG5019, CDC3, Septin family protein [Cell division and chromosome partitioning / Cytoskeleton]

 Score = 40.4 bits (95), Expect = 6e-04
 Identities = 25/86 (29%), Positives = 47/86 (54%), Gaps = 3/86 (3%)

Query: 185 RRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEK-KKKKK 243
           R ++    K   E   +E  E +  E+++E KK  K  EK +EK+K+ ++ ++   +++K
Sbjct: 288 RTEKLSGLKNSGEPSLKEIHEARLNEEERELKK--KFTEKIREKEKRLEELEQNLIEERK 345

Query: 244 EKKKKKEEKKKEKKKKKKKKEKKKKK 269
           E   K EE +K+ +  +K+ EK K  
Sbjct: 346 ELNSKLEEIQKKLEDLEKRLEKLKSN 371

Length = 373

>gnl|CDD|224415 COG1498, SIK1, Protein implicated in ribosomal biogenesis, Nop56p homolog [Translation, ribosomal structure and biogenesis]

 Score = 40.5 bits (95), Expect = 6e-04
 Identities = 14/61 (22%), Positives = 35/61 (57%)

Query: 205 EEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKKKEKKKKKKKKE 264
            E      +E+ +++ +K K+K  K   K K E+ KK++  + ++++K+K+ K +++  +
Sbjct: 335 GEPDGISLREELEKRIEKLKEKPPKPPTKAKPERDKKERPGRYRRKKKEKKAKSERRGLQ 394

Query: 265 K 265
            
Sbjct: 395 N 395

Length = 395

>gnl|CDD|223683 COG0610, COG0610, Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]

 Score = 40.9 bits (96), Expect = 6e-04
 Identities = 19/87 (21%), Positives = 39/87 (44%), Gaps = 4/87 (4%)

Query: 187 KRKRKRKKEEEEKEEEKKEEKKKEKKKEK--KKEKKKKEKKKEKKKKKKKKKEKKKKKKE 244
            + R +K +  EK EE     KKE++ ++  ++E   +E+            +  +   E
Sbjct: 865 NQYRAKKLDTAEKLEELYILAKKEEEFKQFAEEEGLNEEELAFYDDLALNGGKLPENGTE 924

Query: 245 KKKK--KEEKKKEKKKKKKKKEKKKKK 269
             +K  KE+  +EK K   K +++ + 
Sbjct: 925 LVEKLAKEKSLREKNKDDWKAKEEVEA 951

Length = 962

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 40.9 bits (95), Expect = 7e-04
 Identities = 33/102 (32%), Positives = 61/102 (59%), Gaps = 3/102 (2%)

Query: 177  KKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKK 236
            ++ER+ +  RK +  +K E  +K EE K++ ++ KK E+++  ++  K +E +     ++
Sbjct: 1209 EEERKAEEARKAEDAKKAEAVKKAEEAKKDAEEAKKAEEERNNEEIRKFEEARMAHFARR 1268

Query: 237  EKKKKKKEKKKKKEEKKKEKKKKK---KKKEKKKKKDEGRRR 275
            +   K +E +K  E KK E+KKK    KK E+KKK DE +++
Sbjct: 1269 QAAIKAEEARKADELKKAEEKKKADEAKKAEEKKKADEAKKK 1310

Length = 2084

>gnl|CDD|191187 pfam05087, Rota_VP2, Rotavirus VP2 protein

 Score = 40.7 bits (95), Expect = 7e-04
 Identities = 20/85 (23%), Positives = 38/85 (44%), Gaps = 8/85 (9%)

Query: 188 RKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKE-KKKEKKKKKKKKKEKKKKKKEKK 246
           R R+              ++ +EK  EK+ +K + E K+K   KK++   +      +++
Sbjct: 4   RNRREANI-------NNNDRMQEKDDEKQDQKNRMELKEKVLDKKEEVVTDNVDSPVKEQ 56

Query: 247 KKKEEKKKEKKKKKKKKEKKKKKDE 271
             +E  K   + KK  KE+ K+  E
Sbjct: 57  SSQENLKIADEVKKSTKEESKQLLE 81

Rotavirus particles consist of three concentric proteinaceous capsid layers. The innermost capsid (core) is made of VP2. The genomic RNA and the two minor proteins VP1 and VP3 are encapsidated within this layer. The N-terminus of rotavirus VP2 is necessary for the encapsidation of VP1 and VP3. Length = 887

>gnl|CDD|217051 pfam02463, SMC_N, RecF/RecN/SMC N terminal domain

 Score = 40.7 bits (95), Expect = 7e-04
 Identities = 23/94 (24%), Positives = 60/94 (63%)

Query: 176 GKKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKK 235
            ++E +   + + + K +  + E+ +   EEK KE +KE KK +K+ +K+KE+ ++ +K+
Sbjct: 285 QEEELKLLAKEEEELKSELLKLERRKVDDEEKLKESEKELKKLEKELKKEKEEIEELEKE 344

Query: 236 KEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKK 269
            ++ + K+E ++++EE+ ++ ++K ++ E++   
Sbjct: 345 LKELEIKREAEEEEEEQLEKLQEKLEQLEEELLA 378

This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination. Length = 1162

>gnl|CDD|235640 PRK05901, PRK05901, RNA polymerase sigma factor; Provisional

 Score = 40.4 bits (95), Expect = 7e-04
 Identities = 14/83 (16%), Positives = 27/83 (32%)

Query: 189 KRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKK 248
           K      E +  ++K +   K    +   +KK K++    KK +KK    K       K 
Sbjct: 64  KDTDDATESDIPKKKTKTAAKAAAAKAPAKKKLKDELDSSKKAEKKNALDKDDDLNYVKD 123

Query: 249 KEEKKKEKKKKKKKKEKKKKKDE 271
            +   +         +     D+
Sbjct: 124 IDVLNQADDDDDDDDDDDLDDDD 146

Length = 509

>gnl|CDD|114011 pfam05262, Borrelia_P83, Borrelia P83/100 protein

 Score = 40.4 bits (94), Expect = 7e-04
 Identities = 24/88 (27%), Positives = 45/88 (51%), Gaps = 3/88 (3%)

Query: 177 KKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKK 236
            + R+KQ+  K   K       KE+++  E    +K+E +K + + +K  E+  K K  K
Sbjct: 248 DEVRQKQQEAKNLPKPADTSSPKEDKQVAE---NQKREIEKAQIEIKKNDEEALKAKDHK 304

Query: 237 EKKKKKKEKKKKKEEKKKEKKKKKKKKE 264
               K++ K  +KE + KE + +KK++ 
Sbjct: 305 AFDLKQESKASEKEAEDKELEAQKKREP 332

This family consists of several Borrelia P83/P100 antigen proteins. Length = 489

>gnl|CDD|178945 PRK00247, PRK00247, putative inner membrane protein translocase component YidC; Validated

 Score = 40.2 bits (94), Expect = 7e-04
 Identities = 20/99 (20%), Positives = 43/99 (43%), Gaps = 8/99 (8%)

Query: 179 ERRKQRRRKRKRKRKKEEEEKEEE--------KKEEKKKEKKKEKKKEKKKKEKKKEKKK 230
           E+R Q R K+K K+      +           +  E   E  + KK    +K + K +KK
Sbjct: 289 EQRAQYREKQKEKKAFLWTLRRNRLRMIITPWRAPELHAENAEIKKTRTAEKNEAKARKK 348

Query: 231 KKKKKKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKK 269
           +  +K+   +++  ++ ++E      + + ++   K KK
Sbjct: 349 EIAQKRRAAEREINREARQERAAAMARARARRAAVKAKK 387

Length = 429

>gnl|CDD|234767 PRK00448, polC, DNA polymerase III PolC; Validated

 Score = 40.6 bits (96), Expect = 7e-04
 Identities = 23/79 (29%), Positives = 45/79 (56%)

Query: 194 KEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKK 253
            ++ ++E EK E +K+E+ ++  KE  +  KK E +KKK+ K    K+   +  KK +K+
Sbjct: 165 IDDSKEELEKFEAQKEEEDEKLAKEALEAMKKLEAEKKKQSKNFDPKEGPVQIGKKIDKE 224

Query: 254 KEKKKKKKKKEKKKKKDEG 272
           +    K+  +E+++   EG
Sbjct: 225 EITPMKEINEEERRVVVEG 243

Length = 1437

>gnl|CDD|222160 pfam13476, AAA_23, AAA domain

 Score = 39.5 bits (92), Expect = 7e-04
 Identities = 19/64 (29%), Positives = 43/64 (67%)

Query: 197 EEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKKKEK 256
            ++  E+ + K+KEKK+  ++ +K+ E+ +++K   +K  E+K+KKKE ++ KEE ++  
Sbjct: 141 GQERLEELKFKRKEKKERLEELEKELEELEDEKDLLEKLLEEKEKKKELEELKEELEELL 200

Query: 257 KKKK 260
           ++ +
Sbjct: 201 EELE 204

Length = 204

>gnl|CDD|218734 pfam05758, Ycf1, Ycf1

 Score = 40.4 bits (95), Expect = 7e-04
 Identities = 17/72 (23%), Positives = 36/72 (50%)

Query: 181 RKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKK 240
            K+ +   + + ++EE + E E   E K  K++++   ++      E+K+   K ++  K
Sbjct: 223 TKKLKETSETEEREEETDVEIETTSETKGTKQEQEGSTEEDPSLFSEEKEDPDKTEDLDK 282

Query: 241 KKKEKKKKKEEK 252
            +  K+KK EE 
Sbjct: 283 LEILKEKKDEEL 294

The chloroplast genomes of most higher plants contain two giant open reading frames designated ycf1 and ycf2. Although the function of Ycf1 is unknown, it is known to be an essential gene. Length = 832

>gnl|CDD|225606 COG3064, TolA, Membrane protein involved in colicin uptake [Cell envelope biogenesis, outer membrane]

 Score = 40.3 bits (94), Expect = 7e-04
 Identities = 25/86 (29%), Positives = 41/86 (47%)

Query: 189 KRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKK 248
           K+K ++  +  EE K + +    KK+ + E K   +K + + + K K EKK +   ++K 
Sbjct: 170 KKKAEEAAKAAEEAKAKAEAAAAKKKAEAEAKAAAEKAKAEAEAKAKAEKKAEAAAEEKA 229

Query: 249 KEEKKKEKKKKKKKKEKKKKKDEGRR 274
             EKKK   K K  K     K   R+
Sbjct: 230 AAEKKKAAAKAKADKAAAAAKAAERK 255

Length = 387

>gnl|CDD|225606 COG3064, TolA, Membrane protein involved in colicin uptake [Cell envelope biogenesis, outer membrane]

 Score = 40.3 bits (94), Expect = 7e-04
 Identities = 22/91 (24%), Positives = 58/91 (63%)

Query: 177 KKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKK 236
           K E++++++ ++  +  K ++  E+E+ ++ +KE+ K ++++K+ +E +K+ + ++K+++
Sbjct: 76  KGEQQRKKKEEQVAEELKPKQAAEQERLKQLEKERLKAQEQQKQAEEAEKQAQLEQKQQE 135

Query: 237 EKKKKKKEKKKKKEEKKKEKKKKKKKKEKKK 267
           E+ +K   ++KKK E  K K   +  K K  
Sbjct: 136 EQARKAAAEQKKKAEAAKAKAAAEAAKLKAA 166

Length = 387

>gnl|CDD|235175 PRK03918, PRK03918, chromosome segregation protein; Provisional

 Score = 40.8 bits (96), Expect = 7e-04
 Identities = 27/111 (24%), Positives = 63/111 (56%), Gaps = 7/111 (6%)

Query: 172 GYKGGKKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKK 231
           G K   +E+ ++   + +  +K+ EE +E+ K+ ++ KEK +E  K  +  E+  ++ ++
Sbjct: 252 GSKRKLEEKIRELEERIEELKKEIEELEEKVKELKELKEKAEEYIKLSEFYEEYLDELRE 311

Query: 232 KKKKKEKK-------KKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDEGRRR 275
            +K+  +        +++ ++ ++KEE+ +E KKK K+ EK+ ++ E R  
Sbjct: 312 IEKRLSRLEEEINGIEERIKELEEKEERLEELKKKLKELEKRLEELEERHE 362

Length = 880

>gnl|CDD|223496 COG0419, SbcC, ATPase involved in DNA repair [DNA replication, recombination, and repair]

 Score = 40.5 bits (95), Expect = 7e-04
 Identities = 21/94 (22%), Positives = 52/94 (55%), Gaps = 1/94 (1%)

Query: 173 YKGGKKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKK 232
                 E  +++  + + + ++E +  E E++ E+K E+ ++ ++E ++  ++ E+  KK
Sbjct: 651 LLQAALEELEEKVEELEAEIRRELQRIENEEQLEEKLEELEQLEEELEQLREELEELLKK 710

Query: 233 KKKKEKKKKK-KEKKKKKEEKKKEKKKKKKKKEK 265
             + E+  ++ + +K + EE KKE +K +K  E 
Sbjct: 711 LGEIEQLIEELESRKAELEELKKELEKLEKALEL 744

Length = 908

>gnl|CDD|204414 pfam10211, Ax_dynein_light, Axonemal dynein light chain

 Score = 39.5 bits (93), Expect = 7e-04
 Identities = 21/79 (26%), Positives = 49/79 (62%), Gaps = 3/79 (3%)

Query: 190 RKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKK 249
           RK  + E+ K E    E++ +K +E+K+E +K+  + E K +  +K+E+++++ E+K+  
Sbjct: 113 RKALQAEQGKSEL---EQEIKKLEEEKEELEKRVAELEAKLEAIEKREEEERQIEEKRHA 169

Query: 250 EEKKKEKKKKKKKKEKKKK 268
           +E    KK+ ++ K + ++
Sbjct: 170 DEIAFLKKQNQQLKSQLEQ 188

Axonemal dynein light chain proteins play a dynamic role in flagellar and cilia motility. Eukaryotic cilia and flagella are complex organelles consisting of a core structure, the axoneme, which is composed of nine microtubule doublets forming a cylinder that surrounds a pair of central singlet microtubules. This ultra-structural arrangement seems to be one of the most stable micro-tubular assemblies known and is responsible for the flagellar and ciliary movement of a large number of organisms ranging from protozoan to mammals. This light chain interacts directly with the N-terminal half of the heavy chains. Length = 189

>gnl|CDD|226894 COG4499, COG4499, Predicted membrane protein [Function unknown]

 Score = 40.2 bits (94), Expect = 8e-04
 Identities = 16/71 (22%), Positives = 44/71 (61%)

Query: 175 GGKKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKK 234
           G K++   +   K+ +   K+  E ++E    ++ E K +++K K+++ +KK+K++  + 
Sbjct: 364 GDKRQELLKEYNKKLQDYTKKLGEVKDETDASEEAEAKAKEEKLKQEENEKKQKEQADED 423

Query: 235 KKEKKKKKKEK 245
           K++++K +++K
Sbjct: 424 KEKRQKDERKK 434

Length = 434

>gnl|CDD|130141 TIGR01069, mutS2, MutS2 family protein

 Score = 40.6 bits (95), Expect = 8e-04
 Identities = 24/84 (28%), Positives = 47/84 (55%), Gaps = 1/84 (1%)

Query: 185 RRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKK-EKKKKEKKKEKKKKKKKKKEKKKKKK 243
           + K      KEE     EK    +KE +++ +  EK  KE++K KK+ +++ +E K++++
Sbjct: 501 QAKTFYGEFKEEINVLIEKLSALEKELEQKNEHLEKLLKEQEKLKKELEQEMEELKERER 560

Query: 244 EKKKKKEEKKKEKKKKKKKKEKKK 267
            KK + E++ +E  K  KK+ +  
Sbjct: 561 NKKLELEKEAQEALKALKKEVESI 584

Function of MutS2 is unknown. It should not be considered a DNA mismatch repair protein. It is likely a DNA mismatch binding protein of unknown cellular function [DNA metabolism, Other]. Length = 771

>gnl|CDD|237035 PRK12280, rplW, 50S ribosomal protein L23; Reviewed

 Score = 38.6 bits (90), Expect = 8e-04
 Identities = 28/63 (44%), Positives = 40/63 (63%)

Query: 191 KRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKE 250
           +++++E  KE E+KE  K +K+K++KKEKK  EK  +KK  K  K   KK  K+   KKE
Sbjct: 96  EKEQKEVSKETEEKEAIKAKKEKKEKKEKKVAEKLAKKKSTKTTKNTTKKATKKTTTKKE 155

Query: 251 EKK 253
           E K
Sbjct: 156 EGK 158

Length = 158

>gnl|CDD|219868 pfam08496, Peptidase_S49_N, Peptidase family S49 N-terminal

 Score = 38.7 bits (91), Expect = 8e-04
 Identities = 22/70 (31%), Positives = 37/70 (52%), Gaps = 5/70 (7%)

Query: 185 RRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKE 244
            +K+K K+ + E     E+ ++ K+  +     +K+ K  +K +KK      EK K K E
Sbjct: 32  AQKKKGKKGELEITDLNEEYKDLKESLEAALLDKKELKAWEKAEKKA-----EKAKAKAE 86

Query: 245 KKKKKEEKKK 254
           KKK K+E+ K
Sbjct: 87  KKKAKKEEPK 96

This domain is found to the N-terminus of bacterial signal peptidases of the S49 family (pfam01343). Length = 154

>gnl|CDD|150884 pfam10278, Med19, Mediator of RNA pol II transcription subunit 19

 Score = 39.0 bits (91), Expect = 8e-04
 Identities = 22/68 (32%), Positives = 41/68 (60%)

Query: 197 EEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKKKEK 256
           +  +++ K + KK + ++   E+   + +  K  +KK KK+K +  KE+KKKK+EKKK+K
Sbjct: 107 QPPKKKHKHKHKKHRTQDPLPEETPSDSEGLKGHEKKHKKKKHEDDKERKKKKKEKKKKK 166

Query: 257 KKKKKKKE 264
           K+   +  
Sbjct: 167 KRHSPEHP 174

Med19 represents a family of conserved proteins which are members of the multi-protein co-activator Mediator complex. Mediator is required for activation of RNA polymerase II transcription by DNA binding transactivators. Length = 178

>gnl|CDD|224415 COG1498, SIK1, Protein implicated in ribosomal biogenesis, Nop56p homolog [Translation, ribosomal structure and biogenesis]

 Score = 40.1 bits (94), Expect = 8e-04
 Identities = 17/53 (32%), Positives = 30/53 (56%)

Query: 223 EKKKEKKKKKKKKKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDEGRRR 275
              +E+ +K+ +K ++K  K   K K E  KKE+  + ++K+K+KK    RR 
Sbjct: 340 ISLREELEKRIEKLKEKPPKPPTKAKPERDKKERPGRYRRKKKEKKAKSERRG 392

Length = 395

>gnl|CDD|223783 COG0711, AtpF, F0F1-type ATP synthase, subunit b [Energy production and conversion]

 Score = 38.8 bits (91), Expect = 8e-04
 Identities = 18/89 (20%), Positives = 49/89 (55%)

Query: 187 KRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKK 246
           +R+ K   +  E E  K+E +    + E++ E+ +++  +  ++ KK+ ++  ++ K + 
Sbjct: 37  ERQAKIADDLAEAERLKEEAQALLAEYEQELEEAREQASEIIEQAKKEAEQIAEEIKAEA 96

Query: 247 KKKEEKKKEKKKKKKKKEKKKKKDEGRRR 275
           +++ E+ KE  + + + EK++  +E R  
Sbjct: 97  EEELERIKEAAEAEIEAEKERALEELRAE 125

Length = 161

>gnl|CDD|220271 pfam09507, CDC27, DNA polymerase subunit Cdc27

 Score = 40.2 bits (94), Expect = 8e-04
 Identities = 25/99 (25%), Positives = 43/99 (43%)

Query: 174 KGGKKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKK 233
             GK+   K  +     + K +  +K ++  +E   EK + K   K    K+   KK   
Sbjct: 158 ANGKRPSSKPPKSIMSPEVKVKSAKKTQDTSKETTTEKTEGKTSVKAASLKRNPPKKSNI 217

Query: 234 KKKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDEG 272
                KKK KEKK+KKE  +   K++ +++  K+     
Sbjct: 218 MSSFFKKKTKEKKEKKEASESTVKEESEEESGKRDVILE 256

This protein forms the C subunit of DNA polymerase delta. It carries the essential residues for binding to the Pol1 subunit of polymerase alpha, from residues 293-332, which are characterized by the motif D--G--VT, referred to as the DPIM motif. The first 160 residues of the protein form the minimal domain for binding to the B subunit, Cdc1, of polymerase delta, the final 10 C-terminal residues, 362-372, being the DNA sliding clamp, PCNA, binding motif. Length = 427

>gnl|CDD|214661 smart00435, TOPEUc, DNA Topoisomerase I (eukaryota)

 Score = 40.0 bits (94), Expect = 9e-04
 Identities = 27/81 (33%), Positives = 42/81 (51%), Gaps = 3/81 (3%)

Query: 173 YKGGKKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKK 232
            K   K  +K           K + + + E+  EK   + KEKKKEKKK+EK   KKK+ 
Sbjct: 289 LKYQLKRLKKMILLFEMISDLKRKLKSKFERDNEKLDAEVKEKKKEKKKEEK---KKKQI 345

Query: 233 KKKKEKKKKKKEKKKKKEEKK 253
           ++ +E+ +K + +   KEE K
Sbjct: 346 ERLEERIEKLEVQATDKEENK 366

DNA Topoisomerase I (eukaryota), DNA topoisomerase V, Vaccina virus topoisomerase, Variola virus topoisomerase, Shope fibroma virus topoisomeras. Length = 391

>gnl|CDD|236545 PRK09510, tolA, cell envelope integrity inner membrane protein TolA; Provisional

 Score = 39.8 bits (93), Expect = 9e-04
 Identities = 30/101 (29%), Positives = 47/101 (46%), Gaps = 7/101 (6%)

Query: 178 KERRKQRRRKRKRKRKKEEEEK---EEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKK 234
           K+  K+R   +++K++ EE  K    ++K+ E+   K     K K + E K+     KK 
Sbjct: 104 KQLEKERLAAQEQKKQAEEAAKQAALKQKQAEEAAAKAAAAAKAKAEAEAKRAAAAAKKA 163

Query: 235 KKEKKKKKKEKKKKKEE----KKKEKKKKKKKKEKKKKKDE 271
             E KKK + +  KK      KK E +   K   + KKK E
Sbjct: 164 AAEAKKKAEAEAAKKAAAEAKKKAEAEAAAKAAAEAKKKAE 204

Length = 387

>gnl|CDD|187751 cd09270, RNase_H2-B, Ribonuclease H2-B is a subunit of the eukaryotic RNase H complex which cleaves RNA-DNA hybrids

 Score = 39.2 bits (92), Expect = 9e-04
 Identities = 22/56 (39%), Positives = 33/56 (58%)

Query: 220 KKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDEGRRR 275
            KK ++ +KK+   K+ E  + KK+    +EEKKK+KKK  KKK+ KK    G + 
Sbjct: 150 LKKVERLKKKELDIKEAEAARDKKKSNNAEEEKKKKKKKSAKKKKLKKVAAVGMKA 205

Ribonuclease H2B is one of the three proteins of eukaryotic RNase H2 complex that is required for nucleic acid binding and hydrolysis. RNase H is classified into two families, type I (prokaryotic RNase HI, eukaryotic RNase H1 and viral RNase H) and type II (prokaryotic RNase HII and HIII, and eukaryotic RNase H2/HII). RNase H endonucleolytically hydrolyzes an RNA strand when it is annealed to a complementary DNA strand in the presence of divalent cations, in DNA replication and repair. The enzyme can be found in bacteria, archaea, and eukaryotes. Most prokaryotic and eukaryotic genomes contain multiple RNase H genes. Despite a lack of evidence for homology from sequence comparisons, type I and type II RNase H share a common fold and similar steric configurations of the four acidic active-site residues, suggesting identical or very similar catalytic mechanisms. Eukaryotic RNase HII is active during replication and is believed to play a role in removal of Okazaki fragment primers and single ribonucleotides in DNA-DNA duplexes. Eukaryotic RNase HII is functional when it forms a complex with RNase H2B and RNase H2C proteins. It is speculated that the two accessory subunits are required for correct folding of the catalytic subunit of RNase HII. Mutations in the three subunits of human RNase HII cause neurological disorder. Length = 211

>gnl|CDD|200340 TIGR03927, T7SS_EssA_Firm, type VII secretion protein EssA

 Score = 38.5 bits (90), Expect = 9e-04
 Identities = 16/79 (20%), Positives = 38/79 (48%)

Query: 193 KKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEK 252
           KK+ E   +  +EE + +K+    +E+KK   +K K+K ++++ + +   +   +    K
Sbjct: 33  KKDIEINTDYLQEETELDKELFTPEEQKKITFQKHKEKPEQEELKNQLFSENATENNTVK 92

Query: 253 KKEKKKKKKKKEKKKKKDE 271
             +K+    + E+     E
Sbjct: 93  ATKKQLFSSEYEQTSSSSE 111

Members of this family are associated with type VII secretion of WXG100 family targets in the Firmicutes, but not in the Actinobacteria. This highly divergent protein family consists largely of a central region of highly polar low-complexity sequence containing occasional LF motifs in weak repeats about 17 residues in length, flanked by hydrophobic N- and C-terminal regions [Protein fate, Protein and peptide secretion and trafficking]. Length = 150

>gnl|CDD|224415 COG1498, SIK1, Protein implicated in ribosomal biogenesis, Nop56p homolog [Translation, ribosomal structure and biogenesis]

 Score = 40.1 bits (94), Expect = 9e-04
 Identities = 15/62 (24%), Positives = 33/62 (53%)

Query: 190 RKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKK 249
                    +EE +K  +K ++K  K   K K E+ K+++  + ++K+K+KK K +++  
Sbjct: 334 SGEPDGISLREELEKRIEKLKEKPPKPPTKAKPERDKKERPGRYRRKKKEKKAKSERRGL 393

Query: 250 EE 251
           + 
Sbjct: 394 QN 395

Length = 395

>gnl|CDD|220237 pfam09428, DUF2011, Fungal protein of unknown function (DUF2011)

 Score = 38.0 bits (89), Expect = 9e-04
 Identities = 18/61 (29%), Positives = 46/61 (75%)

Query: 209 KEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKK 268
           K +K+  ++++KKK++K+  KK++   + ++++ KE+ +K++  +K ++KK K+++K+K+
Sbjct: 70  KVEKELLREKEKKKKRKRPGKKRRIALRLRRERTKERAEKEKRTRKNREKKFKRRQKEKE 129

Query: 269 K 269
           K
Sbjct: 130 K 130

This is a family of fungal proteins whose function is unknown. Length = 130

>gnl|CDD|235549 PRK05658, PRK05658, RNA polymerase sigma factor RpoD; Validated

 Score = 40.2 bits (95), Expect = 9e-04
 Identities = 23/73 (31%), Positives = 39/73 (53%), Gaps = 2/73 (2%)

Query: 193 KKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEK 252
           + EE + +E+++EE+ +        E +  EK  E  K K   K+ KK +K ++KK E +
Sbjct: 188 ELEELDDDEDEEEEEDENDDSLAADESELPEKVLE--KFKALAKQYKKLRKAQEKKVEGR 245

Query: 253 KKEKKKKKKKKEK 265
             + KK  K +EK
Sbjct: 246 LAQHKKYAKLREK 258

Length = 619

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 40.1 bits (93), Expect = 0.001
 Identities = 34/100 (34%), Positives = 62/100 (62%), Gaps = 2/100 (2%)

Query: 174  KGGKKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKK--K 231
            K  +++++ +  +K +  +     + EE KK E+ + ++  K  E++KK K +E KK  +
Sbjct: 1558 KKAEEKKKAEEAKKAEEDKNMALRKAEEAKKAEEARIEEVMKLYEEEKKMKAEEAKKAEE 1617

Query: 232  KKKKKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDE 271
             K K E+ KK +E+KKK E+ KK++ ++KKK E+ KK +E
Sbjct: 1618 AKIKAEELKKAEEEKKKVEQLKKKEAEEKKKAEELKKAEE 1657

Length = 2084

>gnl|CDD|219655 pfam07946, DUF1682, Protein of unknown function (DUF1682)

 Score = 39.5 bits (93), Expect = 0.001
 Identities = 16/50 (32%), Positives = 34/50 (68%), Gaps = 2/50 (4%)

Query: 173 YKGGKKERRKQRRRKRKRKRKKEEEEKEEE--KKEEKKKEKKKEKKKEKK 220
            K  ++ER+++ + K++ K+K+E E K  +   +E++K E+K+ KK+ +K
Sbjct: 273 LKAAEEERQEEAQEKKEEKKKEEREAKLAKLSPEEQRKLEEKERKKQARK 322

The members of this family are all hypothetical eukaryotic proteins of unknown function. One member is described as being an adipocyte-specific protein, but no evidence of this was found. Length = 322

>gnl|CDD|219655 pfam07946, DUF1682, Protein of unknown function (DUF1682)

 Score = 39.2 bits (92), Expect = 0.001
 Identities = 17/52 (32%), Positives = 34/52 (65%), Gaps = 3/52 (5%)

Query: 177 KKERRKQRRRKRKRKRKKEEEEKEEEKKEEKK---KEKKKEKKKEKKKKEKK 225
           K  +  +  R+ + + KKEE++KEE + +  K   +E++K ++KE+KK+ +K
Sbjct: 271 KILKAAEEERQEEAQEKKEEKKKEEREAKLAKLSPEEQRKLEEKERKKQARK 322

The members of this family are all hypothetical eukaryotic proteins of unknown function. One member is described as being an adipocyte-specific protein, but no evidence of this was found. Length = 322

>gnl|CDD|215214 PLN02381, PLN02381, valyl-tRNA synthetase

 Score = 40.3 bits (94), Expect = 0.001
 Identities = 20/59 (33%), Positives = 35/59 (59%)

Query: 217 KEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDEGRRR 275
           ++K   E++ E+KKKK++K ++K+ KK K  +KE K K + ++        KK E + R
Sbjct: 9   EKKILTEEELERKKKKEEKAKEKELKKLKAAQKEAKAKLQAQQASDGTNVPKKSEKKSR 67

Length = 1066

>gnl|CDD|217051 pfam02463, SMC_N, RecF/RecN/SMC N terminal domain

 Score = 40.3 bits (94), Expect = 0.001
 Identities = 27/104 (25%), Positives = 64/104 (61%)

Query: 168 NLEYGYKGGKKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKE 227
             E   K  ++ + + ++ K +++    ++ +E + K  ++ +  ++K KEK+++E+K  
Sbjct: 698 RQEEIKKKEQRIKEELKKLKLEKEELLADKVQEAQDKINEELKLLEQKIKEKEEEEEKSR 757

Query: 228 KKKKKKKKKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDE 271
            KK+++++++ +   KEK+  +EE+K EK K +++KE+K K  E
Sbjct: 758 LKKEEEEEEKSELSLKEKELAEEEEKTEKLKVEEEKEEKLKAQE 801

This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination. Length = 1162

>gnl|CDD|217051 pfam02463, SMC_N, RecF/RecN/SMC N terminal domain

 Score = 39.6 bits (92), Expect = 0.001
 Identities = 22/81 (27%), Positives = 43/81 (53%)

Query: 191  KRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKE 250
               K E E EE   EE  +++K+E  KE++++  K+    K++          E ++K+E
Sbjct: 930  ILLKYESEPEELLLEEADEKEKEEDNKEEEEERNKRLLLAKEELGNVNLMAIAEFEEKEE 989

Query: 251  EKKKEKKKKKKKKEKKKKKDE 271
               K++ KK++ +E+KK+   
Sbjct: 990  RYNKDELKKERLEEEKKELLR 1010

This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination. Length = 1162

>gnl|CDD|235640 PRK05901, PRK05901, RNA polymerase sigma factor; Provisional

 Score = 39.6 bits (93), Expect = 0.001
 Identities = 13/87 (14%), Positives = 26/87 (29%)

Query: 185 RRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKE 244
                 K+K +   K    K   KK+ K E    KK ++K    K       +      +
Sbjct: 70  TESDIPKKKTKTAAKAAAAKAPAKKKLKDELDSSKKAEKKNALDKDDDLNYVKDIDVLNQ 129

Query: 245 KKKKKEEKKKEKKKKKKKKEKKKKKDE 271
                ++   +        +    +D+
Sbjct: 130 ADDDDDDDDDDDLDDDDIDDDDDDEDD 156

Length = 509

>gnl|CDD|223880 COG0810, TonB, Periplasmic protein TonB, links inner and outer membranes [Cell envelope biogenesis, outer membrane]

 Score = 39.4 bits (92), Expect = 0.001
 Identities = 19/79 (24%), Positives = 29/79 (36%)

Query: 194 KEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKK 253
            E E   E    + K++ K EKK +K K + K + K K K K + K KK   K   +   
Sbjct: 71  TEPETPPEPTPPKPKEKPKPEKKPKKPKPKPKPKPKPKPKVKPQPKPKKPPSKTAAKAPA 130

Query: 254 KEKKKKKKKKEKKKKKDEG 272
              +  +            
Sbjct: 131 APNQPARPPSAASASGAAT 149

Length = 244

>gnl|CDD|114011 pfam05262, Borrelia_P83, Borrelia P83/100 protein

 Score = 40.0 bits (93), Expect = 0.001
 Identities = 23/105 (21%), Positives = 51/105 (48%), Gaps = 13/105 (12%)

Query: 181 RKQRRRKRKRKRKKEEEEKEEEKKEEKK--KEKKKEKKKEKKKKEKKKEKKKKKKK---- 234
           R + R+K++  +   +       KE+K+  + +K+E +K + + +K  E+  K K     
Sbjct: 247 RDEVRQKQQEAKNLPKPADTSSPKEDKQVAENQKREIEKAQIEIKKNDEEALKAKDHKAF 306

Query: 235 --KKEKKKKKKEKKKKKEEKKKEKKK-----KKKKKEKKKKKDEG 272
             K+E K  +KE + K+ E +K+++      +K K + + +    
Sbjct: 307 DLKQESKASEKEAEDKELEAQKKREPVAEDLQKTKPQVEAQPTSL 351

This family consists of several Borrelia P83/P100 antigen proteins. Length = 489

>gnl|CDD|114011 pfam05262, Borrelia_P83, Borrelia P83/100 protein

 Score = 39.6 bits (92), Expect = 0.001
 Identities = 22/102 (21%), Positives = 47/102 (46%)

Query: 167 DNLEYGYKGGKKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKK 226
           D +    +  K   +       K  ++  E +K E +K + + +K  E+  + K  +   
Sbjct: 248 DEVRQKQQEAKNLPKPADTSSPKEDKQVAENQKREIEKAQIEIKKNDEEALKAKDHKAFD 307

Query: 227 EKKKKKKKKKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKK 268
            K++ K  +KE + K+ E +KK+E   ++ +K K + E +  
Sbjct: 308 LKQESKASEKEAEDKELEAQKKREPVAEDLQKTKPQVEAQPT 349

This family consists of several Borrelia P83/P100 antigen proteins. Length = 489

>gnl|CDD|114011 pfam05262, Borrelia_P83, Borrelia P83/100 protein

 Score = 39.6 bits (92), Expect = 0.001
 Identities = 25/100 (25%), Positives = 51/100 (51%), Gaps = 3/100 (3%)

Query: 177 KKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKE-KKKEKKKK--EKKKEKKKKKK 233
           K+E  K++    K ++K +  +   +K+ ++ ++K++E K   K       K++K+  + 
Sbjct: 219 KEELDKKQIDADKAQQKADFAQDNADKQRDEVRQKQQEAKNLPKPADTSSPKEDKQVAEN 278

Query: 234 KKKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDEGR 273
           +K+E +K + E KK  EE  K K  K    +++ K  E  
Sbjct: 279 QKREIEKAQIEIKKNDEEALKAKDHKAFDLKQESKASEKE 318

This family consists of several Borrelia P83/P100 antigen proteins. Length = 489

>gnl|CDD|235401 PRK05306, infB, translation initiation factor IF-2; Validated

 Score = 39.4 bits (93), Expect = 0.001
 Identities = 15/78 (19%), Positives = 35/78 (44%)

Query: 198 EKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKKKEKK 257
           EK +E   E K      +++E +K+E K+E +++ K + E+    + +++ K E      
Sbjct: 22  EKLKELGIEVKSHSSTVEEEEARKEEAKREAEEEAKAEAEEAAAAEAEEEAKAEAAAAAP 81

Query: 258 KKKKKKEKKKKKDEGRRR 275
            ++  +     +   R  
Sbjct: 82  AEEAAEAAAAAEAAARPA 99

Length = 746

>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]

 Score = 40.1 bits (94), Expect = 0.001
 Identities = 24/89 (26%), Positives = 60/89 (67%)

Query: 183 QRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKK 242
           ++RR+R  +  +E EE+ EE +E+  + +++ ++ EK+ +E K+E ++ + +K+E + + 
Sbjct: 820 EQRRERLEQEIEELEEEIEELEEKLDELEEELEELEKELEELKEELEELEAEKEELEDEL 879

Query: 243 KEKKKKKEEKKKEKKKKKKKKEKKKKKDE 271
           KE +++KEE ++E ++ + +  + K++ E
Sbjct: 880 KELEEEKEELEEELRELESELAELKEEIE 908

Length = 1163

>gnl|CDD|172341 PRK13808, PRK13808, adenylate kinase; Provisional

 Score = 39.9 bits (93), Expect = 0.001
 Identities = 29/102 (28%), Positives = 43/102 (42%)

Query: 174 KGGKKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKK 233
           K G K+   + +   K+  KK+  +     K+  K   K  KK +K  K+  K+  K  K
Sbjct: 209 KSGAKKASAKAKSAAKKVSKKKAAKTAVSAKKAAKTAAKAAKKAKKTAKKALKKAAKAVK 268

Query: 234 KKKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDEGRRR 275
           K  +K  K   K  K   K  + K K KKK  KK     + +
Sbjct: 269 KAAKKAAKAAAKAAKGAAKATKGKAKAKKKAGKKAAAGSKAK 310

Length = 333

>gnl|CDD|236545 PRK09510, tolA, cell envelope integrity inner membrane protein TolA; Provisional

 Score = 39.8 bits (93), Expect = 0.001
 Identities = 22/92 (23%), Positives = 45/92 (48%)

Query: 174 KGGKKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKK 233
           K   ++ R ++  K +   ++++++ EE  K+   K+K+ E+   K     K + + + K
Sbjct: 95  KQAAEQERLKQLEKERLAAQEQKKQAEEAAKQAALKQKQAEEAAAKAAAAAKAKAEAEAK 154

Query: 234 KKKEKKKKKKEKKKKKEEKKKEKKKKKKKKEK 265
           +     KK   + KKK E +  KK   + K+K
Sbjct: 155 RAAAAAKKAAAEAKKKAEAEAAKKAAAEAKKK 186

Length = 387

>gnl|CDD|240246 PTZ00053, PTZ00053, methionine aminopeptidase 2; Provisional

 Score = 39.7 bits (93), Expect = 0.001
 Identities = 19/86 (22%), Positives = 39/86 (45%)

Query: 166 GDNLEYGYKGGKKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKK 225
           G+N     K   K++  +++ K+ +K   +++    E   E ++ + K+  K+KKKK+KK
Sbjct: 6   GENEVKQQKQQNKQKGTKKKNKKSKKDVDDDDAFLAELISENQEAENKQNNKKKKKKKKK 65

Query: 226 KEKKKKKKKKKEKKKKKKEKKKKKEE 251
           K+KK   +                 +
Sbjct: 66  KKKKNLGEAYDLAYDLPVVWSSAAFQ 91

Length = 470

>gnl|CDD|240246 PTZ00053, PTZ00053, methionine aminopeptidase 2; Provisional

 Score = 39.7 bits (93), Expect = 0.001
 Identities = 22/84 (26%), Positives = 42/84 (50%)

Query: 166 GDNLEYGYKGGKKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKK 225
            +N E   K  K++ +++  +K+ +K KK+ ++ +    E   + ++ E K+  KKK+KK
Sbjct: 3   NENGENEVKQQKQQNKQKGTKKKNKKSKKDVDDDDAFLAELISENQEAENKQNNKKKKKK 62

Query: 226 KEKKKKKKKKKEKKKKKKEKKKKK 249
           K+KKKKK   +             
Sbjct: 63  KKKKKKKNLGEAYDLAYDLPVVWS 86

Length = 470

>gnl|CDD|237035 PRK12280, rplW, 50S ribosomal protein L23; Reviewed

 Score = 38.2 bits (89), Expect = 0.001
 Identities = 21/63 (33%), Positives = 40/63 (63%)

Query: 189 KRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKK 248
           ++++K+  +E EE++  + KKEKK++K+K+  +K  KK+  K  K   +K  KK   KK+
Sbjct: 96  EKEQKEVSKETEEKEAIKAKKEKKEKKEKKVAEKLAKKKSTKTTKNTTKKATKKTTTKKE 155

Query: 249 KEE 251
           + +
Sbjct: 156 EGK 158

Length = 158

>gnl|CDD|227446 COG5116, RPN2, 26S proteasome regulatory complex component [Posttranslational modification, protein turnover, chaperones]

 Score = 40.3 bits (94), Expect = 0.001
 Identities = 15/65 (23%), Positives = 31/65 (47%)

Query: 211 KKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKD 270
           K   + K+K K++   +K+ K +    + + ++   K++EEK  +       K+KK  K 
Sbjct: 792 KAAARAKQKPKEKGPNDKEIKIESPSVETEGERCTIKQREEKGIDAPAILNVKKKKPYKV 851

Query: 271 EGRRR 275
           +   R
Sbjct: 852 DNMTR 856

Length = 926

>gnl|CDD|217756 pfam03839, Sec62, Translocation protein Sec62

 Score = 39.0 bits (91), Expect = 0.001
 Identities = 19/64 (29%), Positives = 32/64 (50%)

Query: 180 RRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKK 239
           R  +  + +  K K   E   +   ++K  EK K   K +  +  KK   ++KK++K+K 
Sbjct: 14  RALESEKYKANKDKGNPEIYNKINSQDKAIEKFKLLIKAQMAERVKKLHSQEKKEEKKKP 73

Query: 240 KKKK 243
           KKKK
Sbjct: 74  KKKK 77

Length = 217

>gnl|CDD|188306 TIGR03319, RNase_Y, ribonuclease Y

 Score = 39.5 bits (93), Expect = 0.001
 Identities = 19/78 (24%), Positives = 43/78 (55%)

Query: 194 KEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKK 253
           K   EK+    EE  K   +E KKE +  +K+   + K++  K + + ++E K+++ E +
Sbjct: 20  KRIAEKKLGSAEELAKRIIEEAKKEAETLKKEALLEAKEEVHKLRAELERELKERRNELQ 79

Query: 254 KEKKKKKKKKEKKKKKDE 271
           + +++  +++E   +K E
Sbjct: 80  RLERRLLQREETLDRKME 97

Members of this family are RNase Y, an endoribonuclease. The member from Bacillus subtilis, YmdA, has been shown to be involved in turnover of yitJ riboswitch [Transcription, Degradation of RNA]. Length = 514

>gnl|CDD|236048 PRK07561, PRK07561, DNA topoisomerase I subunit omega; Validated

 Score = 39.8 bits (94), Expect = 0.001
 Identities = 9/45 (20%), Positives = 17/45 (37%)

Query: 217 KEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKKKEKKKKKK 261
             +K ++ +       K    KK   K  +K K++    +K  K 
Sbjct: 814 LAEKPEKLRYLADAPAKDPAGKKAAVKFSRKTKQQYVASEKDGKA 858

Length = 859

>gnl|CDD|235971 PRK07219, PRK07219, DNA topoisomerase I; Validated

 Score = 40.0 bits (94), Expect = 0.001
 Identities = 11/74 (14%), Positives = 23/74 (31%)

Query: 197 EEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKKKEK 256
           +    ++       K    +K+KK+KE K E +  K    +  +K K+   +        
Sbjct: 747 KGGFGDELGCCNNPKCNYTEKQKKEKESKSELEALKGVGAKTAEKLKDAGVETVTDLTAA 806

Query: 257 KKKKKKKEKKKKKD 270
                  +      
Sbjct: 807 DPDAVAAKVDGVSA 820

Length = 822

>gnl|CDD|235971 PRK07219, PRK07219, DNA topoisomerase I; Validated

 Score = 40.0 bits (94), Expect = 0.001
 Identities = 12/78 (15%), Positives = 25/78 (32%)

Query: 191 KRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKE 250
           + K    ++       K    +K+KK+++ K E +  K    K  ++ K    E      
Sbjct: 745 RVKGGFGDELGCCNNPKCNYTEKQKKEKESKSELEALKGVGAKTAEKLKDAGVETVTDLT 804

Query: 251 EKKKEKKKKKKKKEKKKK 268
               +    K       +
Sbjct: 805 AADPDAVAAKVDGVSADR 822

Length = 822

>gnl|CDD|206039 pfam13868, Trichoplein, Tumour suppressor, Mitostatin

 Score = 39.5 bits (93), Expect = 0.001
 Identities = 24/104 (23%), Positives = 68/104 (65%), Gaps = 11/104 (10%)

Query: 177 KKERRKQRRRKRKRKRKKEEEEKEEEKK--EEKKKEKKKEKKKEKKKKEKKKE------- 227
            KER  Q   K++ K +++EEE+  ++   EE+ K   +E+++E+K+KE+++E       
Sbjct: 19  NKERDAQIEEKKRIKAEEKEEERRIDEMMEEERLKALAEEEERERKRKEERREGRAVLQE 78

Query: 228 --KKKKKKKKKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKK 269
             ++++K++++E +++ +E+++  E  ++ +++ + + ++K++K
Sbjct: 79  QIEEREKRRQEEYEERLQEREQMDEIIERIQEEDEAEAQEKREK 122

Trichoplein or mitostatin, was first defined as a meiosis-specific nuclear structural protein. It has since been linked with mitochondrial movement. It is associated with the mitochondrial outer membrane, and over-expression leads to reduction in mitochondrial motility whereas lack of it enhances mitochondrial movement. The activity appears to be mediated through binding the mitochondria to the actin intermediate filaments (IFs). Length = 349

>gnl|CDD|227519 COG5192, BMS1, GTP-binding protein required for 40S ribosome biogenesis [Translation, ribosomal structure and biogenesis]

 Score = 40.1 bits (93), Expect = 0.001
 Identities = 16/66 (24%), Positives = 41/66 (62%)

Query: 210  EKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKK 269
             + +EK + K +  K++ K +++K++ E  ++ KE++  K+EK++E++ +K   +  K+ 
Sbjct: 1009 PECREKHEIKDRIVKERIKDQEEKERMESLQRAKEEEIGKKEKEREQRIRKTIHDNYKEM 1068

Query: 270  DEGRRR 275
             + R +
Sbjct: 1069 AKKRLK 1074

Length = 1077

>gnl|CDD|227352 COG5019, CDC3, Septin family protein [Cell division and chromosome partitioning / Cytoskeleton]

 Score = 39.2 bits (92), Expect = 0.001
 Identities = 18/74 (24%), Positives = 35/74 (47%)

Query: 168 NLEYGYKGGKKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKE 227
                     +   ++R  K+K   K  E+EK  E+ E+   E++KE   + ++ +KK E
Sbjct: 300 EPSLKEIHEARLNEEERELKKKFTEKIREKEKRLEELEQNLIEERKELNSKLEEIQKKLE 359

Query: 228 KKKKKKKKKEKKKK 241
             +K+ +K +  K 
Sbjct: 360 DLEKRLEKLKSNKS 373

Length = 373

>gnl|CDD|184900 PRK14907, rplD, 50S ribosomal protein L4; Provisional

 Score = 39.2 bits (91), Expect = 0.001
 Identities = 33/87 (37%), Positives = 40/87 (45%), Gaps = 3/87 (3%)

Query: 187 KRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKK---KKEKKKEKKKKKKKKKEKKKKKK 243
           K+  K+K  EE+K   KK    KE  K KK  K    K  KK  K KK K  K   KK  
Sbjct: 5   KKTTKKKTTEEKKPAAKKATTSKETAKTKKTAKTTSTKAAKKAAKVKKTKSVKTTTKKVT 64

Query: 244 EKKKKKEEKKKEKKKKKKKKEKKKKKD 270
            K +K E  KKE   KK  K++    +
Sbjct: 65  VKFEKTESVKKESVAKKTVKKEAVSAE 91

Length = 295

>gnl|CDD|235175 PRK03918, PRK03918, chromosome segregation protein; Provisional

 Score = 40.0 bits (94), Expect = 0.001
 Identities = 22/98 (22%), Positives = 55/98 (56%), Gaps = 2/98 (2%)

Query: 178 KERRKQRRRKRKRKRKKEE--EEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKK 235
           +E  K  +  ++ +  KEE  E ++E +  E  K K +EK +E +++ ++ +K+ ++ ++
Sbjct: 221 EELEKLEKEVKELEELKEEIEELEKELESLEGSKRKLEEKIRELEERIEELKKEIEELEE 280

Query: 236 KEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDEGR 273
           K K+ K+ ++K ++  K  E  ++   + ++ +K   R
Sbjct: 281 KVKELKELKEKAEEYIKLSEFYEEYLDELREIEKRLSR 318

Length = 880

>gnl|CDD|235175 PRK03918, PRK03918, chromosome segregation protein; Provisional

 Score = 39.7 bits (93), Expect = 0.001
 Identities = 25/102 (24%), Positives = 54/102 (52%), Gaps = 3/102 (2%)

Query: 177 KKERRKQRRRKRKRKRKKEEE---EKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKK 233
            +    +   ++  K  KE E   E+ EE ++E +  +  ++K E+K +E ++  ++ KK
Sbjct: 214 SELPELREELEKLEKEVKELEELKEEIEELEKELESLEGSKRKLEEKIRELEERIEELKK 273

Query: 234 KKKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDEGRRR 275
           + +E ++K KE K+ KE+ ++  K  +  +E   +  E  +R
Sbjct: 274 EIEELEEKVKELKELKEKAEEYIKLSEFYEEYLDELREIEKR 315

Length = 880

>gnl|CDD|224415 COG1498, SIK1, Protein implicated in ribosomal biogenesis, Nop56p homolog [Translation, ribosomal structure and biogenesis]

 Score = 39.3 bits (92), Expect = 0.001
 Identities = 17/51 (33%), Positives = 31/51 (60%)

Query: 219 KKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKK 269
           +++ EK+ EK K+K  K   K K +  KK++  + + KKK+KK K +++  
Sbjct: 343 REELEKRIEKLKEKPPKPPTKAKPERDKKERPGRYRRKKKEKKAKSERRGL 393

Length = 395

>gnl|CDD|223496 COG0419, SbcC, ATPase involved in DNA repair [DNA replication, recombination, and repair]

 Score = 39.7 bits (93), Expect = 0.001
 Identities = 12/93 (12%), Positives = 50/93 (53%), Gaps = 2/93 (2%)

Query: 181 RKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKK 240
            ++     +R  + EEE++  E+ + +  E +  + +  K +E++  + ++  ++ E+K 
Sbjct: 231 EQEIEALEERLAELEEEKERLEELKARLLEIESLELEALKIREEELRELERLLEELEEKI 290

Query: 241 K--KKEKKKKKEEKKKEKKKKKKKKEKKKKKDE 271
           +  ++ +++ +E +++ +  +   +E ++  ++
Sbjct: 291 ERLEELEREIEELEEELEGLRALLEELEELLEK 323

Length = 908

>gnl|CDD|221937 pfam13148, DUF3987, Protein of unknown function (DUF3987)

 Score = 39.6 bits (93), Expect = 0.001
 Identities = 22/57 (38%), Positives = 35/57 (61%)

Query: 195 EEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEE 251
           EEE +EE ++E K+ E +KE  + +KK  +KK KK  KK K E+   ++  + + EE
Sbjct: 67  EEELREEYEEELKEYEAEKEIWEAEKKGLEKKAKKAIKKGKDEEALAEELLELEAEE 123

A family of uncharacterized proteins found by clustering human gut metagenomic sequences. Length = 379

>gnl|CDD|204414 pfam10211, Ax_dynein_light, Axonemal dynein light chain

 Score = 38.7 bits (91), Expect = 0.001
 Identities = 18/73 (24%), Positives = 46/73 (63%)

Query: 199 KEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKKKEKKK 258
           ++  + E+ K E ++E KK +++KE+ +++  + + K E  +K++E++++ EEK+   + 
Sbjct: 113 RKALQAEQGKSELEQEIKKLEEEKEELEKRVAELEAKLEAIEKREEEERQIEEKRHADEI 172

Query: 259 KKKKKEKKKKKDE 271
              KK+ ++ K +
Sbjct: 173 AFLKKQNQQLKSQ 185

Axonemal dynein light chain proteins play a dynamic role in flagellar and cilia motility. Eukaryotic cilia and flagella are complex organelles consisting of a core structure, the axoneme, which is composed of nine microtubule doublets forming a cylinder that surrounds a pair of central singlet microtubules. This ultra-structural arrangement seems to be one of the most stable micro-tubular assemblies known and is responsible for the flagellar and ciliary movement of a large number of organisms ranging from protozoan to mammals. This light chain interacts directly with the N-terminal half of the heavy chains. Length = 189

>gnl|CDD|220237 pfam09428, DUF2011, Fungal protein of unknown function (DUF2011)

 Score = 37.6 bits (88), Expect = 0.001
 Identities = 22/62 (35%), Positives = 44/62 (70%)

Query: 208 KKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKK 267
           KK   K +K+  ++KEKKK++K+  KK++   + ++E+ K++ EK+K  +K ++KK K++
Sbjct: 65  KKHNAKVEKELLREKEKKKKRKRPGKKRRIALRLRRERTKERAEKEKRTRKNREKKFKRR 124

Query: 268 KK 269
           +K
Sbjct: 125 QK 126

This is a family of fungal proteins whose function is unknown. Length = 130

>gnl|CDD|220237 pfam09428, DUF2011, Fungal protein of unknown function (DUF2011)

 Score = 37.6 bits (88), Expect = 0.001
 Identities = 21/59 (35%), Positives = 43/59 (72%)

Query: 204 KEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKKKEKKKKKKK 262
           K EK+  ++KEKKK++K+  KK+    + ++++ K++ +KEK+ +K  +KK K+++K+K
Sbjct: 70  KVEKELLREKEKKKKRKRPGKKRRIALRLRRERTKERAEKEKRTRKNREKKFKRRQKEK 128

This is a family of fungal proteins whose function is unknown. Length = 130

>gnl|CDD|237855 PRK14900, valS, valyl-tRNA synthetase; Provisional

 Score = 40.4 bits (94), Expect = 0.001
 Identities = 27/83 (32%), Positives = 36/83 (43%), Gaps = 1/83 (1%)

Query: 181  RKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKK 240
             +  R+  +R  KK    +   KK+  KK   K K   KK   KK   KKK  KK   KK
Sbjct: 971  AEAVRKTVRRSVKKAAATRAAMKKKVAKKAPAK-KAAAKKAAAKKAAAKKKVAKKAPAKK 1029

Query: 241  KKKEKKKKKEEKKKEKKKKKKKK 263
              ++   KK  KK  +K   +K 
Sbjct: 1030 VARKPAAKKAAKKPARKAAGRKA 1052

Length = 1052

>gnl|CDD|129022 smart00786, SHR3_chaperone, ER membrane protein SH3

 Score = 38.9 bits (91), Expect = 0.001
 Identities = 15/39 (38%), Positives = 22/39 (56%)

Query: 210 EKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKK 248
           E+K  K+KE+   E++KE      KK    +K + KKKK
Sbjct: 158 ERKDAKQKEEFAAEERKEALAAAAKKSATPQKVETKKKK 196

This family of proteins are membrane localised chaperones that are required for correct plasma membrane localisation of amino acid permeases (AAPs). Shr3 prevents AAPs proteins from aggregating and assists in their correct folding. In the absence of Shr3, AAPs are retained in the ER. Length = 196

>gnl|CDD|223095 COG0016, PheS, Phenylalanyl-tRNA synthetase alpha subunit [Translation, ribosomal structure and biogenesis]

 Score = 39.5 bits (93), Expect = 0.001
 Identities = 17/95 (17%), Positives = 33/95 (34%), Gaps = 2/95 (2%)

Query: 182 KQRRRKRKRKRKKEEEEKEEEKKEEKKKEKK-KEKKKEKKKKEKKKEKKKKKKKKKEKKK 240
            ++            +  EE K +   K+    +  K+  K    +E+K+      E KK
Sbjct: 10  AKKGIAAIELASDLLKALEELKVKYLGKKGVLTDLLKKLGKLSPLEERKEVGALINELKK 69

Query: 241 K-KKEKKKKKEEKKKEKKKKKKKKEKKKKKDEGRR 274
           + +    +   E +     ++   EK      GRR
Sbjct: 70  EVEDAITELTPELEAAGLWERLAFEKIDVTLPGRR 104

Length = 335

>gnl|CDD|235334 PRK05035, PRK05035, electron transport complex protein RnfC; Provisional

 Score = 39.5 bits (93), Expect = 0.001
 Identities = 18/95 (18%), Positives = 36/95 (37%), Gaps = 2/95 (2%)

Query: 177 KKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKK 236
           K E  K R   R+ + ++E+  +E   K  K  E +  K K+       + K KK    +
Sbjct: 447 KAEEAKARFEARQARLEREKAAREARHK--KAAEARAAKDKDAVAAALARVKAKKAAATQ 504

Query: 237 EKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDE 271
               K   +          + +K + + ++ +K  
Sbjct: 505 PIVIKAGARPDNSAVIAAREARKAQARARQAEKQA 539

Length = 695

>gnl|CDD|233758 TIGR02169, SMC_prok_A, chromosome segregation protein SMC, primarily archaeal type

 Score = 39.7 bits (93), Expect = 0.001
 Identities = 20/93 (21%), Positives = 52/93 (55%)

Query: 177 KKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKK 236
           K+ +  Q +R   +++ K  E++ E    +K++ +++ ++ E   ++ +      KK++ 
Sbjct: 833 KEIQELQEQRIDLKEQIKSIEKEIENLNGKKEELEEELEELEAALRDLESRLGDLKKERD 892

Query: 237 EKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKK 269
           E + + +E ++K EE + + +KK+K+  + K K
Sbjct: 893 ELEAQLRELERKIEELEAQIEKKRKRLSELKAK 925

SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]. Length = 1164

>gnl|CDD|226889 COG4487, COG4487, Uncharacterized protein conserved in bacteria [Function unknown]

 Score = 39.4 bits (92), Expect = 0.001
 Identities = 22/90 (24%), Positives = 47/90 (52%)

Query: 179 ERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEK 238
           E+    +R + R  KK+E  + EE+   +KKE+K    ++ K+ E   + +  K +  E 
Sbjct: 48  EKEANEKRAQYRSAKKKELSQLEEQLINQKKEQKNLFNEQIKQFELALQDEIAKLEALEL 107

Query: 239 KKKKKEKKKKKEEKKKEKKKKKKKKEKKKK 268
              +K+K+ +  EK+ ++  K+ +K+ +  
Sbjct: 108 LNLEKDKELELLEKELDELSKELQKQLQNT 137

Length = 438

>gnl|CDD|223562 COG0488, Uup, ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]

 Score = 39.5 bits (93), Expect = 0.001
 Identities = 19/81 (23%), Positives = 40/81 (49%), Gaps = 4/81 (4%)

Query: 196 EEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKK-KKKEEKKK 254
            E+K E  ++E    +K++K   +  KE++  ++ K    K KK K + K+ +K E +  
Sbjct: 239 LEQKAERLRQEAAAYEKQQK---ELAKEQEWIRRGKAAASKAKKAKSRIKRLEKLEARLA 295

Query: 255 EKKKKKKKKEKKKKKDEGRRR 275
           E++  ++ K    +     +R
Sbjct: 296 EERPVEEGKPLAFRFPPPGKR 316

Length = 530

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 39.0 bits (90), Expect = 0.002
 Identities = 32/102 (31%), Positives = 61/102 (59%), Gaps = 2/102 (1%)

Query: 174  KGGKKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKK 233
            K  ++ ++    +K + K+K +E +K EE K  K +EKKK ++ +K +++K    +K ++
Sbjct: 1528 KKAEEAKKADEAKKAEEKKKADELKKAEELK--KAEEKKKAEEAKKAEEDKNMALRKAEE 1585

Query: 234  KKKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDEGRRR 275
             KK ++ + +E  K  EE+KK K ++ KK E+ K K E  ++
Sbjct: 1586 AKKAEEARIEEVMKLYEEEKKMKAEEAKKAEEAKIKAEELKK 1627

Length = 2084

>gnl|CDD|215214 PLN02381, PLN02381, valyl-tRNA synthetase

 Score = 39.5 bits (92), Expect = 0.002
 Identities = 17/64 (26%), Positives = 38/64 (59%)

Query: 212 KKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDE 271
            + +KK   ++E +++KKK++K K+++ KK K  +K+ + K + ++        KK + +
Sbjct: 6   SEAEKKILTEEELERKKKKEEKAKEKELKKLKAAQKEAKAKLQAQQASDGTNVPKKSEKK 65

Query: 272 GRRR 275
            R+R
Sbjct: 66  SRKR 69

Length = 1066

>gnl|CDD|219746 pfam08208, RNA_polI_A34, DNA-directed RNA polymerase I subunit RPA34

 Score = 37.8 bits (88), Expect = 0.002
 Identities = 21/66 (31%), Positives = 44/66 (66%)

Query: 210 EKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKK 269
            +   + +  +K+   K +K+ + +++EKK+KKK+K+ KKE+K+K+ KK+K  + K  KK
Sbjct: 126 SELGSESETSEKETTAKVEKEAEVEEEEKKEKKKKKEVKKEKKEKKDKKEKMVEPKGSKK 185

Query: 270 DEGRRR 275
            + +++
Sbjct: 186 KKKKKK 191

5. This is a family of proteins conserved from yeasts to human. Subunit A34.5 of RNA polymerase I is a non-essential subunit which is thought to help Pol I overcome topological constraints imposed on ribosomal DNA during the process of transcription. Length = 193

>gnl|CDD|217051 pfam02463, SMC_N, RecF/RecN/SMC N terminal domain

 Score = 39.6 bits (92), Expect = 0.002
 Identities = 27/94 (28%), Positives = 51/94 (54%), Gaps = 1/94 (1%)

Query: 178 KERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKE 237
           +E   +   +++ K   E  E+EE+  +E+KKE+ K  ++ ++  E K+ K  ++K++  
Sbjct: 396 EELELKNEEEKEAKLLLELSEQEEDLLKEEKKEELKIVEELEESLETKQGKLTEEKEE-L 454

Query: 238 KKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDE 271
           +K+  K  K K E KK E   K+ K  K  ++ E
Sbjct: 455 EKQALKLLKDKLELKKSEDLLKETKLVKLLEQLE 488

This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination. Length = 1162

>gnl|CDD|217051 pfam02463, SMC_N, RecF/RecN/SMC N terminal domain

 Score = 39.6 bits (92), Expect = 0.002
 Identities = 23/88 (26%), Positives = 45/88 (51%)

Query: 177 KKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKK 236
             E  +Q     K ++K+E +  EE ++  + K+ K  ++KE+ +K+  K  K K + KK
Sbjct: 411 LLELSEQEEDLLKEEKKEELKIVEELEESLETKQGKLTEEKEELEKQALKLLKDKLELKK 470

Query: 237 EKKKKKKEKKKKKEEKKKEKKKKKKKKE 264
            +   K+ K  K  E+ +    ++K +E
Sbjct: 471 SEDLLKETKLVKLLEQLELLLLRQKLEE 498

This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination. Length = 1162

>gnl|CDD|217051 pfam02463, SMC_N, RecF/RecN/SMC N terminal domain

 Score = 39.2 bits (91), Expect = 0.002
 Identities = 19/82 (23%), Positives = 43/82 (52%)

Query: 188 RKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKK 247
            K +R+ E EE+    +E++KK+++ +K  E+ +   +     ++ K +E K K++ KK 
Sbjct: 151 MKPERRLEIEEEAAGSREKRKKKERLKKLIEETENLAELIIDLEELKLQELKLKEQAKKA 210

Query: 248 KKEEKKKEKKKKKKKKEKKKKK 269
            +  + KEK + +++       
Sbjct: 211 LEYYQLKEKLELEEENLLYLDY 232

This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination. Length = 1162

>gnl|CDD|235640 PRK05901, PRK05901, RNA polymerase sigma factor; Provisional

 Score = 38.8 bits (91), Expect = 0.002
 Identities = 15/79 (18%), Positives = 25/79 (31%)

Query: 193 KKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEK 252
             E +  +++ K   K    K   K+K K E    KK +KK   +K       K      
Sbjct: 69  ATESDIPKKKTKTAAKAAAAKAPAKKKLKDELDSSKKAEKKNALDKDDDLNYVKDIDVLN 128

Query: 253 KKEKKKKKKKKEKKKKKDE 271
           + +        +     D 
Sbjct: 129 QADDDDDDDDDDDLDDDDI 147

Length = 509

>gnl|CDD|223880 COG0810, TonB, Periplasmic protein TonB, links inner and outer membranes [Cell envelope biogenesis, outer membrane]

 Score = 38.6 bits (90), Expect = 0.002
 Identities = 17/56 (30%), Positives = 26/56 (46%)

Query: 189 KRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKE 244
           +   +    + +E+ K EKK +K K K K K K + K + + K KK   K   K  
Sbjct: 74  ETPPEPTPPKPKEKPKPEKKPKKPKPKPKPKPKPKPKVKPQPKPKKPPSKTAAKAP 129

Length = 244

>gnl|CDD|234750 PRK00409, PRK00409, recombination and DNA strand exchange inhibitor protein; Reviewed

 Score = 39.0 bits (92), Expect = 0.002
 Identities = 23/74 (31%), Positives = 47/74 (63%), Gaps = 7/74 (9%)

Query: 197 EEKEE-----EKKEEKKKEKKKEKKKEKKKKEKKKEKKKKK-KKKKEKKKKKKEKKKKKE 250
           E+KE+        EE ++E + +K +E +   K+ EK K++ ++KKEK +++++K  ++ 
Sbjct: 513 EDKEKLNELIASLEELERELE-QKAEEAEALLKEAEKLKEELEEKKEKLQEEEDKLLEEA 571

Query: 251 EKKKEKKKKKKKKE 264
           EK+ ++  K+ KKE
Sbjct: 572 EKEAQQAIKEAKKE 585

Length = 782

>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]

 Score = 38.9 bits (91), Expect = 0.002
 Identities = 15/97 (15%), Positives = 50/97 (51%), Gaps = 3/97 (3%)

Query: 178 KERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKK---KKEKKKEKKKKKKK 234
           +E +++   K     ++ EE  E  ++E  + E +  + + +    K+E +  +++ ++ 
Sbjct: 357 EEAKEELEEKLSALLEELEELFEALREELAELEAELAEIRNELEELKREIESLEERLERL 416

Query: 235 KKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDE 271
            +  +  K+E K+ + E ++ + + ++  E+ ++ +E
Sbjct: 417 SERLEDLKEELKELEAELEELQTELEELNEELEELEE 453

Length = 1163

>gnl|CDD|237753 PRK14552, PRK14552, C/D box methylation guide ribonucleoprotein complex aNOP56 subunit; Provisional

 Score = 39.2 bits (92), Expect = 0.002
 Identities = 23/50 (46%), Positives = 34/50 (68%)

Query: 178 KERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKE 227
           KE   +R  + K K  K  ++K EEKK +K+K+KKK KKK KK+K+K ++
Sbjct: 365 KEELNKRIEEIKEKYPKPPKKKREEKKPQKRKKKKKRKKKGKKRKKKGRK 414

Length = 414

>gnl|CDD|215774 pfam00183, HSP90, Hsp90 protein

 Score = 39.0 bits (91), Expect = 0.002
 Identities = 22/64 (34%), Positives = 45/64 (70%)

Query: 206 EKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKKKEKKKKKKKKEK 265
           EK+ EK+   ++E+++KE+KKE+++K   K+E+  +++EK++KK++ KK K+   + +  
Sbjct: 28  EKEVEKEVPDEEEEEEKEEKKEEEEKTTDKEEEVDEEEEKEEKKKKTKKVKETTTEWELL 87

Query: 266 KKKK 269
            K K
Sbjct: 88  NKTK 91

Length = 529

>gnl|CDD|236545 PRK09510, tolA, cell envelope integrity inner membrane protein TolA; Provisional

 Score = 39.0 bits (91), Expect = 0.002
 Identities = 23/93 (24%), Positives = 45/93 (48%)

Query: 177 KKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKK 236
           +K++ ++  ++   K+K+ EE   +     K K + + K+     K+   E KKK + + 
Sbjct: 116 QKKQAEEAAKQAALKQKQAEEAAAKAAAAAKAKAEAEAKRAAAAAKKAAAEAKKKAEAEA 175

Query: 237 EKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKK 269
            KK   + KKK + E   +   + KKK + + K
Sbjct: 176 AKKAAAEAKKKAEAEAAAKAAAEAKKKAEAEAK 208

Length = 387

>gnl|CDD|236545 PRK09510, tolA, cell envelope integrity inner membrane protein TolA; Provisional

 Score = 39.0 bits (91), Expect = 0.002
 Identities = 24/93 (25%), Positives = 47/93 (50%), Gaps = 3/93 (3%)

Query: 180 RRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKK 239
           ++KQ   + + K+ ++E    +E+K++ ++  K+   K+K+ +E   +     K K E +
Sbjct: 93  QQKQAAEQERLKQLEKERLAAQEQKKQAEEAAKQAALKQKQAEEAAAKAAAAAKAKAEAE 152

Query: 240 KKKKE---KKKKKEEKKKEKKKKKKKKEKKKKK 269
            K+     KK   E KKK + +  KK   + KK
Sbjct: 153 AKRAAAAAKKAAAEAKKKAEAEAAKKAAAEAKK 185

Length = 387

>gnl|CDD|178945 PRK00247, PRK00247, putative inner membrane protein translocase component YidC; Validated

 Score = 38.7 bits (90), Expect = 0.002
 Identities = 16/93 (17%), Positives = 36/93 (38%), Gaps = 6/93 (6%)

Query: 177 KKERR------KQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKK 230
           KK R       K R+++  +KR+  E E   E ++E+     + + +    K KKK    
Sbjct: 333 KKTRTAEKNEAKARKKEIAQKRRAAEREINREARQERAAAMARARARRAAVKAKKKGLID 392

Query: 231 KKKKKKEKKKKKKEKKKKKEEKKKEKKKKKKKK 263
               +    + ++ K    + +     +  ++ 
Sbjct: 393 ASPNEDTPSENEESKGSPPQVEATTTAEPNREP 425

Length = 429

>gnl|CDD|178945 PRK00247, PRK00247, putative inner membrane protein translocase component YidC; Validated

 Score = 38.7 bits (90), Expect = 0.002
 Identities = 11/70 (15%), Positives = 31/70 (44%), Gaps = 2/70 (2%)

Query: 184 RRRKRKRKRKKEEEE--KEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKK 241
              K+ R  +K E +  K+E  ++ +  E++  ++  +++       + ++   K KKK 
Sbjct: 330 AEIKKTRTAEKNEAKARKKEIAQKRRAAEREINREARQERAAAMARARARRAAVKAKKKG 389

Query: 242 KKEKKKKKEE 251
             +    ++ 
Sbjct: 390 LIDASPNEDT 399

Length = 429

>gnl|CDD|235322 PRK04950, PRK04950, ProP expression regulator; Provisional

 Score = 38.0 bits (89), Expect = 0.002
 Identities = 15/68 (22%), Positives = 34/68 (50%)

Query: 187 KRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKK 246
           K + +R +++ +K E   E++K  +++ K K K  ++K+K + +K + +        E  
Sbjct: 109 KVQAQRAEQQAKKREAAGEKEKAPRRERKPKPKAPRKKRKPRAQKPEPQHTPVSDISELT 168

Query: 247 KKKEEKKK 254
             +  K K
Sbjct: 169 VGQAVKVK 176

Length = 213

>gnl|CDD|220383 pfam09756, DDRGK, DDRGK domain

 Score = 37.8 bits (88), Expect = 0.002
 Identities = 20/73 (27%), Positives = 59/73 (80%)

Query: 199 KEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKKKEKKK 258
           K   KK  K +EK+  +++ + ++E+++E+KK ++K++ ++K+++E ++++E+KK+E+++
Sbjct: 2   KIGAKKRAKLEEKQARRQQREAEEEEREERKKLEEKREGERKEEEELEEEREKKKEEEER 61

Query: 259 KKKKKEKKKKKDE 271
           K+++++ +K+++E
Sbjct: 62  KEREEQARKEQEE 74

This is a family of proteins of approximately 300 residues, found in plants and vertebrates. They contain a highly conserved DDRGK motif. Length = 189

>gnl|CDD|220383 pfam09756, DDRGK, DDRGK domain

 Score = 37.8 bits (88), Expect = 0.002
 Identities = 21/79 (26%), Positives = 63/79 (79%), Gaps = 2/79 (2%)

Query: 190 RKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKK 249
           +K   ++  K EEK  + ++++++ +++E+++++K +EK++ ++K++E+ ++++EKKK++
Sbjct: 1   KKIGAKKRAKLEEK--QARRQQREAEEEEREERKKLEEKREGERKEEEELEEEREKKKEE 58

Query: 250 EEKKKEKKKKKKKKEKKKK 268
           EE+K+ +++ +K++E+ +K
Sbjct: 59  EERKEREEQARKEQEEYEK 77

This is a family of proteins of approximately 300 residues, found in plants and vertebrates. They contain a highly conserved DDRGK motif. Length = 189

>gnl|CDD|219408 pfam07423, DUF1510, Protein of unknown function (DUF1510)

 Score = 38.2 bits (89), Expect = 0.002
 Identities = 15/81 (18%), Positives = 48/81 (59%)

Query: 189 KRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKK 248
           +++ KK ++++  E +E K++EK+    ++K+ K   +++ ++ +++ E++ ++   + +
Sbjct: 48  EQEAKKSDDQETAEIEEVKEEEKEAANSEDKEDKGDAEKEDEESEEENEEEDEESSDENE 107

Query: 249 KEEKKKEKKKKKKKKEKKKKK 269
           KE ++K +   +K+      K
Sbjct: 108 KETEEKTESNVEKEITNPSWK 128

This family consists of several hypothetical bacterial proteins of around 200 residues in length. The function of this family is unknown. Length = 214

>gnl|CDD|218177 pfam04615, Utp14, Utp14 protein

 Score = 38.9 bits (91), Expect = 0.002
 Identities = 29/105 (27%), Positives = 54/105 (51%), Gaps = 9/105 (8%)

Query: 177 KKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKK 236
           +  ++   RRK   +  ++E E ++ KKE K + K+K++  E+++ E ++E K +K   K
Sbjct: 414 EPSKKNVGRRKFGPENGEKEAESKKLKKENKNEFKEKKESDEEEELEDEEEAKVEKVANK 473

Query: 237 EKKKKKKEKKKKKEE---------KKKEKKKKKKKKEKKKKKDEG 272
             K+ +K +K+++EE         K      K  KK+  KKK   
Sbjct: 474 LLKRSEKAQKEEEEEELDEENPWLKTTSSVGKSAKKQDSKKKSSS 518

This protein is found to be part of a large ribonucleoprotein complex containing the U3 snoRNA. Depletion of the Utp proteins impedes production of the 18S rRNA, indicating that they are part of the active pre-rRNA processing complex. This large RNP complex has been termed the small subunit (SSU) processome. Length = 728

>gnl|CDD|218177 pfam04615, Utp14, Utp14 protein

 Score = 38.9 bits (91), Expect = 0.002
 Identities = 25/95 (26%), Positives = 42/95 (44%)

Query: 177 KKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKK 236
              +  +R  K +++ ++EE ++E    +      K  KK++ KKK   K  K   K  K
Sbjct: 470 VANKLLKRSEKAQKEEEEEELDEENPWLKTTSSVGKSAKKQDSKKKSSSKLDKAANKISK 529

Query: 237 EKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDE 271
              K KK+KKK+K     +    ++   K    DE
Sbjct: 530 AAVKVKKKKKKEKSIDLDDDLIDEEDSIKLDVDDE 564

This protein is found to be part of a large ribonucleoprotein complex containing the U3 snoRNA. Depletion of the Utp proteins impedes production of the 18S rRNA, indicating that they are part of the active pre-rRNA processing complex. This large RNP complex has been termed the small subunit (SSU) processome. Length = 728

>gnl|CDD|218177 pfam04615, Utp14, Utp14 protein

 Score = 38.9 bits (91), Expect = 0.002
 Identities = 22/83 (26%), Positives = 50/83 (60%), Gaps = 4/83 (4%)

Query: 194 KEEEEKEEEKKEEKKK----EKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKK 249
           +EE E+  +K   ++K      +KE + +K KKE K E K+KK+  +E++ + +E+ K +
Sbjct: 409 EEENEEPSKKNVGRRKFGPENGEKEAESKKLKKENKNEFKEKKESDEEEELEDEEEAKVE 468

Query: 250 EEKKKEKKKKKKKKEKKKKKDEG 272
           +   K  K+ +K ++++++++  
Sbjct: 469 KVANKLLKRSEKAQKEEEEEELD 491

This protein is found to be part of a large ribonucleoprotein complex containing the U3 snoRNA. Depletion of the Utp proteins impedes production of the 18S rRNA, indicating that they are part of the active pre-rRNA processing complex. This large RNP complex has been termed the small subunit (SSU) processome. Length = 728

>gnl|CDD|221733 pfam12720, DUF3807, Protein of unknown function (DUF3807)

 Score = 38.2 bits (89), Expect = 0.002
 Identities = 12/71 (16%), Positives = 30/71 (42%)

Query: 183 QRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKK 242
            R R+ K + + EEE + +   +      +    +++ +++   +K+K  + K+ K  K 
Sbjct: 66  LRERELKEEAEAEEEGEVDASPDAGAVAGESSADRKEAEQQGAAQKRKSCRDKERKSAKD 125

Query: 243 KEKKKKKEEKK 253
                +    K
Sbjct: 126 PRGGTQDVVDK 136

This is a family of conserved fungal proteins of unknown function. Length = 169

>gnl|CDD|221275 pfam11861, DUF3381, Domain of unknown function (DUF3381)

 Score = 37.7 bits (88), Expect = 0.002
 Identities = 15/68 (22%), Positives = 46/68 (67%)

Query: 208 KKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKK 267
           +K+ +K    +KK+KE+++E++ + ++  E+++  +  +K+  + K+EK+++ ++K+K+ 
Sbjct: 87  RKKVRKLLGLDKKEKEEEEEEEVEVEELDEEEQIDELLEKELAKLKREKRRENERKQKEI 146

Query: 268 KKDEGRRR 275
            K++ +  
Sbjct: 147 LKEQMKML 154

This domain is functionally uncharacterized. This domain is found in eukaryotes. This presumed domain is typically between 156 to 174 amino acids in length. This domain is found associated with pfam07780, pfam01728. Length = 154

>gnl|CDD|218737 pfam05764, YL1, YL1 nuclear protein

 Score = 38.5 bits (90), Expect = 0.002
 Identities = 24/77 (31%), Positives = 37/77 (48%), Gaps = 1/77 (1%)

Query: 194 KEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKK 253
            +EEE E+E + E++ +KKK + K K  KE  K+KKKK     +  K    + KKK E+ 
Sbjct: 69  DDEEEGEKELQREERLKKKK-RVKTKAYKEPTKKKKKKDPTAAKSPKAAAPRPKKKSERI 127

Query: 254 KEKKKKKKKKEKKKKKD 270
                      +K  + 
Sbjct: 128 SWAPTLLDSPRRKSSRS 144

The proteins in this family are designated YL1. These proteins have been shown to be DNA-binding and may be a transcription factor. Length = 238

>gnl|CDD|218737 pfam05764, YL1, YL1 nuclear protein

 Score = 38.5 bits (90), Expect = 0.002
 Identities = 24/106 (22%), Positives = 56/106 (52%), Gaps = 6/106 (5%)

Query: 176 GKKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKK 235
           G+KE +++ R K+K++ K +  ++  +KK++K     K  K    + +KK E+       
Sbjct: 74  GEKELQREERLKKKKRVKTKAYKEPTKKKKKKDPTAAKSPKAAAPRPKKKSERISWAPTL 133

Query: 236 KEKKKKK------KEKKKKKEEKKKEKKKKKKKKEKKKKKDEGRRR 275
            +  ++K       + K+   E+ KE++ ++KK + K +K + +++
Sbjct: 134 LDSPRRKSSRSSTVQNKEATHERLKEREIRRKKIQAKARKRKEKKK 179

The proteins in this family are designated YL1. These proteins have been shown to be DNA-binding and may be a transcription factor. Length = 238

>gnl|CDD|236048 PRK07561, PRK07561, DNA topoisomerase I subunit omega; Validated

 Score = 39.4 bits (93), Expect = 0.002
 Identities = 10/44 (22%), Positives = 16/44 (36%)

Query: 226 KEKKKKKKKKKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKK 269
             +K +K +       K    KK   K   K K++    +K  K
Sbjct: 814 LAEKPEKLRYLADAPAKDPAGKKAAVKFSRKTKQQYVASEKDGK 857

Length = 859

>gnl|CDD|236048 PRK07561, PRK07561, DNA topoisomerase I subunit omega; Validated

 Score = 39.0 bits (92), Expect = 0.002
 Identities = 11/43 (25%), Positives = 17/43 (39%)

Query: 201 EEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKK 243
            EK E+ +       K    KK   K  +K K++    +K  K
Sbjct: 815 AEKPEKLRYLADAPAKDPAGKKAAVKFSRKTKQQYVASEKDGK 857

Length = 859

>gnl|CDD|236048 PRK07561, PRK07561, DNA topoisomerase I subunit omega; Validated

 Score = 39.0 bits (92), Expect = 0.002
 Identities = 13/51 (25%), Positives = 21/51 (41%)

Query: 197 EEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKK 247
           EE  E   E+ +K +       K    KK   K  +K K++    +K+ K 
Sbjct: 808 EEALELLAEKPEKLRYLADAPAKDPAGKKAAVKFSRKTKQQYVASEKDGKA 858

Length = 859

>gnl|CDD|222636 pfam14265, DUF4355, Domain of unknown function (DUF4355)

 Score = 37.2 bits (87), Expect = 0.002
 Identities = 22/68 (32%), Positives = 40/68 (58%)

Query: 208 KKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKK 267
           + E++K    ++  K   KEK K +KK++EKK + ++  K   E+K E + +K +KE ++
Sbjct: 1   EPEEEKTFTDKEVDKAIAKEKAKWEKKQEEKKSEAEKLAKMSAEEKAEYELEKLEKELEE 60

Query: 268 KKDEGRRR 275
            + E  RR
Sbjct: 61  LEAELARR 68

This family of proteins is found in bacteria and viruses. Proteins in this family are typically between 180 and 214 amino acids in length. Length = 125

>gnl|CDD|206039 pfam13868, Trichoplein, Tumour suppressor, Mitostatin

 Score = 38.7 bits (91), Expect = 0.002
 Identities = 19/93 (20%), Positives = 65/93 (69%)

Query: 179 ERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEK 238
           E   + + KR++++K  EE  E  ++  ++KE++KE+++E++ K  + +++K +++++ +
Sbjct: 111 EDEAEAQEKREKQKKLREEIDEFNEERIERKEEEKEREREEELKILEYQREKAEREEERE 170

Query: 239 KKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDE 271
            ++++ K++K+ E  + + ++++ ++++++ DE
Sbjct: 171 AERRERKEEKEREVARLRAQQEEAEDEREELDE 203

Trichoplein or mitostatin, was first defined as a meiosis-specific nuclear structural protein. It has since been linked with mitochondrial movement. It is associated with the mitochondrial outer membrane, and over-expression leads to reduction in mitochondrial motility whereas lack of it enhances mitochondrial movement. The activity appears to be mediated through binding the mitochondria to the actin intermediate filaments (IFs). Length = 349

>gnl|CDD|206039 pfam13868, Trichoplein, Tumour suppressor, Mitostatin

 Score = 38.4 bits (90), Expect = 0.002
 Identities = 20/95 (21%), Positives = 66/95 (69%), Gaps = 11/95 (11%)

Query: 188 RKRKRKKEEEEKEEEKK-----------EEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKK 236
           R+++R++E EE+ +E++           E++ + ++K +K++K ++E  +  +++ ++K+
Sbjct: 83  REKRRQEEYEERLQEREQMDEIIERIQEEDEAEAQEKREKQKKLREEIDEFNEERIERKE 142

Query: 237 EKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDE 271
           E+K++++E++ K  E ++EK ++++++E ++++ +
Sbjct: 143 EEKEREREEELKILEYQREKAEREEEREAERRERK 177

Trichoplein or mitostatin, was first defined as a meiosis-specific nuclear structural protein. It has since been linked with mitochondrial movement. It is associated with the mitochondrial outer membrane, and over-expression leads to reduction in mitochondrial motility whereas lack of it enhances mitochondrial movement. The activity appears to be mediated through binding the mitochondria to the actin intermediate filaments (IFs). Length = 349

>gnl|CDD|225606 COG3064, TolA, Membrane protein involved in colicin uptake [Cell envelope biogenesis, outer membrane]

 Score = 38.4 bits (89), Expect = 0.002
 Identities = 26/95 (27%), Positives = 55/95 (57%)

Query: 177 KKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKK 236
            K+  +Q R K+  K + + +E++++ +E +K+ + ++K++E++ ++   E+KKK +  K
Sbjct: 94  PKQAAEQERLKQLEKERLKAQEQQKQAEEAEKQAQLEQKQQEEQARKAAAEQKKKAEAAK 153

Query: 237 EKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDE 271
            K   +  K K   E KK+ ++  K  E+ K K E
Sbjct: 154 AKAAAEAAKLKAAAEAKKKAEEAAKAAEEAKAKAE 188

Length = 387

>gnl|CDD|235175 PRK03918, PRK03918, chromosome segregation protein; Provisional

 Score = 39.3 bits (92), Expect = 0.002
 Identities = 26/96 (27%), Positives = 57/96 (59%)

Query: 174 KGGKKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKK 233
           K  + E   +   +   +  +  EE E+ +KE K+ E+ KE+ +E +K+ +  E  K+K 
Sbjct: 198 KEKELEEVLREINEISSELPELREELEKLEKEVKELEELKEEIEELEKELESLEGSKRKL 257

Query: 234 KKKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKK 269
           ++K ++ +++ ++ KKE ++ E+K K+ K+ K+K +
Sbjct: 258 EEKIRELEERIEELKKEIEELEEKVKELKELKEKAE 293

Length = 880

>gnl|CDD|235175 PRK03918, PRK03918, chromosome segregation protein; Provisional

 Score = 39.3 bits (92), Expect = 0.002
 Identities = 21/90 (23%), Positives = 53/90 (58%)

Query: 177 KKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKK 236
                 +   +    R++ E+ ++E K+ E+ KE+ +E +KE +  E  K K ++K ++ 
Sbjct: 205 VLREINEISSELPELREELEKLEKEVKELEELKEEIEELEKELESLEGSKRKLEEKIREL 264

Query: 237 EKKKKKKEKKKKKEEKKKEKKKKKKKKEKK 266
           E++ ++ +K+ ++ E+K ++ K+ K+K ++
Sbjct: 265 EERIEELKKEIEELEEKVKELKELKEKAEE 294

Length = 880

>gnl|CDD|219124 pfam06658, DUF1168, Protein of unknown function (DUF1168)

 Score = 37.3 bits (87), Expect = 0.002
 Identities = 28/83 (33%), Positives = 58/83 (69%)

Query: 177 KKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKK 236
           KKE   +  ++++ ++K+++EEK  +K+ +++K+K+K+KKK+K KK  KKE+K+  K  +
Sbjct: 60  KKETEDEEFQQKREEKKRKDEEKTAKKRAKRQKKKQKKKKKKKAKKGNKKEEKEGSKSSE 119

Query: 237 EKKKKKKEKKKKKEEKKKEKKKK 259
           E   +++E ++ K+E+  E  +K
Sbjct: 120 ESSDEEEEGEEDKQEEPVEIMEK 142

This family consists of several hypothetical eukaryotic proteins of unknown function. Length = 142

>gnl|CDD|224415 COG1498, SIK1, Protein implicated in ribosomal biogenesis, Nop56p homolog [Translation, ribosomal structure and biogenesis]

 Score = 39.3 bits (92), Expect = 0.002
 Identities = 14/56 (25%), Positives = 32/56 (57%)

Query: 200 EEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKKKE 255
              ++E +K+ +K ++K  K   + K E+ KK++  + ++KKK++K K +    + 
Sbjct: 340 ISLREELEKRIEKLKEKPPKPPTKAKPERDKKERPGRYRRKKKEKKAKSERRGLQN 395

Length = 395

>gnl|CDD|224415 COG1498, SIK1, Protein implicated in ribosomal biogenesis, Nop56p homolog [Translation, ribosomal structure and biogenesis]

 Score = 39.3 bits (92), Expect = 0.002
 Identities = 15/52 (28%), Positives = 32/52 (61%)

Query: 220 KKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDE 271
           +++ +K+ +K K+K  K   K K E+ KK+   +  +KKK+KK + +++  +
Sbjct: 343 REELEKRIEKLKEKPPKPPTKAKPERDKKERPGRYRRKKKEKKAKSERRGLQ 394

Length = 395

>gnl|CDD|223496 COG0419, SbcC, ATPase involved in DNA repair [DNA replication, recombination, and repair]

 Score = 39.0 bits (91), Expect = 0.002
 Identities = 19/103 (18%), Positives = 54/103 (52%)

Query: 169 LEYGYKGGKKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEK 228
           L+      +    +  + + +  R+ E   +E E+K E+ +E ++E ++ +++ E  +  
Sbjct: 254 LKARLLEIESLELEALKIREEELRELERLLEELEEKIERLEELEREIEELEEELEGLRAL 313

Query: 229 KKKKKKKKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDE 271
            ++ ++  EK K  +E+ +K EEK ++ + + ++  ++K +  
Sbjct: 314 LEELEELLEKLKSLEERLEKLEEKLEKLESELEELAEEKNELA 356

Length = 908

>gnl|CDD|223496 COG0419, SbcC, ATPase involved in DNA repair [DNA replication, recombination, and repair]

 Score = 39.0 bits (91), Expect = 0.002
 Identities = 22/100 (22%), Positives = 56/100 (56%)

Query: 176 GKKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKK 235
            +KE  +    + +   ++   EKEE +  E+ +E +KE ++ +++  +  E ++  K++
Sbjct: 471 HEKELLELYELELEELEEELSREKEEAELREEIEELEKELRELEEELIELLELEEALKEE 530

Query: 236 KEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDEGRRR 275
            E+K +K E   ++ E+ KEK + ++ KE+ ++ ++  + 
Sbjct: 531 LEEKLEKLENLLEELEELKEKLQLQQLKEELRQLEDRLQE 570

Length = 908

>gnl|CDD|223496 COG0419, SbcC, ATPase involved in DNA repair [DNA replication, recombination, and repair]

 Score = 39.0 bits (91), Expect = 0.002
 Identities = 25/108 (23%), Positives = 60/108 (55%)

Query: 167 DNLEYGYKGGKKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKK 226
             L   Y+   +E  ++  R+++    +EE E+ E++  E ++E  +  + E+  KE+ +
Sbjct: 473 KELLELYELELEELEEELSREKEEAELREEIEELEKELRELEEELIELLELEEALKEELE 532

Query: 227 EKKKKKKKKKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDEGRR 274
           EK +K +   E+ ++ KEK + ++ K++ ++ + + +E K+  +E R 
Sbjct: 533 EKLEKLENLLEELEELKEKLQLQQLKEELRQLEDRLQELKELLEELRL 580

Length = 908

>gnl|CDD|223496 COG0419, SbcC, ATPase involved in DNA repair [DNA replication, recombination, and repair]

 Score = 39.0 bits (91), Expect = 0.002
 Identities = 20/92 (21%), Positives = 53/92 (57%)

Query: 178 KERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKE 237
           +E  +    + + K ++ E E   E +  + +E+ +EK +E ++ E++ E+ +++ ++  
Sbjct: 649 EELLQAALEELEEKVEELEAEIRRELQRIENEEQLEEKLEELEQLEEELEQLREELEELL 708

Query: 238 KKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKK 269
           KK  + E+  ++ E +K + ++ KK+ +K +K
Sbjct: 709 KKLGEIEQLIEELESRKAELEELKKELEKLEK 740

Length = 908

>gnl|CDD|149343 pfam08229, SHR3_chaperone, ER membrane protein SH3

 Score = 38.1 bits (89), Expect = 0.002
 Identities = 14/38 (36%), Positives = 21/38 (55%), Gaps = 1/38 (2%)

Query: 194 KEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKK 231
           K+ +  EE   EE +      K++E  + EKK+ KKKK
Sbjct: 160 KDAKLLEEFAAEEAEAAAAA-KEEESAEGEKKESKKKK 196

This family of proteins are membrane localised chaperones that are required for correct plasma membrane localisation of amino acid permeases (AAPs). SH3 prevents AAPs proteins from aggregating and assists in their correct folding. In the absence of SH3, AAPs are retained in the ER. Length = 196

>gnl|CDD|223683 COG0610, COG0610, Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]

 Score = 38.9 bits (91), Expect = 0.002
 Identities = 25/92 (27%), Positives = 40/92 (43%), Gaps = 3/92 (3%)

Query: 178 KERRKQRRRKRKRKRKKEEEEKEEEKKEEKKK---EKKKEKKKEKKKKEKKKEKKKKKKK 234
            E   Q R K+    +K EE     KKEE+ K   E++   ++E    +       K  +
Sbjct: 861 IEAINQYRAKKLDTAEKLEELYILAKKEEEFKQFAEEEGLNEEELAFYDDLALNGGKLPE 920

Query: 235 KKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKK 266
              +  +K  K+K   EK K+  K K++ E K
Sbjct: 921 NGTELVEKLAKEKSLREKNKDDWKAKEEVEAK 952

Length = 962

>gnl|CDD|129022 smart00786, SHR3_chaperone, ER membrane protein SH3

 Score = 38.1 bits (89), Expect = 0.002
 Identities = 13/38 (34%), Positives = 20/38 (52%)

Query: 185 RRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKK 222
           R+  K+K +   EE++E      KK    +K + KKKK
Sbjct: 159 RKDAKQKEEFAAEERKEALAAAAKKSATPQKVETKKKK 196

This family of proteins are membrane localised chaperones that are required for correct plasma membrane localisation of amino acid permeases (AAPs). Shr3 prevents AAPs proteins from aggregating and assists in their correct folding. In the absence of Shr3, AAPs are retained in the ER. Length = 196

>gnl|CDD|129022 smart00786, SHR3_chaperone, ER membrane protein SH3

 Score = 38.1 bits (89), Expect = 0.002
 Identities = 15/39 (38%), Positives = 22/39 (56%)

Query: 197 EEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKK 235
           E K+ ++KEE   E++KE      KK    +K + KKKK
Sbjct: 158 ERKDAKQKEEFAAEERKEALAAAAKKSATPQKVETKKKK 196

This family of proteins are membrane localised chaperones that are required for correct plasma membrane localisation of amino acid permeases (AAPs). Shr3 prevents AAPs proteins from aggregating and assists in their correct folding. In the absence of Shr3, AAPs are retained in the ER. Length = 196

>gnl|CDD|235334 PRK05035, PRK05035, electron transport complex protein RnfC; Provisional

 Score = 38.8 bits (91), Expect = 0.002
 Identities = 19/92 (20%), Positives = 36/92 (39%), Gaps = 4/92 (4%)

Query: 186 RKRKRKRKKEEEEKE--EEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKK 243
           R  ++++KK EE K   E ++   + E++K  ++ + KK  +    K K        + K
Sbjct: 439 RAIEQEKKKAEEAKARFEARQA--RLEREKAAREARHKKAAEARAAKDKDAVAAALARVK 496

Query: 244 EKKKKKEEKKKEKKKKKKKKEKKKKKDEGRRR 275
            KK    +    K   +          E R+ 
Sbjct: 497 AKKAAATQPIVIKAGARPDNSAVIAAREARKA 528

Length = 695

>gnl|CDD|218899 pfam06102, DUF947, Domain of unknown function (DUF947)

 Score = 38.0 bits (89), Expect = 0.002
 Identities = 29/99 (29%), Positives = 52/99 (52%)

Query: 177 KKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKK 236
            +E  K  ++ +  + K+E +   +  K   K  K K++++E  K+ KK+EK+  K+ KK
Sbjct: 65  IEELEKALKKTKDSEEKEELKRTLQSMKSRLKTLKNKDREREILKEHKKQEKELIKEGKK 124

Query: 237 EKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDEGRRR 275
               KK E KK   +KK ++ KK K+ +K  +K   +  
Sbjct: 125 PYYLKKSEIKKLVLKKKFDELKKSKQLDKALEKKRKKNA 163

Family of eukaryotic proteins with unknown function. Length = 168

>gnl|CDD|220369 pfam09731, Mitofilin, Mitochondrial inner membrane protein

 Score = 39.2 bits (92), Expect = 0.002
 Identities = 24/79 (30%), Positives = 51/79 (64%)

Query: 193 KKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEK 252
           K EEEE+ E   +EK++E   + ++E   + + KE   +K+ + E +++K+E +KK EEK
Sbjct: 183 KAEEEEELERALKEKREELLSKLEEELLARLESKEAALEKQLRLEFEREKEELRKKYEEK 242

Query: 253 KKEKKKKKKKKEKKKKKDE 271
            +++ +++ +  ++K K+E
Sbjct: 243 LRQELERQAEAHEQKLKNE 261

Mitofilin controls mitochondrial cristae morphology. Mitofilin is enriched in the narrow space between the inner boundary and the outer membranes, where it forms a homotypic interaction and assembles into a large multimeric protein complex. The first 78 amino acids contain a typical amino-terminal-cleavable mitochondrial presequence rich in positive-charged and hydroxylated residues and a membrane anchor domain. In addition, it has three centrally located coiled coil domains. Length = 493

>gnl|CDD|222571 pfam14153, Spore_coat_CotO, Spore coat protein CotO

 Score = 38.3 bits (89), Expect = 0.002
 Identities = 22/85 (25%), Positives = 54/85 (63%)

Query: 186 RKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEK 245
             +K   K+EE+E  +E  + K++E+K E ++ +K+KE  + +++   +++EK++  +E+
Sbjct: 32  IIKKADEKEEEKENSDEHVKSKEEEQKIEYEEAEKEKEAGEPEREDIAEQQEKEEIAQEE 91

Query: 246 KKKKEEKKKEKKKKKKKKEKKKKKD 270
           +K++E +  ++++    K KK  K+
Sbjct: 92  EKEEEAEDVKQQEVFSFKRKKPFKE 116

Bacillus spores are protected by a protein shell consisting of over 50 different polypeptides, known as the coat. This family of proteins has an important morphogenetic role in coat assembly, it is involved in the assembly of at least 5 different coat proteins including CotB, CotG, CotS, CotSA and CotW. It is likely to act at a late stage of coat assembly. Length = 185

>gnl|CDD|221028 pfam11208, DUF2992, Protein of unknown function (DUF2992)

 Score = 37.2 bits (87), Expect = 0.002
 Identities = 23/78 (29%), Positives = 48/78 (61%), Gaps = 8/78 (10%)

Query: 197 EEKEEEKKEEKKKEKKKEKKKEKKKKEKKKE--------KKKKKKKKKEKKKKKKEKKKK 248
           E  +   K++KK   K+ +++  K+ +K           K + ++ K+EKKK+ KEKK++
Sbjct: 53  EAVKVSIKKQKKINPKRLQRQAAKEVKKPGISTKAQQALKLEHERNKQEKKKRSKEKKEE 112

Query: 249 KEEKKKEKKKKKKKKEKK 266
           ++E+K++ K++KKK + +
Sbjct: 113 EKERKRQLKQQKKKAKHR 130

This bacterial family of proteins has no known function. However, the cis-regulatory yjdF motif, just upstream from the gene encoding the proteins for this family, is a small non-coding RNA, Rfam:RF01764. The yjdF motif is found in many Firmicutes, including Bacillus subtilis. In most cases, it resides in potential 5' UTRs of homologues of the yjdF gene whose function is unknown. However, in Streptococcus thermophilus, a yjdF RNA motif is associated with an operon whose protein products synthesise nicotinamide adenine dinucleotide (NAD+). Also, the S. thermophilus yjdF RNA lacks typical yjdF motif consensus features downstream of and including the P4 stem. Thus, if yjdF RNAs are riboswitch aptamers, the S. thermophilus RNAs might sense a distinct compound that structurally resembles the ligand bound by other yjdF RNAs. On the ohter hand, perhaps these RNAs have an alternative solution forming a similar binding site, as is observed with some SAM riboswitches. Length = 132

>gnl|CDD|221028 pfam11208, DUF2992, Protein of unknown function (DUF2992)

 Score = 36.8 bits (86), Expect = 0.002
 Identities = 29/79 (36%), Positives = 47/79 (59%), Gaps = 7/79 (8%)

Query: 201 EEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKK-----KKEKKKKKKEKKKKKEEKKKE 255
           E  K   KK+KK   K+ +++  K+ +K     K     K E ++ K+EKKK+ +EKK+E
Sbjct: 53  EAVKVSIKKQKKINPKRLQRQAAKEVKKPGISTKAQQALKLEHERNKQEKKKRSKEKKEE 112

Query: 256 KKKKK--KKKEKKKKKDEG 272
           +K++K   K++KKK K  G
Sbjct: 113 EKERKRQLKQQKKKAKHRG 131

This bacterial family of proteins has no known function. However, the cis-regulatory yjdF motif, just upstream from the gene encoding the proteins for this family, is a small non-coding RNA, Rfam:RF01764. The yjdF motif is found in many Firmicutes, including Bacillus subtilis. In most cases, it resides in potential 5' UTRs of homologues of the yjdF gene whose function is unknown. However, in Streptococcus thermophilus, a yjdF RNA motif is associated with an operon whose protein products synthesise nicotinamide adenine dinucleotide (NAD+). Also, the S. thermophilus yjdF RNA lacks typical yjdF motif consensus features downstream of and including the P4 stem. Thus, if yjdF RNAs are riboswitch aptamers, the S. thermophilus RNAs might sense a distinct compound that structurally resembles the ligand bound by other yjdF RNAs. On the ohter hand, perhaps these RNAs have an alternative solution forming a similar binding site, as is observed with some SAM riboswitches. Length = 132

>gnl|CDD|237867 PRK14953, PRK14953, DNA polymerase III subunits gamma and tau; Provisional

 Score = 39.0 bits (91), Expect = 0.002
 Identities = 28/123 (22%), Positives = 57/123 (46%), Gaps = 21/123 (17%)

Query: 173 YKGGKKERRKQRRRKRKRKRKKEEEEKEE---------------EKKEEKKKEKKKEKKK 217
            K G K+  K++  K++ ++++ + +K                 +  E K++E K   K 
Sbjct: 364 LKEGSKQETKEQPEKKEEEKEELDIDKIILQIIKNEGKIISAILKNAEIKEEEGKITIKV 423

Query: 218 EKKKKEKKKEKKKKKKKK------KEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDE 271
           EK +++    + K  KK       +E KK+K+++K++ E  +K  +  K  K    KK +
Sbjct: 424 EKSEEDTLDLEIKSIKKYFPFIEFEEVKKEKEKEKERPEFVEKVLELFKGSKIITYKKKK 483

Query: 272 GRR 274
           G+ 
Sbjct: 484 GKD 486

Length = 486

>gnl|CDD|184287 PRK13735, PRK13735, conjugal transfer mating pair stabilization protein TraG; Provisional

 Score = 39.3 bits (92), Expect = 0.002
 Identities = 13/89 (14%), Positives = 34/89 (38%), Gaps = 1/89 (1%)

Query: 175 GGKKERRKQRRRKRKRKRKKEEEEKEEEKKEEKK-KEKKKEKKKEKKKKEKKKEKKKKKK 233
           G + + + Q             + +   + EE   K +  E +   K +   +  K  ++
Sbjct: 854 GIRNDVKHQVDNMVTEYEGNIGDTQNSIRGEENTVKGQYSELQNHHKTEALSQNNKYNEE 913

Query: 234 KKKEKKKKKKEKKKKKEEKKKEKKKKKKK 262
           K  +++    +  ++  ++ KE + K K 
Sbjct: 914 KSAQERMPGADSPEELMKRAKEYQDKHKG 942

Length = 942

>gnl|CDD|227708 COG5421, COG5421, Transposase [DNA replication, recombination, and repair]

 Score = 38.9 bits (91), Expect = 0.002
 Identities = 22/80 (27%), Positives = 40/80 (50%), Gaps = 2/80 (2%)

Query: 194 KEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKK 253
           +++EE+    + EK+ EK ++  ++ K +E   E  K  +   EK  K     +  E   
Sbjct: 279 QKKEEQTLRTRIEKELEKAEKSLEKLKGREFNCE--KDARIAAEKILKDYSSVEFLEVDF 336

Query: 254 KEKKKKKKKKEKKKKKDEGR 273
           K KKK+++ K  + +KDE  
Sbjct: 337 KSKKKREEAKRGRPRKDEEL 356

Length = 480

>gnl|CDD|221049 pfam11262, Tho2, Transcription factor/nuclear export subunit protein 2

 Score = 38.5 bits (90), Expect = 0.002
 Identities = 23/61 (37%), Positives = 34/61 (55%), Gaps = 2/61 (3%)

Query: 212 KKEKKK-EKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKKKEKKKKKKKKEK-KKKK 269
            KE ++ EK+ KE         KKKKEKK+ K   KK +EE KK  +  +K K++  ++K
Sbjct: 30  DKEIERLEKQIKELDSSSSGIDKKKKEKKRLKSLIKKLEEELKKHIEHNEKTKKRLSEEK 89

Query: 270 D 270
            
Sbjct: 90  S 90

THO and TREX form a eukaryotic complex which functions in messenger ribonucleoprotein metabolism and plays a role in preventing the transcription-associated genetic instability. Tho2, along with four other subunits forms THO. Length = 296

>gnl|CDD|236553 PRK09535, btuC, corrinoid ABC transporter permease; Reviewed

 Score = 38.6 bits (90), Expect = 0.002
 Identities = 27/85 (31%), Positives = 38/85 (44%), Gaps = 7/85 (8%)

Query: 59  ASVGRGAAESIAECQHQFRHHRWNCSSGGPGAGGGGGGKSESTTAPSVLPPTLHIGSREA 118
           A+VG   A +    Q  FR+   + S  G  +G   G       A  VLP  +  G + A
Sbjct: 103 ATVGFALAAAGTVMQGFFRNPMADPSIIGVSSGAAVGA-----VAAIVLPLAVPFGLQAA 157

Query: 119 AFTHAIATAGVVYAVARSCKDGSLP 143
           AF  A+  A  VYA+A   ++G  P
Sbjct: 158 AFAGALVAAFGVYAIA--TENGRTP 180

Length = 366

>gnl|CDD|240370 PTZ00342, PTZ00342, acyl-CoA synthetase; Provisional

 Score = 38.9 bits (91), Expect = 0.002
 Identities = 18/92 (19%), Positives = 33/92 (35%), Gaps = 9/92 (9%)

Query: 189 KRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKE-KKKEKKKKKKKKKEKKKKKKEKKK 247
           K K     +E++           K  K+++K      + E       + +K+K +K K  
Sbjct: 212 KSKEININKEEKNNGSNVNNNGNKNNKEEQKGNDLSNELEDISLGPLEYDKEKLEKIKDL 271

Query: 248 KKEEKKKEKK--------KKKKKKEKKKKKDE 271
           K++ KK            K K    K + +D 
Sbjct: 272 KEKAKKLGISIILFDDMTKNKTTNYKIQNEDP 303

Length = 746

>gnl|CDD|225288 COG2433, COG2433, Uncharacterized conserved protein [Function unknown]

 Score = 38.9 bits (91), Expect = 0.002
 Identities = 21/100 (21%), Positives = 56/100 (56%), Gaps = 2/100 (2%)

Query: 178 KERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKE 237
           +E+      +R+     E+  K+ E+  E+ +E+  E K+E ++ +++ EK + + ++  
Sbjct: 404 REKEGTEEEERREITVYEKRIKKLEETVERLEEENSELKRELEELKREIEKLESELERFR 463

Query: 238 KKKKKKEKKKKKEEKKKEK--KKKKKKKEKKKKKDEGRRR 275
           ++ + K +K ++   +  +  + +K+ +EKKK+ +E  R+
Sbjct: 464 REVRDKVRKDREIRARDRRIERLEKELEEKKKRVEELERK 503

Length = 652

>gnl|CDD|220431 pfam09831, DUF2058, Uncharacterized protein conserved in bacteria (DUF2058)

 Score = 37.6 bits (88), Expect = 0.002
 Identities = 16/61 (26%), Positives = 35/61 (57%), Gaps = 8/61 (13%)

Query: 214 EKKKEKKKKEKKKEKKKKKKK--------KKEKKKKKKEKKKKKEEKKKEKKKKKKKKEK 265
           +KK +K KKEK+K++K+ +K         K+  ++ K EK ++  E  ++++ + ++K  
Sbjct: 14  KKKAKKAKKEKRKQRKQARKGADDGDDELKQAAEEAKAEKAERDRELNRQRQAEAEQKAI 73

Query: 266 K 266
            
Sbjct: 74  V 74

This domain, found in various prokaryotic proteins, has no known function. Length = 177

>gnl|CDD|114629 pfam05917, DUF874, Helicobacter pylori protein of unknown function (DUF874)

 Score = 38.7 bits (89), Expect = 0.002
 Identities = 28/95 (29%), Positives = 56/95 (58%)

Query: 177 KKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKK 236
           KKE    R R  K   + E+EE++ E++++K +++  E    + K E++K+K +++K+K 
Sbjct: 134 KKEAENARDRANKSGIELEQEEQKTEQEKQKTEKEGIELANSQIKAEQEKQKTEQEKQKT 193

Query: 237 EKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDE 271
           E++K+K      K   + E++K+K + EK+    E
Sbjct: 194 EQEKQKTSNIANKNAIELEQEKQKTENEKQDLIKE 228

This family consists of several hypothetical proteins specific to Helicobacter pylori. The function of this family is unknown. Length = 417

>gnl|CDD|148630 pfam07133, Merozoite_SPAM, Merozoite surface protein (SPAM)

 Score = 37.5 bits (87), Expect = 0.002
 Identities = 15/84 (17%), Positives = 49/84 (58%)

Query: 191 KRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKE 250
           K +K+E+++EEE+++E++ E+ ++ + E++  E ++E+++ ++   + K  +K+      
Sbjct: 44  KDEKQEDDEEEEEEDEEEIEEPEDIEDEEEIVEDEEEEEEDEEDNVDLKDIEKKNINDIF 103

Query: 251 EKKKEKKKKKKKKEKKKKKDEGRR 274
              ++   +    +  KK ++ ++
Sbjct: 104 NSTQDDNAQNLISKNYKKNEKSKK 127

This family consists of several Plasmodium falciparum SPAM (secreted polymorphic antigen associated with merozoites) proteins. Variation among SPAM alleles is the result of deletions and amino acid substitutions in non-repetitive sequences within and flanking the alanine heptad-repeat domain. Heptad repeats in which the a and d position contain hydrophobic residues generate amphipathic alpha-helices which give rise to helical bundles or coiled-coil structures in proteins. SPAM is an example of a P. falciparum antigen in which a repetitive sequence has features characteristic of a well-defined structural element. Length = 164

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 38.6 bits (89), Expect = 0.003
 Identities = 31/94 (32%), Positives = 62/94 (65%), Gaps = 3/94 (3%)

Query: 178  KERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKE 237
            K++  + ++K +  +K EEE K + ++ +K+ E+ K+K +E KK E++K+K    KK++E
Sbjct: 1708 KKKEAEEKKKAEELKKAEEENKIKAEEAKKEAEEDKKKAEEAKKDEEEKKKIAHLKKEEE 1767

Query: 238  KKKKKKEKKKK---KEEKKKEKKKKKKKKEKKKK 268
            KK ++  K+K+   +EE  +E +K++ + +KK K
Sbjct: 1768 KKAEEIRKEKEAVIEEELDEEDEKRRMEVDKKIK 1801

Length = 2084

>gnl|CDD|217051 pfam02463, SMC_N, RecF/RecN/SMC N terminal domain

 Score = 38.8 bits (90), Expect = 0.003
 Identities = 20/88 (22%), Positives = 45/88 (51%)

Query: 177 KKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKK 236
            +   ++    ++ K+++ +  +E E+  E K+ K  E+K+E +K+  K  K K + KK 
Sbjct: 412 LELSEQEEDLLKEEKKEELKIVEELEESLETKQGKLTEEKEELEKQALKLLKDKLELKKS 471

Query: 237 EKKKKKKEKKKKKEEKKKEKKKKKKKKE 264
           E   K+ +  K  E+ +    ++K ++ 
Sbjct: 472 EDLLKETKLVKLLEQLELLLLRQKLEEA 499

This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination. Length = 1162

>gnl|CDD|217051 pfam02463, SMC_N, RecF/RecN/SMC N terminal domain

 Score = 38.4 bits (89), Expect = 0.003
 Identities = 24/95 (25%), Positives = 63/95 (66%)

Query: 177 KKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKK 236
           KK + ++      + ++ +++  EE K  E+K ++K+E++++ + K++++E++K +   K
Sbjct: 714 KKLKLEKEELLADKVQEAQDKINEELKLLEQKIKEKEEEEEKSRLKKEEEEEEKSELSLK 773

Query: 237 EKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDE 271
           EK+  ++E+K +K + ++EK++K K +E++ +  E
Sbjct: 774 EKELAEEEEKTEKLKVEEEKEEKLKAQEEELRALE 808

This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination. Length = 1162

>gnl|CDD|220252 pfam09468, RNase_H2-Ydr279, Ydr279p protein family (RNase H2 complex component)

 Score = 37.7 bits (88), Expect = 0.003
 Identities = 22/63 (34%), Positives = 31/63 (49%)

Query: 213 KEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDEG 272
            +  KE  K     E K   K  KE KKKK+E ++  E  +   +KK+K KE+ KKK   
Sbjct: 205 PDLYKELLKSLLIPEFKPLDKYLKESKKKKRETEEDVEAAESRAEKKRKSKEEIKKKKPK 264

Query: 273 RRR 275
             +
Sbjct: 265 ESK 267

RNases H are enzymes that specifically hydrolyse RNA when annealed to a complementary DNA and are present in all living organisms. In yeast RNase H2 is composed of a complex of three proteins (Rnh2Ap, Ydr279p and Ylr154p), this family represents the homologues of Ydr279p. It is not known whether non yeast proteins in this family fulfil the same function. Length = 287

>gnl|CDD|114011 pfam05262, Borrelia_P83, Borrelia P83/100 protein

 Score = 38.4 bits (89), Expect = 0.003
 Identities = 21/98 (21%), Positives = 50/98 (51%), Gaps = 1/98 (1%)

Query: 179 ERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEK 238
           E  ++   K    R+   + KE E +E+ K+ ++ +++ +KK+ +  K ++K    +   
Sbjct: 184 EALREDNEKGVNFRRDMTDLKERESQEDAKRAQQLKEELDKKQIDADKAQQKADFAQDNA 243

Query: 239 KKKKKE-KKKKKEEKKKEKKKKKKKKEKKKKKDEGRRR 275
            K++ E ++K++E K   K       ++ K+  E ++R
Sbjct: 244 DKQRDEVRQKQQEAKNLPKPADTSSPKEDKQVAENQKR 281

This family consists of several Borrelia P83/P100 antigen proteins. Length = 489

>gnl|CDD|235401 PRK05306, infB, translation initiation factor IF-2; Validated

 Score = 38.3 bits (90), Expect = 0.003
 Identities = 12/73 (16%), Positives = 33/73 (45%)

Query: 197 EEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKKKEK 256
           +E   E K      +++E +KE+ K+E ++E K + ++    + +++ K +       E+
Sbjct: 25  KELGIEVKSHSSTVEEEEARKEEAKREAEEEAKAEAEEAAAAEAEEEAKAEAAAAAPAEE 84

Query: 257 KKKKKKKEKKKKK 269
             +     +   +
Sbjct: 85  AAEAAAAAEAAAR 97

Length = 746

>gnl|CDD|221952 pfam13166, AAA_13, AAA domain

 Score = 38.8 bits (91), Expect = 0.003
 Identities = 23/95 (24%), Positives = 40/95 (42%)

Query: 177 KKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKK 236
           KKE +K   +  + + + E++E+E EK + K  +K  +K  +K      +  K    KK 
Sbjct: 101 KKELKKLEEKIEQLEAEIEKKEEELEKAKNKFLDKAWKKLAKKYDSNLSEALKGLNYKKN 160

Query: 237 EKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDE 271
            K+K  KE K            ++ K + K     
Sbjct: 161 FKEKLLKELKSVILNASSLLSLEELKAKIKTLFSS 195

This family of domains contain a P-loop motif that is characteristic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins. This family includes the PrrC protein that is thought to be the active component of the anticodon nuclease. Length = 713

>gnl|CDD|221952 pfam13166, AAA_13, AAA domain

 Score = 38.8 bits (91), Expect = 0.003
 Identities = 29/98 (29%), Positives = 40/98 (40%), Gaps = 6/98 (6%)

Query: 178 KERRKQRRRKRKRKRKKEE-----EEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKK 232
            E   Q    +K  +K EE     E + E+K+EE +K K K   K  KK  KK +    +
Sbjct: 91  IEIEAQIEELKKELKKLEEKIEQLEAEIEKKEEELEKAKNKFLDKAWKKLAKKYDSNLSE 150

Query: 233 KKKKEKKKKK-KEKKKKKEEKKKEKKKKKKKKEKKKKK 269
             K    KK  KEK  K+ +            E+ K K
Sbjct: 151 ALKGLNYKKNFKEKLLKELKSVILNASSLLSLEELKAK 188

This family of domains contain a P-loop motif that is characteristic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins. This family includes the PrrC protein that is thought to be the active component of the anticodon nuclease. Length = 713

>gnl|CDD|221952 pfam13166, AAA_13, AAA domain

 Score = 38.5 bits (90), Expect = 0.003
 Identities = 16/74 (21%), Positives = 37/74 (50%)

Query: 186 RKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEK 245
           R+   K    ++EK + KK+       + K+     +++KK  +K     +++ K+ + +
Sbjct: 378 REHNEKIDNLKKEKNKAKKKLWLHLVAELKEDIDAYQKEKKGLEKAINSLEKEIKQLEAE 437

Query: 246 KKKKEEKKKEKKKK 259
            K  E++ KE +K+
Sbjct: 438 IKALEKEIKELEKQ 451

This family of domains contain a P-loop motif that is characteristic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins. This family includes the PrrC protein that is thought to be the active component of the anticodon nuclease. Length = 713

>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]

 Score = 38.9 bits (91), Expect = 0.003
 Identities = 20/97 (20%), Positives = 57/97 (58%), Gaps = 3/97 (3%)

Query: 178 KERRKQRRRKRKRKRKKEE--EEKEEEKKEEKKK-EKKKEKKKEKKKKEKKKEKKKKKKK 234
           KER+++  RK +R  +  E  E+  EE +++ +K E++ EK +  ++ + +  + +    
Sbjct: 171 KERKEEAERKLERTEENLERLEDLLEELEKQLEKLERQAEKAERYQELKAELRELELALL 230

Query: 235 KKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDE 271
             + K+ +KE ++ +EE  + +++ ++ +E+ ++ ++
Sbjct: 231 LAKLKELRKELEELEEELSRLEEELEELQEELEEAEK 267

Length = 1163

>gnl|CDD|236545 PRK09510, tolA, cell envelope integrity inner membrane protein TolA; Provisional

 Score = 38.2 bits (89), Expect = 0.003
 Identities = 19/94 (20%), Positives = 58/94 (61%)

Query: 182 KQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKK 241
           +Q  R++++++  +  E++ +KKE+++ E+ ++K+  ++++ K+ EK++   ++++K+ +
Sbjct: 62  EQYNRQQQQQKSAKRAEEQRKKKEQQQAEELQQKQAAEQERLKQLEKERLAAQEQKKQAE 121

Query: 242 KKEKKKKKEEKKKEKKKKKKKKEKKKKKDEGRRR 275
           +  K+   ++K+ E+   K     K K +   +R
Sbjct: 122 EAAKQAALKQKQAEEAAAKAAAAAKAKAEAEAKR 155

Length = 387

>gnl|CDD|240402 PTZ00399, PTZ00399, cysteinyl-tRNA-synthetase; Provisional

 Score = 38.5 bits (90), Expect = 0.003
 Identities = 14/42 (33%), Positives = 31/42 (73%)

Query: 234 KKKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDEGRRR 275
           K  +K++ ++EK++K+  K++++ +K KK+E+KKKK+  +  
Sbjct: 546 KLDDKEELQREKEEKEALKEQKRLRKLKKQEEKKKKELEKLE 587

Length = 651

>gnl|CDD|220383 pfam09756, DDRGK, DDRGK domain

 Score = 37.4 bits (87), Expect = 0.003
 Identities = 23/79 (29%), Positives = 58/79 (73%), Gaps = 1/79 (1%)

Query: 174 KGGKKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKK 233
           K  ++++R+    +R+ ++K EE ++E E+KEE++ E+++EKKKE++++++++E+ +K++
Sbjct: 14  KQARRQQREAEEEEREERKKLEE-KREGERKEEEELEEEREKKKEEEERKEREEQARKEQ 72

Query: 234 KKKEKKKKKKEKKKKKEEK 252
           ++ EK K     +++  +K
Sbjct: 73  EEYEKLKSSFVVEEEGTDK 91

This is a family of proteins of approximately 300 residues, found in plants and vertebrates. They contain a highly conserved DDRGK motif. Length = 189

>gnl|CDD|200340 TIGR03927, T7SS_EssA_Firm, type VII secretion protein EssA

 Score = 37.0 bits (86), Expect = 0.003
 Identities = 15/65 (23%), Positives = 33/65 (50%), Gaps = 2/65 (3%)

Query: 189 KRKRKKEEEEKEEEKKEEKKKEKKKEKKK--EKKKKEKKKEKKKKKKKKKEKKKKKKEKK 246
           K+  +   +  +EE + +K+    +E+KK   +K KEK ++++ K +   E   +    K
Sbjct: 33  KKDIEINTDYLQEETELDKELFTPEEQKKITFQKHKEKPEQEELKNQLFSENATENNTVK 92

Query: 247 KKKEE 251
             K++
Sbjct: 93  ATKKQ 97

Members of this family are associated with type VII secretion of WXG100 family targets in the Firmicutes, but not in the Actinobacteria. This highly divergent protein family consists largely of a central region of highly polar low-complexity sequence containing occasional LF motifs in weak repeats about 17 residues in length, flanked by hydrophobic N- and C-terminal regions [Protein fate, Protein and peptide secretion and trafficking]. Length = 150

>gnl|CDD|219563 pfam07767, Nop53, Nop53 (60S ribosomal biogenesis)

 Score = 38.1 bits (89), Expect = 0.003
 Identities = 26/99 (26%), Positives = 52/99 (52%), Gaps = 18/99 (18%)

Query: 194 KEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKK---- 249
             EEE ++E   E  + + +   K  + K K K ++ K+K++KE +++ KE+K+ K    
Sbjct: 248 DGEEESDDESAWEGFESEYEPINKPVRPKRKTKAQRNKEKRRKELEREAKEEKQLKKKLA 307

Query: 250 --------------EEKKKEKKKKKKKKEKKKKKDEGRR 274
                         +EK + +KK+++K+  +KKK + R+
Sbjct: 308 QLARLKEIAKEVAQKEKARARKKEQRKERGEKKKLKRRK 346

This nucleolar family of proteins are involved in 60S ribosomal biogenesis. They are specifically involved in the processing beyond the 27S stage of 25S rRNA maturation. This family contains sequences that bear similarity to the glioma tumour suppressor candidate region gene 2 protein (p60). This protein has been found to interact with herpes simplex type 1 regulatory proteins. Length = 387

>gnl|CDD|222160 pfam13476, AAA_23, AAA domain

 Score = 37.9 bits (88), Expect = 0.003
 Identities = 17/61 (27%), Positives = 42/61 (68%)

Query: 193 KKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEK 252
           + EE + + ++K+E+ +E +KE ++ + +K+  ++  ++K+KKKE ++ K+E ++  EE 
Sbjct: 144 RLEELKFKRKEKKERLEELEKELEELEDEKDLLEKLLEEKEKKKELEELKEELEELLEEL 203

Query: 253 K 253
           +
Sbjct: 204 E 204

Length = 204

>gnl|CDD|222636 pfam14265, DUF4355, Domain of unknown function (DUF4355)

 Score = 36.5 bits (85), Expect = 0.003
 Identities = 19/77 (24%), Positives = 42/77 (54%)

Query: 186 RKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEK 245
           +    K   +   KE+ K E+K++EKK E +K  K   ++K + + +K +KE ++ + E 
Sbjct: 6   KTFTDKEVDKAIAKEKAKWEKKQEEKKSEAEKLAKMSAEEKAEYELEKLEKELEELEAEL 65

Query: 246 KKKKEEKKKEKKKKKKK 262
            +++ + + +K   +K 
Sbjct: 66  ARRELKAEAKKMLSEKG 82

This family of proteins is found in bacteria and viruses. Proteins in this family are typically between 180 and 214 amino acids in length. Length = 125

>gnl|CDD|222636 pfam14265, DUF4355, Domain of unknown function (DUF4355)

 Score = 36.5 bits (85), Expect = 0.003
 Identities = 19/80 (23%), Positives = 48/80 (60%)

Query: 193 KKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEK 252
           ++E+   ++E  +   KEK K +KK+++KK + ++  K   ++K + + +K +K+ +E +
Sbjct: 3   EEEKTFTDKEVDKAIAKEKAKWEKKQEEKKSEAEKLAKMSAEEKAEYELEKLEKELEELE 62

Query: 253 KKEKKKKKKKKEKKKKKDEG 272
            +  +++ K + KK   ++G
Sbjct: 63  AELARRELKAEAKKMLSEKG 82

This family of proteins is found in bacteria and viruses. Proteins in this family are typically between 180 and 214 amino acids in length. Length = 125

>gnl|CDD|206039 pfam13868, Trichoplein, Tumour suppressor, Mitostatin

 Score = 38.0 bits (89), Expect = 0.003
 Identities = 19/95 (20%), Positives = 66/95 (69%)

Query: 177 KKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKK 236
           ++ERR     + +R +   EEE+ E K++E+++E +   +++ +++EK+++++ +++ ++
Sbjct: 38  EEERRIDEMMEEERLKALAEEEERERKRKEERREGRAVLQEQIEEREKRRQEEYEERLQE 97

Query: 237 EKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDE 271
            ++  +  ++ ++E++ + ++K++K+K+ +++ DE
Sbjct: 98  REQMDEIIERIQEEDEAEAQEKREKQKKLREEIDE 132

Trichoplein or mitostatin, was first defined as a meiosis-specific nuclear structural protein. It has since been linked with mitochondrial movement. It is associated with the mitochondrial outer membrane, and over-expression leads to reduction in mitochondrial motility whereas lack of it enhances mitochondrial movement. The activity appears to be mediated through binding the mitochondria to the actin intermediate filaments (IFs). Length = 349

>gnl|CDD|225606 COG3064, TolA, Membrane protein involved in colicin uptake [Cell envelope biogenesis, outer membrane]

 Score = 38.4 bits (89), Expect = 0.003
 Identities = 25/97 (25%), Positives = 49/97 (50%)

Query: 174 KGGKKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKK 233
           K  +++++ +   K+ +  +K++EE+  +   E+KK+ +  K K   +  K K   + KK
Sbjct: 112 KAQEQQKQAEEAEKQAQLEQKQQEEQARKAAAEQKKKAEAAKAKAAAEAAKLKAAAEAKK 171

Query: 234 KKKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKD 270
           K +E  K  +E K K E    +KK + + K   +K  
Sbjct: 172 KAEEAAKAAEEAKAKAEAAAAKKKAEAEAKAAAEKAK 208

Length = 387

>gnl|CDD|225606 COG3064, TolA, Membrane protein involved in colicin uptake [Cell envelope biogenesis, outer membrane]

 Score = 38.0 bits (88), Expect = 0.003
 Identities = 25/95 (26%), Positives = 55/95 (57%)

Query: 177 KKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKK 236
            K+  K+R + ++++++ EE EK+ + ++++++E+ ++   E+KKK +  + K   +  K
Sbjct: 103 LKQLEKERLKAQEQQKQAEEAEKQAQLEQKQQEEQARKAAAEQKKKAEAAKAKAAAEAAK 162

Query: 237 EKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDE 271
            K   + +KK ++  K  E+ K K +    KKK E
Sbjct: 163 LKAAAEAKKKAEEAAKAAEEAKAKAEAAAAKKKAE 197

Length = 387

>gnl|CDD|224415 COG1498, SIK1, Protein implicated in ribosomal biogenesis, Nop56p homolog [Translation, ribosomal structure and biogenesis]

 Score = 38.1 bits (89), Expect = 0.003
 Identities = 20/61 (32%), Positives = 32/61 (52%)

Query: 196 EEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKKKE 255
            E      +EE +K  +K K+K  K   K K ++ KK++    ++KKKEKK K E +  +
Sbjct: 335 GEPDGISLREELEKRIEKLKEKPPKPPTKAKPERDKKERPGRYRRKKKEKKAKSERRGLQ 394

Query: 256 K 256
            
Sbjct: 395 N 395

Length = 395

>gnl|CDD|223496 COG0419, SbcC, ATPase involved in DNA repair [DNA replication, recombination, and repair]

 Score = 38.6 bits (90), Expect = 0.003
 Identities = 16/97 (16%), Positives = 50/97 (51%)

Query: 178 KERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKE 237
           +  R       +   K +  E+  EK EEK ++ + E ++  ++K +  +  +++ K+ E
Sbjct: 308 EGLRALLEELEELLEKLKSLEERLEKLEEKLEKLESELEELAEEKNELAKLLEERLKELE 367

Query: 238 KKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDEGRR 274
           ++ ++ EK+ +K  ++ ++ ++  ++ K++  +    
Sbjct: 368 ERLEELEKELEKALERLKQLEEAIQELKEELAELSAA 404

Length = 908

>gnl|CDD|223496 COG0419, SbcC, ATPase involved in DNA repair [DNA replication, recombination, and repair]

 Score = 38.6 bits (90), Expect = 0.003
 Identities = 20/102 (19%), Positives = 54/102 (52%)

Query: 168 NLEYGYKGGKKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKE 227
           NL+   +   +   ++   K +    +   E +  + EE+ +EK +E ++ +++ E+ +E
Sbjct: 643 NLQAELEELLQAALEELEEKVEELEAEIRRELQRIENEEQLEEKLEELEQLEEELEQLRE 702

Query: 228 KKKKKKKKKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKK 269
           + ++  KK  + ++  E+ + ++ + +E KK+ +K EK  + 
Sbjct: 703 ELEELLKKLGEIEQLIEELESRKAELEELKKELEKLEKALEL 744

Length = 908

>gnl|CDD|223496 COG0419, SbcC, ATPase involved in DNA repair [DNA replication, recombination, and repair]

 Score = 38.6 bits (90), Expect = 0.003
 Identities = 13/91 (14%), Positives = 54/91 (59%)

Query: 178 KERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKE 237
           K+  + +  + + + ++E E  EE   E ++++++ E+ K +  + +  E +  K +++E
Sbjct: 216 KKLEEIQEEQEEEELEQEIEALEERLAELEEEKERLEELKARLLEIESLELEALKIREEE 275

Query: 238 KKKKKKEKKKKKEEKKKEKKKKKKKKEKKKK 268
            ++ ++  ++ +E+ ++ ++ +++ +E +++
Sbjct: 276 LRELERLLEELEEKIERLEELEREIEELEEE 306

Length = 908

>gnl|CDD|149343 pfam08229, SHR3_chaperone, ER membrane protein SH3

 Score = 37.3 bits (87), Expect = 0.003
 Identities = 11/34 (32%), Positives = 18/34 (52%)

Query: 189 KRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKK 222
           K   +   EE E     ++++  + EKK+ KKKK
Sbjct: 163 KLLEEFAAEEAEAAAAAKEEESAEGEKKESKKKK 196

This family of proteins are membrane localised chaperones that are required for correct plasma membrane localisation of amino acid permeases (AAPs). SH3 prevents AAPs proteins from aggregating and assists in their correct folding. In the absence of SH3, AAPs are retained in the ER. Length = 196

>gnl|CDD|149343 pfam08229, SHR3_chaperone, ER membrane protein SH3

 Score = 37.3 bits (87), Expect = 0.003
 Identities = 12/39 (30%), Positives = 21/39 (53%)

Query: 210 EKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKK 248
           E K  K  E+   E+ +     K+++  + +KK+ KKKK
Sbjct: 158 EWKDAKLLEEFAAEEAEAAAAAKEEESAEGEKKESKKKK 196

This family of proteins are membrane localised chaperones that are required for correct plasma membrane localisation of amino acid permeases (AAPs). SH3 prevents AAPs proteins from aggregating and assists in their correct folding. In the absence of SH3, AAPs are retained in the ER. Length = 196

>gnl|CDD|235549 PRK05658, PRK05658, RNA polymerase sigma factor RpoD; Validated

 Score = 38.6 bits (91), Expect = 0.003
 Identities = 22/79 (27%), Positives = 39/79 (49%), Gaps = 1/79 (1%)

Query: 194 KEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKK-KEKKKKKKKKKEKKKKKKEKKKKKEEK 252
               E EE   +E ++E++ E        E +  EK  +K K   K+ KK  K ++K+ +
Sbjct: 184 HVGSELEELDDDEDEEEEEDENDDSLAADESELPEKVLEKFKALAKQYKKLRKAQEKKVE 243

Query: 253 KKEKKKKKKKKEKKKKKDE 271
            +  + KK  K ++K K+E
Sbjct: 244 GRLAQHKKYAKLREKLKEE 262

Length = 619

>gnl|CDD|218899 pfam06102, DUF947, Domain of unknown function (DUF947)

 Score = 37.3 bits (87), Expect = 0.003
 Identities = 28/95 (29%), Positives = 52/95 (54%), Gaps = 3/95 (3%)

Query: 177 KKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEK---KKKKK 233
           K +  +++   ++  +  +   K  + K+ +++  K+ KK+EK+  ++ K+    KK + 
Sbjct: 74  KTKDSEEKEELKRTLQSMKSRLKTLKNKDREREILKEHKKQEKELIKEGKKPYYLKKSEI 133

Query: 234 KKKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKK 268
           KK   KKK  E KK K+  K  +KK+KK   K+KK
Sbjct: 134 KKLVLKKKFDELKKSKQLDKALEKKRKKNAGKEKK 168

Family of eukaryotic proteins with unknown function. Length = 168

>gnl|CDD|221049 pfam11262, Tho2, Transcription factor/nuclear export subunit protein 2

 Score = 38.1 bits (89), Expect = 0.003
 Identities = 19/62 (30%), Positives = 35/62 (56%)

Query: 204 KEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKKKEKKKKKKKK 263
            +E ++ +K+ K+ +       K+KK+KK+ K   KK ++E KK  E  +K KK+  ++K
Sbjct: 30  DKEIERLEKQIKELDSSSSGIDKKKKEKKRLKSLIKKLEEELKKHIEHNEKTKKRLSEEK 89

Query: 264 EK 265
             
Sbjct: 90  SS 91

THO and TREX form a eukaryotic complex which functions in messenger ribonucleoprotein metabolism and plays a role in preventing the transcription-associated genetic instability. Tho2, along with four other subunits forms THO. Length = 296

>gnl|CDD|148630 pfam07133, Merozoite_SPAM, Merozoite surface protein (SPAM)

 Score = 37.1 bits (86), Expect = 0.003
 Identities = 23/81 (28%), Positives = 44/81 (54%)

Query: 189 KRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKK 248
           K++  +EEEE++EE+ EE +  + +E+  E +++E++ E+     K  EKK         
Sbjct: 47  KQEDDEEEEEEDEEEIEEPEDIEDEEEIVEDEEEEEEDEEDNVDLKDIEKKNINDIFNST 106

Query: 249 KEEKKKEKKKKKKKKEKKKKK 269
           +++  +    K  KK +K KK
Sbjct: 107 QDDNAQNLISKNYKKNEKSKK 127

This family consists of several Plasmodium falciparum SPAM (secreted polymorphic antigen associated with merozoites) proteins. Variation among SPAM alleles is the result of deletions and amino acid substitutions in non-repetitive sequences within and flanking the alanine heptad-repeat domain. Heptad repeats in which the a and d position contain hydrophobic residues generate amphipathic alpha-helices which give rise to helical bundles or coiled-coil structures in proteins. SPAM is an example of a P. falciparum antigen in which a repetitive sequence has features characteristic of a well-defined structural element. Length = 164

>gnl|CDD|215641 PLN03237, PLN03237, DNA topoisomerase 2; Provisional

 Score = 38.7 bits (90), Expect = 0.003
 Identities = 21/97 (21%), Positives = 39/97 (40%), Gaps = 20/97 (20%)

Query: 195  EEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEE--- 251
            E+E  + +K++ K +E +++ ++   + E    KK  ++  K+   KK  KK  + E   
Sbjct: 1162 EKELDKLDKEDAKAEEAREKLQRAAARGESGAAKKVSRQAPKKPAPKKTTKKASESETTE 1221

Query: 252  -----------------KKKEKKKKKKKKEKKKKKDE 271
                             K K +   KKK     K+ E
Sbjct: 1222 ETYGSSAMETENVAEVVKPKGRAGAKKKAPAAAKEKE 1258

Length = 1465

>gnl|CDD|223250 COG0172, SerS, Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis]

 Score = 38.3 bits (90), Expect = 0.003
 Identities = 18/65 (27%), Positives = 33/65 (50%)

Query: 187 KRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKK 246
           + +RK  +E EE + E+ E  K+  +  K+ E   +E   E K+ K+K KE +    E +
Sbjct: 36  EERRKLLRELEELQAERNELSKEIGRALKRGEDDAEELIAEVKELKEKLKELEAALDELE 95

Query: 247 KKKEE 251
            + + 
Sbjct: 96  AELDT 100

Length = 429

>gnl|CDD|240254 PTZ00069, PTZ00069, 60S ribosomal protein L5; Provisional

 Score = 38.1 bits (89), Expect = 0.003
 Identities = 24/72 (33%), Positives = 39/72 (54%)

Query: 191 KRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKE 250
           K     +  E+  K+     +    K +KKKK+KKK   KK K KK   K++K + K K+
Sbjct: 229 KAGVGPDSLEDMYKKAHAAIRANPSKVKKKKKKKKKVVHKKYKTKKLTGKQRKARVKAKK 288

Query: 251 EKKKEKKKKKKK 262
            +++E+ +KK K
Sbjct: 289 AQRRERLQKKIK 300

Length = 300

>gnl|CDD|235219 PRK04098, PRK04098, sec-independent translocase; Provisional

 Score = 37.0 bits (86), Expect = 0.003
 Identities = 18/81 (22%), Positives = 37/81 (45%)

Query: 191 KRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKE 250
           K+K + EE ++ K   + + K  +   +  KK  +++       ++   + K  ++   +
Sbjct: 78  KKKLKFEELDDLKITAENEIKSIQDLLQDYKKSLEEDTIPNHLNEEVSNETKLTQESSSD 137

Query: 251 EKKKEKKKKKKKKEKKKKKDE 271
           E  KE K   K K KK  K++
Sbjct: 138 ESPKEVKLATKNKTKKHDKEK 158

Length = 158

>gnl|CDD|218896 pfam06098, Radial_spoke_3, Radial spoke protein 3

 Score = 38.1 bits (89), Expect = 0.003
 Identities = 15/63 (23%), Positives = 46/63 (73%)

Query: 196 EEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKKKE 255
           E  +EEE  E ++++++ E+++  +  E ++ ++ ++++++EK+++KK+ K++K+ +K+ 
Sbjct: 147 EVLEEEELAELRQQQRQFEQRRNAELAETQRLEEAERRRREEKERRKKQDKERKQREKET 206

Query: 256 KKK 258
            +K
Sbjct: 207 AEK 209

This family consists of several radial spoke protein 3 (RSP3) sequences. Eukaryotic cilia and flagella present in diverse types of cells perform motile, sensory, and developmental functions in organisms from protists to humans. They are centred by precisely organised, microtubule-based structures, the axonemes. The axoneme consists of two central singlet microtubules, called the central pair, and nine outer doublet microtubules. These structures are well-conserved during evolution. The outer doublet microtubules, each composed of A and B sub-fibres, are connected to each other by nexin links, while the central pair is held at the centre of the axoneme by radial spokes. The radial spokes are T-shaped structures extending from the A-tubule of each outer doublet microtubule to the centre of the axoneme. Radial spoke protein 3 (RSP3), is present at the proximal end of the spoke stalk and helps in anchoring the radial spoke to the outer doublet. It is thought that radial spokes regulate the activity of inner arm dynein through protein phosphorylation and dephosphorylation. Length = 288

>gnl|CDD|217834 pfam03998, Utp11, Utp11 protein

 Score = 37.7 bits (88), Expect = 0.003
 Identities = 24/89 (26%), Positives = 50/89 (56%)

Query: 181 RKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKK 240
            ++++     +      E  + ++   +  + ++     +K++KK  KKK+K  K+ K++
Sbjct: 131 EEEQKSFDPAEYFDTTPELLDRRENRPRISQLEKTSLVDEKQKKKSAKKKRKLYKELKER 190

Query: 241 KKKEKKKKKEEKKKEKKKKKKKKEKKKKK 269
           K++EKK KK E++ E +++  KK K KKK
Sbjct: 191 KEREKKLKKVEQRLELQRELMKKGKGKKK 219

This protein is found to be part of a large ribonucleoprotein complex containing the U3 snoRNA. Depletion of the Utp proteins impedes production of the 18S rRNA, indicating that they are part of the active pre-rRNA processing complex. This large RNP complex has been termed the small subunit (SSU) processome. Length = 239

>gnl|CDD|227594 COG5269, ZUO1, Ribosome-associated chaperone zuotin [Translation, ribosomal structure and biogenesis / Posttranslational modification, protein turnover, chaperones]

 Score = 38.1 bits (88), Expect = 0.003
 Identities = 27/113 (23%), Positives = 48/113 (42%), Gaps = 9/113 (7%)

Query: 167 DNLEYGYKGGKKERRKQRRRKRKRKRKKEEEEK---------EEEKKEEKKKEKKKEKKK 217
           D   Y     +++R K + +   R ++  +  K         +E++KE KK  K + +  
Sbjct: 194 DRKRYSEAKNREKRAKLKNQDNARLKRLVQIAKKRDPRIKSFKEQEKEMKKIRKWEREAG 253

Query: 218 EKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKD 270
            + K     + K + K K E + +        ++K KE  KK  K EKK  K+
Sbjct: 254 ARLKALAALKGKAEAKNKAEIEAEALASATAVKKKAKEVMKKALKMEKKAIKN 306

Length = 379

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 38.2 bits (88), Expect = 0.004
 Identities = 40/118 (33%), Positives = 64/118 (54%), Gaps = 22/118 (18%)

Query: 180  RRKQRRRKRKRKRKKEEEEKEEE--KKEEKKKEKKKEKKKEKKKKEKKKEK--------- 228
            R+ +  RK +  RK E+ +K E   K EE KK+ ++ KK E+++  ++  K         
Sbjct: 1206 RKAEEERKAEEARKAEDAKKAEAVKKAEEAKKDAEEAKKAEEERNNEEIRKFEEARMAHF 1265

Query: 229  -------KKKKKKKKEKKKKKKEKKKKKEEKKKEKKKK----KKKKEKKKKKDEGRRR 275
                   K ++ +K ++ KK +EKKK  E KK E+KKK    KKK E+ KK DE +++
Sbjct: 1266 ARRQAAIKAEEARKADELKKAEEKKKADEAKKAEEKKKADEAKKKAEEAKKADEAKKK 1323

Length = 2084

>gnl|CDD|217051 pfam02463, SMC_N, RecF/RecN/SMC N terminal domain

 Score = 38.4 bits (89), Expect = 0.004
 Identities = 23/96 (23%), Positives = 58/96 (60%)

Query: 176 GKKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKK 235
            K E+  ++ ++   + +KE +E E +++ E+++E++ EK +EK ++ +++   KKK + 
Sbjct: 325 KKLEKELKKEKEEIEELEKELKELEIKREAEEEEEEQLEKLQEKLEQLEEELLAKKKLES 384

Query: 236 KEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDE 271
           +      K K+++ E K +E+K+ K   E  +++++
Sbjct: 385 ERLSSAAKLKEEELELKNEEEKEAKLLLELSEQEED 420

This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination. Length = 1162

>gnl|CDD|217051 pfam02463, SMC_N, RecF/RecN/SMC N terminal domain

 Score = 38.4 bits (89), Expect = 0.004
 Identities = 25/100 (25%), Positives = 49/100 (49%), Gaps = 1/100 (1%)

Query: 168 NLEYGYKGGKKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEK-KKEKKKEKKKKEKKK 226
            LE   +  K+ +      +++    KEE+++E +  EE ++    K+ K  ++K+E +K
Sbjct: 397 ELELKNEEEKEAKLLLELSEQEEDLLKEEKKEELKIVEELEESLETKQGKLTEEKEELEK 456

Query: 227 EKKKKKKKKKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKK 266
           +  K  K K E KK +   K+ K  K  E+ +    ++K 
Sbjct: 457 QALKLLKDKLELKKSEDLLKETKLVKLLEQLELLLLRQKL 496

This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination. Length = 1162

>gnl|CDD|235640 PRK05901, PRK05901, RNA polymerase sigma factor; Provisional

 Score = 38.1 bits (89), Expect = 0.004
 Identities = 11/82 (13%), Positives = 26/82 (31%)

Query: 191 KRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKE 250
             + +  +K+ +   +    K   KKK K + +  K+ +KK    K+      +      
Sbjct: 69  ATESDIPKKKTKTAAKAAAAKAPAKKKLKDELDSSKKAEKKNALDKDDDLNYVKDIDVLN 128

Query: 251 EKKKEKKKKKKKKEKKKKKDEG 272
           +   +              D+ 
Sbjct: 129 QADDDDDDDDDDDLDDDDIDDD 150

Length = 509

>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]

 Score = 38.2 bits (89), Expect = 0.004
 Identities = 20/90 (22%), Positives = 54/90 (60%)

Query: 182 KQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKK 241
           K    + + +  ++E E+ +E+ EE + EK++ + + K+ +E+K+E +++ ++ + +  +
Sbjct: 843 KLDELEEELEELEKELEELKEELEELEAEKEELEDELKELEEEKEELEEELRELESELAE 902

Query: 242 KKEKKKKKEEKKKEKKKKKKKKEKKKKKDE 271
            KE+ +K  E+ +E + K ++ E +  + E
Sbjct: 903 LKEEIEKLRERLEELEAKLERLEVELPELE 932

Length = 1163

>gnl|CDD|215774 pfam00183, HSP90, Hsp90 protein

 Score = 38.2 bits (89), Expect = 0.004
 Identities = 25/65 (38%), Positives = 43/65 (66%), Gaps = 3/65 (4%)

Query: 196 EEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKKKE 255
           E EKE   +EE   E++KE+KKE+++K   KE++  ++++KE+KKKK +K K+   + + 
Sbjct: 30  EVEKEVPDEEE---EEEKEEKKEEEEKTTDKEEEVDEEEEKEEKKKKTKKVKETTTEWEL 86

Query: 256 KKKKK 260
             K K
Sbjct: 87  LNKTK 91

Length = 529

>gnl|CDD|220383 pfam09756, DDRGK, DDRGK domain

 Score = 37.0 bits (86), Expect = 0.004
 Identities = 20/66 (30%), Positives = 55/66 (83%)

Query: 210 EKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKK 269
            KK+ K +EK+ + +++E +++++++++K ++K+E ++K+EE+ +E+++KKK++E++K++
Sbjct: 5   AKKRAKLEEKQARRQQREAEEEEREERKKLEEKREGERKEEEELEEEREKKKEEEERKER 64

Query: 270 DEGRRR 275
           +E  R+
Sbjct: 65  EEQARK 70

This is a family of proteins of approximately 300 residues, found in plants and vertebrates. They contain a highly conserved DDRGK motif. Length = 189

>gnl|CDD|218177 pfam04615, Utp14, Utp14 protein

 Score = 38.1 bits (89), Expect = 0.004
 Identities = 30/101 (29%), Positives = 54/101 (53%), Gaps = 11/101 (10%)

Query: 183 QRRRKRKRKRKKEE-----EEKEEEKKEEKKKEKKKEKKKEKKKK------EKKKEKKKK 231
           QR   RK++    E      E E E++ ++++ ++  KK   ++K      EK+ E KK 
Sbjct: 380 QRAEARKKEENDAEIEELRRELEGEEESDEEENEEPSKKNVGRRKFGPENGEKEAESKKL 439

Query: 232 KKKKKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDEG 272
           KK+ K + K+KKE  +++E + +E+ K +K   K  K+ E 
Sbjct: 440 KKENKNEFKEKKESDEEEELEDEEEAKVEKVANKLLKRSEK 480

This protein is found to be part of a large ribonucleoprotein complex containing the U3 snoRNA. Depletion of the Utp proteins impedes production of the 18S rRNA, indicating that they are part of the active pre-rRNA processing complex. This large RNP complex has been termed the small subunit (SSU) processome. Length = 728

>gnl|CDD|218177 pfam04615, Utp14, Utp14 protein

 Score = 38.1 bits (89), Expect = 0.004
 Identities = 25/95 (26%), Positives = 46/95 (48%)

Query: 177 KKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKK 236
            +E  K  +   K  ++ E+ +KEEE++E  ++    +      K  KK++ KKK   K 
Sbjct: 461 DEEEAKVEKVANKLLKRSEKAQKEEEEEELDEENPWLKTTSSVGKSAKKQDSKKKSSSKL 520

Query: 237 EKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDE 271
           +K   K  K   K +KKK+K+K     +    +++
Sbjct: 521 DKAANKISKAAVKVKKKKKKEKSIDLDDDLIDEED 555

This protein is found to be part of a large ribonucleoprotein complex containing the U3 snoRNA. Depletion of the Utp proteins impedes production of the 18S rRNA, indicating that they are part of the active pre-rRNA processing complex. This large RNP complex has been termed the small subunit (SSU) processome. Length = 728

>gnl|CDD|234767 PRK00448, polC, DNA polymerase III PolC; Validated

 Score = 38.3 bits (90), Expect = 0.004
 Identities = 21/80 (26%), Positives = 41/80 (51%), Gaps = 9/80 (11%)

Query: 193 KKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEK 252
           +KEEE+++  K+  +  +K + +KK++ K    KE   +  KK +K++    K+  +EE+
Sbjct: 178 QKEEEDEKLAKEALEAMKKLEAEKKKQSKNFDPKEGPVQIGKKIDKEEITPMKEINEEER 237

Query: 253 ---------KKEKKKKKKKK 263
                    K E K+ K  +
Sbjct: 238 RVVVEGYVFKVEIKELKSGR 257

Length = 1437

>gnl|CDD|221733 pfam12720, DUF3807, Protein of unknown function (DUF3807)

 Score = 37.0 bits (86), Expect = 0.004
 Identities = 15/81 (18%), Positives = 35/81 (43%)

Query: 192 RKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEE 251
           R++E +E+ E ++E +            +    +KE +++   +K K  + KE+K  K+ 
Sbjct: 67  RERELKEEAEAEEEGEVDASPDAGAVAGESSADRKEAEQQGAAQKRKSCRDKERKSAKDP 126

Query: 252 KKKEKKKKKKKKEKKKKKDEG 272
           +   +    K +      +E 
Sbjct: 127 RGGTQDVVDKSQASLDYGEEE 147

This is a family of conserved fungal proteins of unknown function. Length = 169

>gnl|CDD|222636 pfam14265, DUF4355, Domain of unknown function (DUF4355)

 Score = 36.1 bits (84), Expect = 0.004
 Identities = 23/73 (31%), Positives = 43/73 (58%)

Query: 199 KEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKKKEKKK 258
           + EE+K    KE  K   KEK K EKK+E+KK + +K  K   +++ + + E+ +KE ++
Sbjct: 1   EPEEEKTFTDKEVDKAIAKEKAKWEKKQEEKKSEAEKLAKMSAEEKAEYELEKLEKELEE 60

Query: 259 KKKKKEKKKKKDE 271
            + +  +++ K E
Sbjct: 61  LEAELARRELKAE 73

This family of proteins is found in bacteria and viruses. Proteins in this family are typically between 180 and 214 amino acids in length. Length = 125

>gnl|CDD|236978 PRK11778, PRK11778, putative inner membrane peptidase; Provisional

 Score = 37.9 bits (89), Expect = 0.004
 Identities = 15/60 (25%), Positives = 31/60 (51%)

Query: 215 KKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDEGRR 274
            +++K +K + +     ++ K+ K++ K     KKE K   K +KKK+K++ K      +
Sbjct: 30  AQRKKSQKGELEVTNLNEQYKEMKEELKAALLDKKELKAWHKAQKKKEKQEAKAAKAKSK 89

Length = 330

>gnl|CDD|220371 pfam09736, Bud13, Pre-mRNA-splicing factor of RES complex

 Score = 36.5 bits (85), Expect = 0.004
 Identities = 26/96 (27%), Positives = 52/96 (54%), Gaps = 8/96 (8%)

Query: 172 GYKGGKKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKK 231
           G     +E+R+++ R+++ K +KEE+EKE  K   +K+E++K  ++ +K K K   +   
Sbjct: 9   GRIIDIEEKREEKEREKEEKERKEEKEKEWGKGLVQKEEREKRLEELEKAKNKPLARYAD 68

Query: 232 KKKKKEKKKKKKEK--------KKKKEEKKKEKKKK 259
            +   E+ K+++          +KKKE+  K+ K  
Sbjct: 69  DEDYDEELKEQERWDDPMAQFLRKKKEKTDKKGKPL 104

This entry is characterized by proteins with alternating conserved and low-complexity regions. Bud13 together with Snu17p and a newly identified factor, Pml1p/Ylr016c, form a novel trimeric complex. called The RES complex, pre-mRNA retention and splicing complex. Subunits of this complex are not essential for viability of yeasts but they are required for efficient splicing in vitro and in vivo. Furthermore, inactivation of this complex causes pre-mRNA leakage from the nucleus. Bud13 contains a unique, phylogenetically conserved C-terminal region of unknown function. Length = 141

>gnl|CDD|206039 pfam13868, Trichoplein, Tumour suppressor, Mitostatin

 Score = 38.0 bits (89), Expect = 0.004
 Identities = 30/103 (29%), Positives = 72/103 (69%), Gaps = 5/103 (4%)

Query: 177 KKERRKQRRRKRKRKRKKEE-----EEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKK 231
           +KER+K++    KR+R+K+E     EE+ EEK+E  ++E+ +E+ + ++  EK+ E ++ 
Sbjct: 215 RKERQKEKEEAEKRRRQKQELQRAREEQIEEKEERLQEERAEEEAERERMLEKQAEDEEL 274

Query: 232 KKKKKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDEGRR 274
           +++  EK++ K+ + +++ E++ E+K++++  E++++ +EG R
Sbjct: 275 EQENAEKRRMKRLEHRRELEQQIEEKEERRAAEREEELEEGER 317

Trichoplein or mitostatin, was first defined as a meiosis-specific nuclear structural protein. It has since been linked with mitochondrial movement. It is associated with the mitochondrial outer membrane, and over-expression leads to reduction in mitochondrial motility whereas lack of it enhances mitochondrial movement. The activity appears to be mediated through binding the mitochondria to the actin intermediate filaments (IFs). Length = 349

>gnl|CDD|227352 COG5019, CDC3, Septin family protein [Cell division and chromosome partitioning / Cytoskeleton]

 Score = 37.7 bits (88), Expect = 0.004
 Identities = 20/86 (23%), Positives = 47/86 (54%)

Query: 181 RKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKK 240
           R ++    K   +   +E  E +  E+++E KK+  ++ ++KEK+ E+ ++   ++ K+ 
Sbjct: 288 RTEKLSGLKNSGEPSLKEIHEARLNEEERELKKKFTEKIREKEKRLEELEQNLIEERKEL 347

Query: 241 KKKEKKKKKEEKKKEKKKKKKKKEKK 266
             K ++ +K+ +  EK+ +K K  K 
Sbjct: 348 NSKLEEIQKKLEDLEKRLEKLKSNKS 373

Length = 373

>gnl|CDD|184900 PRK14907, rplD, 50S ribosomal protein L4; Provisional

 Score = 37.6 bits (87), Expect = 0.004
 Identities = 28/76 (36%), Positives = 33/76 (43%), Gaps = 3/76 (3%)

Query: 199 KEEEKKEEKKK---EKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKKKE 255
             E KK  KKK   EKK   KK    KE  K KK  K    +  KK  + KK K  K   
Sbjct: 1   MAETKKTTKKKTTEEKKPAAKKATTSKETAKTKKTAKTTSTKAAKKAAKVKKTKSVKTTT 60

Query: 256 KKKKKKKKEKKKKKDE 271
           KK   K ++ +  K E
Sbjct: 61  KKVTVKFEKTESVKKE 76

Length = 295

>gnl|CDD|184900 PRK14907, rplD, 50S ribosomal protein L4; Provisional

 Score = 37.6 bits (87), Expect = 0.004
 Identities = 22/82 (26%), Positives = 35/82 (42%)

Query: 189 KRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKK 248
           ++K   ++    +E  + KK  K    K  KK  + KK K  K   KK   K +K +  K
Sbjct: 15  EKKPAAKKATTSKETAKTKKTAKTTSTKAAKKAAKVKKTKSVKTTTKKVTVKFEKTESVK 74

Query: 249 KEEKKKEKKKKKKKKEKKKKKD 270
           KE   K+  KK+    +  +  
Sbjct: 75  KESVAKKTVKKEAVSAEVFEAS 96

Length = 295

>gnl|CDD|235175 PRK03918, PRK03918, chromosome segregation protein; Provisional

 Score = 38.1 bits (89), Expect = 0.004
 Identities = 28/100 (28%), Positives = 61/100 (61%), Gaps = 2/100 (2%)

Query: 177 KKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKK 236
           K++  ++  R+      +  E +EE +K EK+ ++ +E K+E ++ EK+ E  +  K+K 
Sbjct: 198 KEKELEEVLREINEISSELPELREELEKLEKEVKELEELKEEIEELEKELESLEGSKRKL 257

Query: 237 EKKKKKKEK--KKKKEEKKKEKKKKKKKKEKKKKKDEGRR 274
           E+K ++ E+  ++ K+E ++ ++K K+ KE K+K +E  +
Sbjct: 258 EEKIRELEERIEELKKEIEELEEKVKELKELKEKAEEYIK 297

Length = 880

>gnl|CDD|223496 COG0419, SbcC, ATPase involved in DNA repair [DNA replication, recombination, and repair]

 Score = 38.2 bits (89), Expect = 0.004
 Identities = 20/95 (21%), Positives = 53/95 (55%)

Query: 177 KKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKK 236
           + ER  +   ++  + ++ E E EE ++E +      E+ +E  +K K  E++ +K ++K
Sbjct: 278 ELERLLEELEEKIERLEELEREIEELEEELEGLRALLEELEELLEKLKSLEERLEKLEEK 337

Query: 237 EKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDE 271
            +K + + ++  +E+ +  K  +++ KE +++ +E
Sbjct: 338 LEKLESELEELAEEKNELAKLLEERLKELEERLEE 372

Length = 908

>gnl|CDD|149343 pfam08229, SHR3_chaperone, ER membrane protein SH3

 Score = 36.9 bits (86), Expect = 0.004
 Identities = 14/39 (35%), Positives = 21/39 (53%), Gaps = 2/39 (5%)

Query: 206 EKKKEKKKEK--KKEKKKKEKKKEKKKKKKKKKEKKKKK 242
           E K  K  E+   +E +     KE++  + +KKE KKKK
Sbjct: 158 EWKDAKLLEEFAAEEAEAAAAAKEEESAEGEKKESKKKK 196

This family of proteins are membrane localised chaperones that are required for correct plasma membrane localisation of amino acid permeases (AAPs). SH3 prevents AAPs proteins from aggregating and assists in their correct folding. In the absence of SH3, AAPs are retained in the ER. Length = 196

>gnl|CDD|220237 pfam09428, DUF2011, Fungal protein of unknown function (DUF2011)

 Score = 36.1 bits (84), Expect = 0.004
 Identities = 23/66 (34%), Positives = 44/66 (66%)

Query: 203 KKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKKKEKKKKKKK 262
           KK   K EK+  ++KEKKKK K+  KK++   +  +++ K+  +K+K  +K  +KK K++
Sbjct: 65  KKHNAKVEKELLREKEKKKKRKRPGKKRRIALRLRRERTKERAEKEKRTRKNREKKFKRR 124

Query: 263 KEKKKK 268
           +++K+K
Sbjct: 125 QKEKEK 130

This is a family of fungal proteins whose function is unknown. Length = 130

>gnl|CDD|220237 pfam09428, DUF2011, Fungal protein of unknown function (DUF2011)

 Score = 36.1 bits (84), Expect = 0.004
 Identities = 19/61 (31%), Positives = 39/61 (63%)

Query: 190 RKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKK 249
            K +KE   ++E+KK+ K+  KK+      +++  K+  +K+K+ +K ++KK K ++K+K
Sbjct: 69  AKVEKELLREKEKKKKRKRPGKKRRIALRLRRERTKERAEKEKRTRKNREKKFKRRQKEK 128

Query: 250 E 250
           E
Sbjct: 129 E 129

This is a family of fungal proteins whose function is unknown. Length = 130

>gnl|CDD|235334 PRK05035, PRK05035, electron transport complex protein RnfC; Provisional

 Score = 38.0 bits (89), Expect = 0.004
 Identities = 20/115 (17%), Positives = 44/115 (38%), Gaps = 16/115 (13%)

Query: 173 YKGGKKERRKQRRRKRK----RKR---KKEEEEKEEEKKEEKKKEKKKEKKKEKKK---- 221
           Y+  K E R   + K+K    + R   ++   E+E+  +E + K+  + +  + K     
Sbjct: 431 YRQAKAEIRAIEQEKKKAEEAKARFEARQARLEREKAAREARHKKAAEARAAKDKDAVAA 490

Query: 222 -----KEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDE 271
                K KK    +    K   +         +E +K + + ++ +K+     D 
Sbjct: 491 ALARVKAKKAAATQPIVIKAGARPDNSAVIAAREARKAQARARQAEKQAAAAADP 545

Length = 695

>gnl|CDD|233758 TIGR02169, SMC_prok_A, chromosome segregation protein SMC, primarily archaeal type

 Score = 38.5 bits (90), Expect = 0.004
 Identities = 20/104 (19%), Positives = 54/104 (51%), Gaps = 10/104 (9%)

Query: 177 KKERRKQRRR----KRKRKRKKEEEEKEEEKKEEKK------KEKKKEKKKEKKKKEKKK 226
           ++E  +   R    ++K  R   E+E  E++ +E +      KE+ K  +KE +    KK
Sbjct: 804 EEEVSRIEARLREIEQKLNRLTLEKEYLEKEIQELQEQRIDLKEQIKSIEKEIENLNGKK 863

Query: 227 EKKKKKKKKKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKD 270
           E+ +++ ++ E   +  E +    +K++++ + + ++ ++K ++
Sbjct: 864 EELEEELEELEAALRDLESRLGDLKKERDELEAQLRELERKIEE 907

SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]. Length = 1164

>gnl|CDD|223250 COG0172, SerS, Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis]

 Score = 38.0 bits (89), Expect = 0.004
 Identities = 18/83 (21%), Positives = 43/83 (51%)

Query: 184 RRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKK 243
           R + +KR     + +K  E  EE++K  ++ ++ + ++ E  KE  +  K+ ++  ++  
Sbjct: 15  REKLKKRGGDALDVDKLLELDEERRKLLRELEELQAERNELSKEIGRALKRGEDDAEELI 74

Query: 244 EKKKKKEEKKKEKKKKKKKKEKK 266
            + K+ +EK KE +    + E +
Sbjct: 75  AEVKELKEKLKELEAALDELEAE 97

Length = 429

>gnl|CDD|203489 pfam06644, ATP11, ATP11 protein

 Score = 37.3 bits (87), Expect = 0.004
 Identities = 27/88 (30%), Positives = 36/88 (40%), Gaps = 10/88 (11%)

Query: 185 RRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKE 244
           R K  +K K+   E  E  K  K  + K EKK+   KK      K+  K K  K  K  +
Sbjct: 5   RSKLLQKAKESGLEFIERLK--KALKDKIEKKEFSAKKPPTGPSKQASKFKTLKPPKPAD 62

Query: 245 KKKKKEEKKK--------EKKKKKKKKE 264
           KKK  ++  K        EK K    +E
Sbjct: 63  KKKPFDKPFKPLSSILDVEKIKDLSAEE 90

This family consists of several eukaryotic ATP11 proteins. In Saccharomyces cerevisiae, expression of functional F1-ATPase requires two proteins encoded by the ATP11 and ATP12 genes. Atp11p is a molecular chaperone of the mitochondrial matrix that participates in the biogenesis pathway to form F1, the catalytic unit of the ATP synthase. Length = 250

>gnl|CDD|221185 pfam11719, Drc1-Sld2, DNA replication and checkpoint protein

 Score = 37.9 bits (88), Expect = 0.004
 Identities = 20/85 (23%), Positives = 41/85 (48%), Gaps = 1/85 (1%)

Query: 177 KKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKK 236
           K ++R  RR K +  R K  +E    + +  + E  K  +K   +         +  + +
Sbjct: 287 KGQKRTTRRVKMRPVRAKPSDEPSLPESDIHE-EIPKLDEKSLSEFLGYMGGIDEDDEDE 345

Query: 237 EKKKKKKEKKKKKEEKKKEKKKKKK 261
           + ++ K+E +KK++ KKK +K+K  
Sbjct: 346 DDEESKEEVEKKQKVKKKPRKRKVN 370

Genome duplication is precisely regulated by cyclin-dependent kinases CDKs, which bring about the onset of S phase by activating replication origins and then prevent relicensing of origins until mitosis is completed. The optimum sequence motif for CDK phosphorylation is S/T-P-K/R-K/R, and Drc1-Sld2 is found to have at least 11 potential phosphorylation sites. Drc1 is required for DNA synthesis and S-M replication checkpoint control. Drc1 associates with Cdc2 and is phosphorylated at the onset of S phase when Cdc2 is activated. Thus Cdc2 promotes DNA replication by phosphorylating Drc1 and regulating its association with Cut5. Sld2 and Sld3 represent the minimal set of S-CDK substrates required for DNA replication. Length = 397

>gnl|CDD|222812 PHA00727, PHA00727, hypothetical protein

 Score = 37.5 bits (87), Expect = 0.004
 Identities = 26/71 (36%), Positives = 44/71 (61%), Gaps = 2/71 (2%)

Query: 200 EEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKKKEKKKK 259
           EEE ++ +  E+ K+K +E +K+    + K  K+  K  +K++ E KK++ E+ K +  K
Sbjct: 11  EEELRKAQSLEELKQKYEEAQKQ--IADGKTLKRLYKVYEKREFELKKQQFEQLKAELSK 68

Query: 260 KKKKEKKKKKD 270
           KKKK KK+K D
Sbjct: 69  KKKKFKKEKVD 79

Length = 278

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	275
KOG3913|consensus	356		100.0
smart00097	305	WNT1 found in Wnt-1.	100.0
PF00110	310	wnt: wnt family; InterPro: IPR005817 Wnt proteins	100.0
KOG4364|consensus	811		92.63
KOG2572|consensus	498		81.93

>KOG3913|consensus

Probab=100.00  E-value=2.4e-52  Score=396.03  Aligned_cols=145  Identities=43%  Similarity=0.786  Sum_probs=134.6

Q ss_pred             hhhhccCCCCCCHHHHHHhhhhhhHHHHHHHHHHHHHHHHHHhhccCcccCCCCCCCCCCCCCCCCCCCCCCCCCCcccc
Q psy17095         33 SARVCSRVPGLSFGQVRQCSLFADHMASVGRGAAESIAECQHQFRHHRWNCSSGGPGAGGGGGGKSESTTAPSVLPPTLH  112 (275)
Q Consensus        33 ~~~iC~~l~GLs~rQ~~LCr~~p~lm~sV~~GaklAI~ECQ~QFr~~RWNCSs~~~~~~~~~~~k~~~~~~~~~fg~iL~  112 (275)
                      ...+|..++||+++|+++|++||++|++|++|+++||+|||||||++|||||+.               +..++|+++|.
T Consensus        44 ~~~~C~~l~gL~~~Q~~~Cr~~p~~~~sv~~G~~~~i~ECq~QFr~~RWNCs~~---------------~~~~~~g~~l~  108 (356)
T KOG3913|consen   44 AKPLCDNLPGLSPRQRRLCRRNPDVMPSVAEGAREGIQECQFQFRFRRWNCSTL---------------DQLPVFGPLLS  108 (356)
T ss_pred             cccchhhccccCHHHHHHHHhCcchHHHHHHHHHHHHHHHHHHHHhhccCCCCC---------------ccccccchhhc
Confidence            345899999999999999999999999999999999999999999999999988               56789999999


Q ss_pred             cCCchhHHHHHHHHHHHHHHHHhhhcCCCCCCccCcCCCCCCCCCCCcccCCCCcchhhhhhhhhhhhhhhHHhHHHHhh
Q psy17095        113 IGSREAAFTHAIATAGVVYAVARSCKDGSLPSCGCSRTARPKDLKREWLWGGCGDNLEYGYKGGKKERRKQRRRKRKRKR  192 (275)
Q Consensus       113 ~GTREtAFV~AItSAGVv~aVTRACS~G~L~~CgCd~~~~~~~~~~~w~WGGCSDNI~fG~~fSr~FlDa~er~~~~r~~  192 (275)
                      .|+||+||||||+||||+|+|||||+.|.|..||||....+...+++|+||||||||.||+.||+.|||+++++++=|..
T Consensus       109 ~g~REsAFv~AIssAgV~havtraCs~G~l~~CgCd~~~~~~~~~~~w~WGGCsDnv~fG~~fsr~FlD~re~~~d~r~l  188 (356)
T KOG3913|consen  109 RGTRETAFVYAISSAGVAHAVTRACSQGNLESCGCDPSPNGKSGPEGWEWGGCSDNVDFGIRFSRKFLDAREKRKDARAL  188 (356)
T ss_pred             ccchHHHHHHHHHHhHHHHHHHHHhcCCCCCCcCCCCCCCCCCCCCCccccCCCCchHHHHHHHHHhccccccccCHHHH
Confidence            99999999999999999999999999999999999987766556677999999999999999999999999887655543

>smart00097 WNT1 found in Wnt-1

Probab=100.00  E-value=1.8e-47  Score=357.19  Aligned_cols=132  Identities=46%  Similarity=0.833  Sum_probs=121.6

Q ss_pred             CCCCCHHHHHHhhhhhhHHHHHHHHHHHHHHHHHHhhccCcccCCCCCCCCCCCCCCCCCCCCCCCCCCcccccCCchhH
Q psy17095         40 VPGLSFGQVRQCSLFADHMASVGRGAAESIAECQHQFRHHRWNCSSGGPGAGGGGGGKSESTTAPSVLPPTLHIGSREAA  119 (275)
Q Consensus        40 l~GLs~rQ~~LCr~~p~lm~sV~~GaklAI~ECQ~QFr~~RWNCSs~~~~~~~~~~~k~~~~~~~~~fg~iL~~GTREtA  119 (275)
                      ++||++.|+++|+.+|++|++|++|+++||+|||+||+++|||||++               +..++|+++|..||||+|
T Consensus         2 ~~~l~~~Q~~~C~~~~~~~~~v~~g~~~ai~ECq~QF~~~rWNCs~~---------------~~~~~~~~~l~~~trEtA   66 (305)
T smart00097        2 LPGLSRRQRRLCRANPDVMISVAEGAQEGIEECQHQFRFRRWNCSTL---------------DNASVFGKVLRQGTRETA   66 (305)
T ss_pred             CcccCHHHHHHHHhCHHHHHHHHHHHHHHHHHHHHHhCCCCCCCCCC---------------cCCcccccccccccchHH
Confidence            67999999999999999999999999999999999999999999987               445789999999999999


Q ss_pred             HHHHHHHHHHHHHHHhhhcCCCCCCccCcCCCCCCCCCCCcccCCCCcchhhhhhhhhhhhhhhHHh
Q psy17095        120 FTHAIATAGVVYAVARSCKDGSLPSCGCSRTARPKDLKREWLWGGCGDNLEYGYKGGKKERRKQRRR  186 (275)
Q Consensus       120 FV~AItSAGVv~aVTRACS~G~L~~CgCd~~~~~~~~~~~w~WGGCSDNI~fG~~fSr~FlDa~er~  186 (275)
                      |||||+||||+|+||+||+.|.|.+||||...++.....+|+||||||||.||+.||+.|||+.+..
T Consensus        67 fv~Ai~sAgv~~~itraCs~G~l~~C~Cd~~~~~~~~~~~w~WgGCsdnv~~G~~~s~~FlD~~~~~  133 (305)
T smart00097       67 FVYAISSAGVAHAVTRACSEGELDSCGCDYRKRGRAGGRGWKWGGCSDNIDFGIRFSREFVDARERG  133 (305)
T ss_pred             HHHHHHHHHHHHHHHHHHhCCCCCCCCCCCCCCCCCCCCCcccCCCCccHHHHHHHHHHHHhccccc
Confidence            9999999999999999999999999999987654333357999999999999999999999987653

>PF00110 wnt: wnt family; InterPro: IPR005817 Wnt proteins constitute a large family of secreted molecules that are involved in intercellular signalling during development

Probab=100.00  E-value=5.7e-48  Score=360.30  Aligned_cols=137  Identities=42%  Similarity=0.855  Sum_probs=87.5

Q ss_pred             hccCCCCCCHHHHHHhhhhhhHHHHHHHHHHHHHHHHHHhhccCcccCCCCCCCCCCCCCCCCCCCCCCCCCCc-ccccC
Q psy17095         36 VCSRVPGLSFGQVRQCSLFADHMASVGRGAAESIAECQHQFRHHRWNCSSGGPGAGGGGGGKSESTTAPSVLPP-TLHIG  114 (275)
Q Consensus        36 iC~~l~GLs~rQ~~LCr~~p~lm~sV~~GaklAI~ECQ~QFr~~RWNCSs~~~~~~~~~~~k~~~~~~~~~fg~-iL~~G  114 (275)
                      ||..++||+++|++||++||++|++|++|+++||+|||+||+++|||||++               +..++|++ +|..|
T Consensus         1 iC~~~~gL~~~Q~~~C~~~p~~m~~i~~G~~~ai~ECq~QF~~~RWNCs~~---------------~~~~~f~~~~~~~g   65 (310)
T PF00110_consen    1 ICDKIPGLTKRQRRLCRRNPDLMPSIAEGAKMAIEECQHQFRNRRWNCSTV---------------DNNPVFGPPILKKG   65 (310)
T ss_dssp             ------------------HHHHHHHHHHHHHHHHHHHHHHTTTSSS--------------------T-THHHH-TT--S-
T ss_pred             CCcccccccccccccccCCHHHHHHHHHHHHHHHHHHHHHHhccCCCCCCC---------------cccccccccccccC
Confidence            799999999999999999999999999999999999999999999999988               44467877 99999


Q ss_pred             CchhHHHHHHHHHHHHHHHHhhhcCCCCCCccCcCCCCCCCCCCCcccCCCCcchhhhhhhhhhhhhhhHHhH
Q psy17095        115 SREAAFTHAIATAGVVYAVARSCKDGSLPSCGCSRTARPKDLKREWLWGGCGDNLEYGYKGGKKERRKQRRRK  187 (275)
Q Consensus       115 TREtAFV~AItSAGVv~aVTRACS~G~L~~CgCd~~~~~~~~~~~w~WGGCSDNI~fG~~fSr~FlDa~er~~  187 (275)
                      |||+||||||+||||+|+||+||+.|.|..|+|+....+...+..|.||||+|||.||+.||+.|||+.+...
T Consensus        66 trE~Afv~Ai~sAgv~~~itraCs~G~l~~C~C~~~~~~~~~~~~~~wggCsdni~~G~~~sr~Fld~~~~~~  138 (310)
T PF00110_consen   66 TRETAFVYAISSAGVAHSITRACSRGKLKSCGCDRNPRGSSSQNTWQWGGCSDNIKFGIKFSRRFLDAREKGS  138 (310)
T ss_dssp             -HHHHHHHHHHHHHHHHHHHHHHHTTT-SS-----TTTTSEEETTEEE-S----HHHHHHHHHHHHHHH--SS
T ss_pred             cccceeeEhhhcCchHHHHHHHhhcccCCcCCCcccccccccccccccCCcccccccchHHHHHHHHhhhhhh
Confidence            9999999999999999999999999999999999888764455569999999999999999999999998433

The name derives from the first 2 members of the family to be discovered: int-1 (mouse) and wingless (Drosophila) []. It is now recognised that Wnt signalling controls many cell fate decisions in a variety of different organisms, including mammals []. Wnt signalling has been implicated in tumourigenesis, early mesodermal patterning of the embryo, morphogenesis of the brain and kidneys, regulation of mammary gland proliferation and Alzheimer's disease [, ]. Wnt-mediated signalling is believed to proceed initially through binding to cell surface receptors of the frizzled family; the signal is subsequently transduced through several cytoplasmic components to B-catenin, which enters the nucleus and activates the transcription of several genes important in development []. Several non-canonical Wnt signalling pathways have also been elucidated that act independently of B-catenin. Canonical and noncanonical Wnt signaling branches are highly interconnected, and cross-regulate each other []. Members of the Wnt gene family are defined by their sequence similarity to mouse Wnt-1 and Wingless in Drosophila. They encode proteins of ~350-400 residues in length, with orthologues identified in several, mostly vertebrate, species. Very little is known about the structure of Wnts as they are notoriously insoluble, but they share the following features characteristics of secretory proteins: a signal peptide, several potential N-glycosylation sites and 22 conserved cysteines [] that are probably involved in disulphide bonds. The Wnt proteins seem to adhere to the plasma membrane of the secreting cells and are therefore likely to signal over only few cell diameters. Fifteen major Wnt gene families have been identified in vertebrates, with multiple subtypes within some classes. In humans, 19 Wnt proteins have been identified that share 27% to 83% amino-acid sequence identity and a conserved pattern of 23 or 24 cysteine residues []. Wnt genes are highly conserved between vertebrate species sharing overall sequence identity and gene structure, and are slightly less conserved between vertebrates and invertebrates.; GO: 0005102 receptor binding, 0007275 multicellular organismal development, 0016055 Wnt receptor signaling pathway, 0005576 extracellular region; PDB: 4F0A_B.

>KOG4364|consensus

Probab=92.63  E-value=1.7  Score=46.09  Aligned_cols=20  Identities=20%  Similarity=0.014  Sum_probs=11.1

Q ss_pred             hhhhHHHHHHHHHHHHHHHH
Q psy17095         53 LFADHMASVGRGAAESIAEC   72 (275)
Q Consensus        53 ~~p~lm~sV~~GaklAI~EC   72 (275)
                      ..+.+|..+..++..-+..|
T Consensus       155 ~~~~~~~~s~~vVl~~~~~~  174 (811)
T KOG4364|consen  155 RDLKIMPSSVRVVLKLRRTC  174 (811)
T ss_pred             cCcccCCCcchhHHhhhhcc
Confidence            34556666666665444444

>KOG2572|consensus

Probab=81.93  E-value=0.52  Score=47.44  Aligned_cols=22  Identities=18%  Similarity=0.181  Sum_probs=12.1

Q ss_pred             CcchhhhccCCCCCCHHHHHHh
Q psy17095         30 LEDSARVCSRVPGLSFGQVRQC   51 (275)
Q Consensus        30 ~~~~~~iC~~l~GLs~rQ~~LC   51 (275)
                      +++...+|+++--|...-.+||
T Consensus       249 l~nI~~l~dqVle~aeyR~qL~  270 (498)
T KOG2572|consen  249 LLNIKELCDQVLELAEYRDQLI  270 (498)
T ss_pred             HHhHHHHHHHHHHHHHHHHHHH
Confidence            4444557777655555444444

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	275
4f0a_B	316	Crystal Structure Of Xwnt8 In Complex With The Cyst		2e-16

>pdb|4F0A|B Chain B, Crystal Structure Of Xwnt8 In Complex With The Cysteine-Rich Domain Of Frizzled 8 Length = 316

Iteration: 1
 Score = 82.4 bits (202), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 42/121 (34%), Positives = 60/121 (49%), Gaps = 15/121 (12%)
Query: 54  FADHMASVGRGAAESIAECQHQFRHHRWNCSSXXXXXXXXXXXKSESTTAPSVLPPTLHI 113
           +  + ASV  GA   I EC++QF   RWNC                 +T        L  
Sbjct: 15  YLTYSASVAVGAQNGIEECKYQFAWERWNCPE---------------STLQLATHNGLRS 59
Query: 114 GSREAAFTHAIATAGVVYAVARSCKDGSLPSCGCSRTARPKDLKREWLWGGCGDNLEYGY 173
            +RE +F HAI++AGV+Y + R+C  G   +CGC  +   +   R W+WGGC DN E+G 
Sbjct: 60  ATRETSFVHAISSAGVMYTLTRNCSMGDFDNCGCDDSRNGRIGGRGWVWGGCSDNAEFGE 119
Query: 174 K 174
           +
Sbjct: 120 R 120

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	275
4f0a_B	316	Protein WNT-8, XWNT-8; WNT signaling, ligand-recep	3e-31
1g8x_A	1010	Myosin II heavy chain fused to alpha-actinin 3; mo	1e-13
1g8x_A	1010	Myosin II heavy chain fused to alpha-actinin 3; mo	4e-13
1g8x_A	1010	Myosin II heavy chain fused to alpha-actinin 3; mo	9e-13
1g8x_A	1010	Myosin II heavy chain fused to alpha-actinin 3; mo	5e-12
1g8x_A	1010	Myosin II heavy chain fused to alpha-actinin 3; mo	8e-12
1g8x_A	1010	Myosin II heavy chain fused to alpha-actinin 3; mo	4e-10
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	7e-12
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	1e-11
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	1e-11
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	5e-11
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	9e-11
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	2e-10
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	2e-10
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	3e-10
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	6e-10
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	1e-09
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	1e-09
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	2e-09
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	3e-09
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	3e-09
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	3e-09
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	7e-09
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	2e-08
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	2e-08
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	2e-07
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	3e-07
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	6e-07
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	1e-06
3lvg_D	190	LCB, clathrin light chain B; SELF assembly, coated	1e-09
3lvg_D	190	LCB, clathrin light chain B; SELF assembly, coated	1e-08
3lvg_D	190	LCB, clathrin light chain B; SELF assembly, coated	3e-08
3lvg_D	190	LCB, clathrin light chain B; SELF assembly, coated	5e-07
3lvg_D	190	LCB, clathrin light chain B; SELF assembly, coated	6e-07
3lvg_D	190	LCB, clathrin light chain B; SELF assembly, coated	4e-04
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	1e-09
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	4e-09
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	4e-09
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	6e-09
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	6e-09
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	6e-09
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	1e-08
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	1e-08
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	2e-08
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	3e-08
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	8e-08
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	2e-07
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	2e-07
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	6e-07
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	6e-07
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	9e-07
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	7e-06
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	1e-05
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	2e-05
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	4e-05
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	1e-04
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	2e-04
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	2e-04
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	5e-04
4ady_A	963	RPN2, 26S proteasome regulatory subunit RPN2; prot	7e-09
4ady_A	963	RPN2, 26S proteasome regulatory subunit RPN2; prot	3e-08
4ady_A	963	RPN2, 26S proteasome regulatory subunit RPN2; prot	4e-08
4ady_A	963	RPN2, 26S proteasome regulatory subunit RPN2; prot	2e-07
4ady_A	963	RPN2, 26S proteasome regulatory subunit RPN2; prot	5e-07
4ady_A	963	RPN2, 26S proteasome regulatory subunit RPN2; prot	2e-06
4ady_A	963	RPN2, 26S proteasome regulatory subunit RPN2; prot	1e-05
4ady_A	963	RPN2, 26S proteasome regulatory subunit RPN2; prot	1e-05
4ady_A	963	RPN2, 26S proteasome regulatory subunit RPN2; prot	2e-04
1b6a_A	478	Methionine aminopeptidase; angiogenesis inhibitor;	8e-08
1b6a_A	478	Methionine aminopeptidase; angiogenesis inhibitor;	1e-06
1b6a_A	478	Methionine aminopeptidase; angiogenesis inhibitor;	2e-06
1b6a_A	478	Methionine aminopeptidase; angiogenesis inhibitor;	2e-06
1b6a_A	478	Methionine aminopeptidase; angiogenesis inhibitor;	3e-06
1b6a_A	478	Methionine aminopeptidase; angiogenesis inhibitor;	2e-04
1f5n_A	592	Interferon-induced guanylate-binding protein 1; GB	2e-07
1f5n_A	592	Interferon-induced guanylate-binding protein 1; GB	2e-06
1f5n_A	592	Interferon-induced guanylate-binding protein 1; GB	3e-04
2zkr_c	421	60S ribosomal protein L4; protein-RNA complex, 60S	1e-06
2zkr_c	421	60S ribosomal protein L4; protein-RNA complex, 60S	9e-06
2zkr_c	421	60S ribosomal protein L4; protein-RNA complex, 60S	2e-05
2zkr_c	421	60S ribosomal protein L4; protein-RNA complex, 60S	2e-05
2zkr_c	421	60S ribosomal protein L4; protein-RNA complex, 60S	3e-05
2zkr_c	421	60S ribosomal protein L4; protein-RNA complex, 60S	3e-05
2zkr_c	421	60S ribosomal protein L4; protein-RNA complex, 60S	5e-04
2qag_B	427	Septin-6, protein NEDD5; cell cycle, cell division	5e-06
2qag_B	427	Septin-6, protein NEDD5; cell cycle, cell division	5e-06
2qag_B	427	Septin-6, protein NEDD5; cell cycle, cell division	7e-06
2qag_B	427	Septin-6, protein NEDD5; cell cycle, cell division	9e-06
2qag_B	427	Septin-6, protein NEDD5; cell cycle, cell division	1e-05
2qag_B	427	Septin-6, protein NEDD5; cell cycle, cell division	2e-05
2qag_B	427	Septin-6, protein NEDD5; cell cycle, cell division	5e-04
3kio_B	332	Ribonuclease H2 subunit B; aicardi-goutieres syndr	9e-06
3kio_B	332	Ribonuclease H2 subunit B; aicardi-goutieres syndr	2e-05
3kio_B	332	Ribonuclease H2 subunit B; aicardi-goutieres syndr	9e-05
3kio_B	332	Ribonuclease H2 subunit B; aicardi-goutieres syndr	2e-04
3kio_B	332	Ribonuclease H2 subunit B; aicardi-goutieres syndr	7e-04
2qag_C	418	Septin-7; cell cycle, cell division, GTP-binding,	1e-05
2qag_C	418	Septin-7; cell cycle, cell division, GTP-binding,	3e-04
3lvh_D	205	LCB, clathrin light chain B; SELF assembly, coated	1e-05
3lvh_D	205	LCB, clathrin light chain B; SELF assembly, coated	3e-05
3lvh_D	205	LCB, clathrin light chain B; SELF assembly, coated	8e-05
3lvh_D	205	LCB, clathrin light chain B; SELF assembly, coated	3e-04
3lvh_D	205	LCB, clathrin light chain B; SELF assembly, coated	4e-04
2zjr_S	237	50S ribosomal protein L25; ribosome, large ribosom	2e-05
2zjr_S	237	50S ribosomal protein L25; ribosome, large ribosom	2e-05
2zjr_S	237	50S ribosomal protein L25; ribosome, large ribosom	3e-05
2zjr_S	237	50S ribosomal protein L25; ribosome, large ribosom	3e-05
2zjr_S	237	50S ribosomal protein L25; ribosome, large ribosom	6e-05
2zjr_S	237	50S ribosomal protein L25; ribosome, large ribosom	8e-05
2zjr_S	237	50S ribosomal protein L25; ribosome, large ribosom	3e-04
1qy5_A	269	Endoplasmin; GRP94, NECA, HSP90, chaperone; HET: N	2e-05
1qy5_A	269	Endoplasmin; GRP94, NECA, HSP90, chaperone; HET: N	2e-05
1qy5_A	269	Endoplasmin; GRP94, NECA, HSP90, chaperone; HET: N	5e-05
1qy5_A	269	Endoplasmin; GRP94, NECA, HSP90, chaperone; HET: N	1e-04
1qy5_A	269	Endoplasmin; GRP94, NECA, HSP90, chaperone; HET: N	2e-04
1qy5_A	269	Endoplasmin; GRP94, NECA, HSP90, chaperone; HET: N	2e-04
1qy5_A	269	Endoplasmin; GRP94, NECA, HSP90, chaperone; HET: N	2e-04
1qy5_A	269	Endoplasmin; GRP94, NECA, HSP90, chaperone; HET: N	4e-04
1qy5_A	269	Endoplasmin; GRP94, NECA, HSP90, chaperone; HET: N	4e-04
1qy5_A	269	Endoplasmin; GRP94, NECA, HSP90, chaperone; HET: N	5e-04
1qy5_A	269	Endoplasmin; GRP94, NECA, HSP90, chaperone; HET: N	6e-04
1a31_A	591	Protein (topoisomerase I); topoisomerase I/DNA, DN	3e-05
1a31_A	591	Protein (topoisomerase I); topoisomerase I/DNA, DN	5e-05
1a31_A	591	Protein (topoisomerase I); topoisomerase I/DNA, DN	1e-04
1a31_A	591	Protein (topoisomerase I); topoisomerase I/DNA, DN	2e-04
1a31_A	591	Protein (topoisomerase I); topoisomerase I/DNA, DN	3e-04
1a31_A	591	Protein (topoisomerase I); topoisomerase I/DNA, DN	4e-04
2p4f_A	299	Similar to SP|P32453 saccharomyces cerevisiae YNL	1e-04
2y9y_A	374	Imitation switch protein 1 (DEL_ATPase); transcrip	2e-04
2y9y_A	374	Imitation switch protein 1 (DEL_ATPase); transcrip	6e-04
2efk_A	301	CDC42-interacting protein 4; EFC domain, structura	2e-04
2efk_A	301	CDC42-interacting protein 4; EFC domain, structura	3e-04
3auy_A	371	DNA double-strand break repair RAD50 ATPase; DNA r	3e-04
3auy_A	371	DNA double-strand break repair RAD50 ATPase; DNA r	3e-04
3vkg_A	3245	Dynein heavy chain, cytoplasmic; AAA+ protein, mol	4e-04
1kxf_A	264	Sindbis virus capsid protein; chymotrypsin-like se	4e-04
2efl_A	305	Formin-binding protein 1; EFC domain, structural g	5e-04
4a17_C	410	RPL4, ribosomal protein L3; eukaryotic ribosome, r	5e-04
2v0o_A	276	FCHO2, FCH domain only protein 2; lipid-binding pr	5e-04
3izc_e	244	60S ribosomal protein RPL7 (L30P); eukaryotic ribo	6e-04
2ycu_A	995	Non muscle myosin 2C, alpha-actinin; motor protein	8e-04

>4f0a_B Protein WNT-8, XWNT-8; WNT signaling, ligand-receptor complex, frizzled, fatty acylation, glycosylation, signaling protein; HET: NAG BMA MAN FUC PAM; 3.25A {Xenopus laevis} Length = 316

 Score =  117 bits (293), Expect = 3e-31
 Identities = 44/151 (29%), Positives = 66/151 (43%), Gaps = 15/151 (9%)

Query: 43  LSFGQVRQCSLFADHMASVGRGAAESIAECQHQFRHHRWNCSSGGPGAGGGGGGKSESTT 102
           ++   +     +  + ASV  GA   I EC++QF   RWNC                 +T
Sbjct: 4   VNNFLMTGPKAYLTYSASVAVGAQNGIEECKYQFAWERWNCPE---------------ST 48

Query: 103 APSVLPPTLHIGSREAAFTHAIATAGVVYAVARSCKDGSLPSCGCSRTARPKDLKREWLW 162
                   L   +RE +F HAI++AGV+Y + R+C  G   +CGC  +   +   R W+W
Sbjct: 49  LQLATHNGLRSATRETSFVHAISSAGVMYTLTRNCSMGDFDNCGCDDSRNGRIGGRGWVW 108

Query: 163 GGCGDNLEYGYKGGKKERRKQRRRKRKRKRK 193
           GGC DN E+G +  K         +  R   
Sbjct: 109 GGCSDNAEFGERISKLFVDGLETGQDARALM 139

>1g8x_A Myosin II heavy chain fused to alpha-actinin 3; motor, lever ARM, protein engineering, structural protein; HET: ADP; 2.80A {Dictyostelium discoideum} SCOP: k.1.1.1 Length = 1010

 Score = 69.7 bits (171), Expect = 1e-13
 Identities = 11/95 (11%), Positives = 28/95 (29%)

Query: 177 KKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKK 236
           K E+      + + KR+K+     ++     KK +     K       +        + K
Sbjct: 865 KAEQEHAEALRIELKRQKKIAVLLQKYNRILKKLENWATTKSVYLGSNETGDSITAVQAK 924

Query: 237 EKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDE 271
            K  +  + + +  E +          +  +    
Sbjct: 925 LKNLEAFDGECQSLEGQSNSDLLSILAQLTELNYN 959

>1g8x_A Myosin II heavy chain fused to alpha-actinin 3; motor, lever ARM, protein engineering, structural protein; HET: ADP; 2.80A {Dictyostelium discoideum} SCOP: k.1.1.1 Length = 1010

 Score = 68.2 bits (167), Expect = 4e-13
 Identities = 10/93 (10%), Positives = 28/93 (30%)

Query: 177 KKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKK 236
           K++++     ++  +  K+ E     K       +  +     + K K  E    + +  
Sbjct: 879 KRQKKIAVLLQKYNRILKKLENWATTKSVYLGSNETGDSITAVQAKLKNLEAFDGECQSL 938

Query: 237 EKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKK 269
           E +          +  +       +  E+K   
Sbjct: 939 EGQSNSDLLSILAQLTELNYNGVPELTERKDTF 971

>1g8x_A Myosin II heavy chain fused to alpha-actinin 3; motor, lever ARM, protein engineering, structural protein; HET: ADP; 2.80A {Dictyostelium discoideum} SCOP: k.1.1.1 Length = 1010

 Score = 67.0 bits (164), Expect = 9e-13
 Identities = 8/93 (8%), Positives = 23/93 (24%)

Query: 177 KKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKK 236
                           + + +  E    E +  E +          +  +       +  
Sbjct: 906 SVYLGSNETGDSITAVQAKLKNLEAFDGECQSLEGQSNSDLLSILAQLTELNYNGVPELT 965

Query: 237 EKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKK 269
           E+K     ++    +   E  K     E ++ +
Sbjct: 966 ERKDTFFAQQWTGVKSSAETYKNTLLAELERLQ 998

>1g8x_A Myosin II heavy chain fused to alpha-actinin 3; motor, lever ARM, protein engineering, structural protein; HET: ADP; 2.80A {Dictyostelium discoideum} SCOP: k.1.1.1 Length = 1010

 Score = 64.7 bits (158), Expect = 5e-12
 Identities = 5/96 (5%), Positives = 24/96 (25%), Gaps = 1/96 (1%)

Query: 177 KKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKK-EKKKEKKKKEKKKEKKKKKKKK 235
               +       +        + + +  E    E +  E +          +  +     
Sbjct: 901 WATTKSVYLGSNETGDSITAVQAKLKNLEAFDGECQSLEGQSNSDLLSILAQLTELNYNG 960

Query: 236 KEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDE 271
             +  ++K+    ++    +   +  K     + + 
Sbjct: 961 VPELTERKDTFFAQQWTGVKSSAETYKNTLLAELER 996

>1g8x_A Myosin II heavy chain fused to alpha-actinin 3; motor, lever ARM, protein engineering, structural protein; HET: ADP; 2.80A {Dictyostelium discoideum} SCOP: k.1.1.1 Length = 1010

 Score = 64.3 bits (157), Expect = 8e-12
 Identities = 10/93 (10%), Positives = 28/93 (30%)

Query: 176  GKKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKK 235
            G  E        + + +  E  + E +  E +          +  +       +  ++K 
Sbjct: 910  GSNETGDSITAVQAKLKNLEAFDGECQSLEGQSNSDLLSILAQLTELNYNGVPELTERKD 969

Query: 236  KEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKK 268
                ++    K   E  K     + ++ +K + 
Sbjct: 970  TFFAQQWTGVKSSAETYKNTLLAELERLQKIED 1002

>1g8x_A Myosin II heavy chain fused to alpha-actinin 3; motor, lever ARM, protein engineering, structural protein; HET: ADP; 2.80A {Dictyostelium discoideum} SCOP: k.1.1.1 Length = 1010

 Score = 59.3 bits (144), Expect = 4e-10
 Identities = 6/89 (6%), Positives = 23/89 (25%)

Query: 177  KKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKK 236
             + + K         +  E +   +      +  +       +  + K     ++    K
Sbjct: 921  VQAKLKNLEAFDGECQSLEGQSNSDLLSILAQLTELNYNGVPELTERKDTFFAQQWTGVK 980

Query: 237  EKKKKKKEKKKKKEEKKKEKKKKKKKKEK 265
               +  K     + E+ ++ +        
Sbjct: 981  SSAETYKNTLLAELERLQKIEDLHHHHHH 1009

>2dfs_A Myosin-5A; myosin-V, inhibited state, cryoelectron tomograp contractIle protein-transport protein complex; 24.00A {Gallus gallus} Length = 1080

 Score = 64.4 bits (157), Expect = 7e-12
 Identities = 17/100 (17%), Positives = 43/100 (43%), Gaps = 1/100 (1%)

Query: 177 KKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKK 236
           K     Q   +R   +++ ++ K E +  E+ K+     + +  + ++K +++ K+ K  
Sbjct: 888 KAIVYLQCCYRRMMAKRELKKLKIEARSVERYKKLHIGLENKIMQLQRKIDEQNKEYKSL 947

Query: 237 EKKKKKKEKKKKKEEKK-KEKKKKKKKKEKKKKKDEGRRR 275
            +K    E     E +K +   ++ +  E++ K    R  
Sbjct: 948 LEKMNNLEITYSTETEKLRSDVERLRMSEEEAKNATNRVL 987

>2dfs_A Myosin-5A; myosin-V, inhibited state, cryoelectron tomograp contractIle protein-transport protein complex; 24.00A {Gallus gallus} Length = 1080

 Score = 63.6 bits (155), Expect = 1e-11
 Identities = 17/98 (17%), Positives = 38/98 (38%), Gaps = 3/98 (3%)

Query: 177 KKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKK---EKKKEKKKKEKKKEKKKKKK 233
           +   R+   ++  +K K E    E  KK     E K    ++K +++ KE K   +K   
Sbjct: 894 QCCYRRMMAKRELKKLKIEARSVERYKKLHIGLENKIMQLQRKIDEQNKEYKSLLEKMNN 953

Query: 234 KKKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDE 271
            +     + ++ +   E  +  +++ K    +     E
Sbjct: 954 LEITYSTETEKLRSDVERLRMSEEEAKNATNRVLSLQE 991

>2dfs_A Myosin-5A; myosin-V, inhibited state, cryoelectron tomograp contractIle protein-transport protein complex; 24.00A {Gallus gallus} Length = 1080

 Score = 63.6 bits (155), Expect = 1e-11
 Identities = 14/100 (14%), Positives = 44/100 (44%)

Query: 176  GKKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKK 235
             + ++       +  + +++ +E+ +E K   +K    E     + ++ + + ++ +  +
Sbjct: 917  ERYKKLHIGLENKIMQLQRKIDEQNKEYKSLLEKMNNLEITYSTETEKLRSDVERLRMSE 976

Query: 236  KEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDEGRRR 275
            +E K         +EE  K +K+  + + +KK  +E   +
Sbjct: 977  EEAKNATNRVLSLQEEIAKLRKELHQTQTEKKTIEEWADK 1016

>2dfs_A Myosin-5A; myosin-V, inhibited state, cryoelectron tomograp contractIle protein-transport protein complex; 24.00A {Gallus gallus} Length = 1080

 Score = 62.0 bits (151), Expect = 5e-11
 Identities = 19/95 (20%), Positives = 40/95 (42%)

Query: 177  KKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKK 236
              E       ++ R   +     EEE K    +    +++  K +KE  + + +KK  ++
Sbjct: 953  NLEITYSTETEKLRSDVERLRMSEEEAKNATNRVLSLQEEIAKLRKELHQTQTEKKTIEE 1012

Query: 237  EKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDE 271
               K K E ++   E K++    K +KE+  ++  
Sbjct: 1013 WADKYKHETEQLVSELKEQNTLLKTEKEELNRRIH 1047

>2dfs_A Myosin-5A; myosin-V, inhibited state, cryoelectron tomograp contractIle protein-transport protein complex; 24.00A {Gallus gallus} Length = 1080

 Score = 61.3 bits (149), Expect = 9e-11
 Identities = 18/95 (18%), Positives = 42/95 (44%)

Query: 177  KKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKK 236
             K  + QR+   + K  K   EK    +     E +K +   ++ +  ++E K    +  
Sbjct: 928  NKIMQLQRKIDEQNKEYKSLLEKMNNLEITYSTETEKLRSDVERLRMSEEEAKNATNRVL 987

Query: 237  EKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDE 271
              +++  + +K+  + + EKK  ++  +K K + E
Sbjct: 988  SLQEEIAKLRKELHQTQTEKKTIEEWADKYKHETE 1022

>2dfs_A Myosin-5A; myosin-V, inhibited state, cryoelectron tomograp contractIle protein-transport protein complex; 24.00A {Gallus gallus} Length = 1080

 Score = 60.1 bits (146), Expect = 2e-10
 Identities = 19/100 (19%), Positives = 39/100 (39%), Gaps = 5/100 (5%)

Query: 177  KKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEK-----KKEKKKK 231
            KK       +  + +RK +E+ KE +   EK    +     E +K        +  +++ 
Sbjct: 920  KKLHIGLENKIMQLQRKIDEQNKEYKSLLEKMNNLEITYSTETEKLRSDVERLRMSEEEA 979

Query: 232  KKKKKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDE 271
            K         ++E  K ++E  + + +KK  +E   K   
Sbjct: 980  KNATNRVLSLQEEIAKLRKELHQTQTEKKTIEEWADKYKH 1019

>2dfs_A Myosin-5A; myosin-V, inhibited state, cryoelectron tomograp contractIle protein-transport protein complex; 24.00A {Gallus gallus} Length = 1080

 Score = 60.1 bits (146), Expect = 2e-10
 Identities = 19/93 (20%), Positives = 41/93 (44%)

Query: 177 KKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKK 236
           K+E +K +   R  +R K+     E K  + +++  ++ K+ K   EK    +     + 
Sbjct: 903 KRELKKLKIEARSVERYKKLHIGLENKIMQLQRKIDEQNKEYKSLLEKMNNLEITYSTET 962

Query: 237 EKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKK 269
           EK +   E+ +  EE+ K    +    +++  K
Sbjct: 963 EKLRSDVERLRMSEEEAKNATNRVLSLQEEIAK 995

>2dfs_A Myosin-5A; myosin-V, inhibited state, cryoelectron tomograp contractIle protein-transport protein complex; 24.00A {Gallus gallus} Length = 1080

 Score = 59.7 bits (145), Expect = 3e-10
 Identities = 16/93 (17%), Positives = 39/93 (41%)

Query: 179  ERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEK 238
            +R+   + K  +   ++    E     E +K +   ++    ++E K    +    ++E 
Sbjct: 934  QRKIDEQNKEYKSLLEKMNNLEITYSTETEKLRSDVERLRMSEEEAKNATNRVLSLQEEI 993

Query: 239  KKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDE 271
             K +KE  + + EKK  ++   K K + ++   
Sbjct: 994  AKLRKELHQTQTEKKTIEEWADKYKHETEQLVS 1026

>2dfs_A Myosin-5A; myosin-V, inhibited state, cryoelectron tomograp contractIle protein-transport protein complex; 24.00A {Gallus gallus} Length = 1080

 Score = 58.6 bits (142), Expect = 6e-10
 Identities = 18/108 (16%), Positives = 48/108 (44%)

Query: 168  NLEYGYKGGKKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKE 227
            NLE  Y    ++ R    R R  + + +         +E+  + +KE  + + +K+  +E
Sbjct: 953  NLEITYSTETEKLRSDVERLRMSEEEAKNATNRVLSLQEEIAKLRKELHQTQTEKKTIEE 1012

Query: 228  KKKKKKKKKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDEGRRR 275
               K K + E+   + +++    + +KE+  ++   + K+  +   ++
Sbjct: 1013 WADKYKHETEQLVSELKEQNTLLKTEKEELNRRIHDQAKEITETMEKK 1060

>2dfs_A Myosin-5A; myosin-V, inhibited state, cryoelectron tomograp contractIle protein-transport protein complex; 24.00A {Gallus gallus} Length = 1080

 Score = 57.8 bits (140), Expect = 1e-09
 Identities = 10/96 (10%), Positives = 41/96 (42%), Gaps = 3/96 (3%)

Query: 178  KERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKK---K 234
            +   + ++     + K  + +++ +++ ++ K   ++    +     + EK +      +
Sbjct: 914  RSVERYKKLHIGLENKIMQLQRKIDEQNKEYKSLLEKMNNLEITYSTETEKLRSDVERLR 973

Query: 235  KKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKD 270
              E++ K    +    +++  K +K+  + + +KK 
Sbjct: 974  MSEEEAKNATNRVLSLQEEIAKLRKELHQTQTEKKT 1009

>2dfs_A Myosin-5A; myosin-V, inhibited state, cryoelectron tomograp contractIle protein-transport protein complex; 24.00A {Gallus gallus} Length = 1080

 Score = 57.8 bits (140), Expect = 1e-09
 Identities = 12/105 (11%), Positives = 42/105 (40%), Gaps = 9/105 (8%)

Query: 176  GKKERRKQRRRK---------RKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKK 226
                +R+ ++ K         +K     E +  + ++K +++ ++ K   ++    E   
Sbjct: 899  RMMAKRELKKLKIEARSVERYKKLHIGLENKIMQLQRKIDEQNKEYKSLLEKMNNLEITY 958

Query: 227  EKKKKKKKKKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDE 271
              + +K +   ++ +  E++ K    +    +++  K +K+    
Sbjct: 959  STETEKLRSDVERLRMSEEEAKNATNRVLSLQEEIAKLRKELHQT 1003

>2dfs_A Myosin-5A; myosin-V, inhibited state, cryoelectron tomograp contractIle protein-transport protein complex; 24.00A {Gallus gallus} Length = 1080

 Score = 57.0 bits (138), Expect = 2e-09
 Identities = 21/102 (20%), Positives = 39/102 (38%), Gaps = 3/102 (2%)

Query: 177 KKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKK 236
           K  R    R    R  K     +   ++   K+E KK K + +  +  KK     + K  
Sbjct: 872 KHVRGWLARVHYHRTLKAIVYLQCCYRRMMAKRELKKLKIEARSVERYKKLHIGLENKIM 931

Query: 237 EKKKK---KKEKKKKKEEKKKEKKKKKKKKEKKKKKDEGRRR 275
           + ++K   + ++ K   EK    +     + +K + D  R R
Sbjct: 932 QLQRKIDEQNKEYKSLLEKMNNLEITYSTETEKLRSDVERLR 973

>2dfs_A Myosin-5A; myosin-V, inhibited state, cryoelectron tomograp contractIle protein-transport protein complex; 24.00A {Gallus gallus} Length = 1080

 Score = 56.7 bits (137), Expect = 3e-09
 Identities = 18/100 (18%), Positives = 40/100 (40%), Gaps = 5/100 (5%)

Query: 177  KKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKK-- 234
             KE +    +    +     E ++     E+ +  ++E K    +    +E+  K +K  
Sbjct: 941  NKEYKSLLEKMNNLEITYSTETEKLRSDVERLRMSEEEAKNATNRVLSLQEEIAKLRKEL 1000

Query: 235  ---KKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDE 271
               + EKK  ++   K K E ++   + K++    K + E
Sbjct: 1001 HQTQTEKKTIEEWADKYKHETEQLVSELKEQNTLLKTEKE 1040

>2dfs_A Myosin-5A; myosin-V, inhibited state, cryoelectron tomograp contractIle protein-transport protein complex; 24.00A {Gallus gallus} Length = 1080

 Score = 56.3 bits (136), Expect = 3e-09
 Identities = 15/96 (15%), Positives = 38/96 (39%), Gaps = 1/96 (1%)

Query: 177  KKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKK-KEKKKEKKKKEKKKEKKKKKKKK 235
            K    +        K + + E     ++E K    +    ++E  K  K+  + + +KK 
Sbjct: 950  KMNNLEITYSTETEKLRSDVERLRMSEEEAKNATNRVLSLQEEIAKLRKELHQTQTEKKT 1009

Query: 236  KEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDE 271
             E+   K + + ++   + +++    K EK++    
Sbjct: 1010 IEEWADKYKHETEQLVSELKEQNTLLKTEKEELNRR 1045

>2dfs_A Myosin-5A; myosin-V, inhibited state, cryoelectron tomograp contractIle protein-transport protein complex; 24.00A {Gallus gallus} Length = 1080

 Score = 56.3 bits (136), Expect = 3e-09
 Identities = 12/101 (11%), Positives = 41/101 (40%), Gaps = 2/101 (1%)

Query: 177  KKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEK--KKEKKKEKKKKEKKKEKKKKKKK 234
            K + + +  +    K    E     E ++ +   +  +  +++ K    +    +++  K
Sbjct: 936  KIDEQNKEYKSLLEKMNNLEITYSTETEKLRSDVERLRMSEEEAKNATNRVLSLQEEIAK 995

Query: 235  KKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDEGRRR 275
             +++  + + +KK  EE   + K + ++   + K+     +
Sbjct: 996  LRKELHQTQTEKKTIEEWADKYKHETEQLVSELKEQNTLLK 1036

>2dfs_A Myosin-5A; myosin-V, inhibited state, cryoelectron tomograp contractIle protein-transport protein complex; 24.00A {Gallus gallus} Length = 1080

 Score = 55.5 bits (134), Expect = 7e-09
 Identities = 16/97 (16%), Positives = 34/97 (35%), Gaps = 2/97 (2%)

Query: 177 KKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKK--EKKKEKKKKKKK 234
            K    Q+  +    R       +     +    +   K++ KK K   +  E+ KK   
Sbjct: 865 HKSIIIQKHVRGWLARVHYHRTLKAIVYLQCCYRRMMAKRELKKLKIEARSVERYKKLHI 924

Query: 235 KKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDE 271
             E K  + ++K  ++ K+ +   +K    +     E
Sbjct: 925 GLENKIMQLQRKIDEQNKEYKSLLEKMNNLEITYSTE 961

>2dfs_A Myosin-5A; myosin-V, inhibited state, cryoelectron tomograp contractIle protein-transport protein complex; 24.00A {Gallus gallus} Length = 1080

 Score = 54.3 bits (131), Expect = 2e-08
 Identities = 13/94 (13%), Positives = 42/94 (44%)

Query: 178  KERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKE 237
            +  R      +    +    ++E  K  ++  + + EKK  ++  +K K + ++   + +
Sbjct: 970  ERLRMSEEEAKNATNRVLSLQEEIAKLRKELHQTQTEKKTIEEWADKYKHETEQLVSELK 1029

Query: 238  KKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDE 271
            ++    + +K++  ++   + K+  +  +KK  E
Sbjct: 1030 EQNTLLKTEKEELNRRIHDQAKEITETMEKKLVE 1063

>2dfs_A Myosin-5A; myosin-V, inhibited state, cryoelectron tomograp contractIle protein-transport protein complex; 24.00A {Gallus gallus} Length = 1080

 Score = 54.0 bits (130), Expect = 2e-08
 Identities = 18/106 (16%), Positives = 47/106 (44%), Gaps = 8/106 (7%)

Query: 178  KERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKK----- 232
            +   ++ +    R    +EE  +  K+  + + +KK  ++   K + + E+   +     
Sbjct: 973  RMSEEEAKNATNRVLSLQEEIAKLRKELHQTQTEKKTIEEWADKYKHETEQLVSELKEQN 1032

Query: 233  ---KKKKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDEGRRR 275
               K +KE+  ++   + K+  +  EKK  ++ K+ +   ++ R R
Sbjct: 1033 TLLKTEKEELNRRIHDQAKEITETMEKKLVEETKQLELDLNDERLR 1078

>2dfs_A Myosin-5A; myosin-V, inhibited state, cryoelectron tomograp contractIle protein-transport protein complex; 24.00A {Gallus gallus} Length = 1080

 Score = 50.9 bits (122), Expect = 2e-07
 Identities = 14/91 (15%), Positives = 43/91 (47%)

Query: 177  KKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKK 236
              +    + RK   + + E++  EE   + K + ++   + +++    K EK++  ++  
Sbjct: 988  SLQEEIAKLRKELHQTQTEKKTIEEWADKYKHETEQLVSELKEQNTLLKTEKEELNRRIH 1047

Query: 237  EKKKKKKEKKKKKEEKKKEKKKKKKKKEKKK 267
            ++ K+  E  +KK  ++ ++ +     E+ +
Sbjct: 1048 DQAKEITETMEKKLVEETKQLELDLNDERLR 1078

>2dfs_A Myosin-5A; myosin-V, inhibited state, cryoelectron tomograp contractIle protein-transport protein complex; 24.00A {Gallus gallus} Length = 1080

 Score = 50.5 bits (121), Expect = 3e-07
 Identities = 16/94 (17%), Positives = 35/94 (37%)

Query: 178 KERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKE 237
           +   +    + K +    E +    +K  +    +    +  K     +   ++   K+E
Sbjct: 846 QALLRGYLVRNKYQMMLREHKSIIIQKHVRGWLARVHYHRTLKAIVYLQCCYRRMMAKRE 905

Query: 238 KKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDE 271
            KK K E +  +  KK     + K  + ++K DE
Sbjct: 906 LKKLKIEARSVERYKKLHIGLENKIMQLQRKIDE 939

>2dfs_A Myosin-5A; myosin-V, inhibited state, cryoelectron tomograp contractIle protein-transport protein complex; 24.00A {Gallus gallus} Length = 1080

 Score = 49.3 bits (118), Expect = 6e-07
 Identities = 17/111 (15%), Positives = 34/111 (30%), Gaps = 8/111 (7%)

Query: 173 YKGGKKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKK 232
            +     +R Q  R      +          K +    + K    +K  +         +
Sbjct: 826 QRMYVVRKRYQCMRDATIALQALLRGYLVRNKYQMMLREHKSIIIQKHVRGWLARVHYHR 885

Query: 233 KKKK--------EKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDEGRRR 275
             K          +   K+E KK K E +  ++ KK     + K  + +R+
Sbjct: 886 TLKAIVYLQCCYRRMMAKRELKKLKIEARSVERYKKLHIGLENKIMQLQRK 936

>2dfs_A Myosin-5A; myosin-V, inhibited state, cryoelectron tomograp contractIle protein-transport protein complex; 24.00A {Gallus gallus} Length = 1080

 Score = 48.6 bits (116), Expect = 1e-06
 Identities = 15/93 (16%), Positives = 33/93 (35%), Gaps = 1/93 (1%)

Query: 183 QRRRKRKRKRKKEEEEKEEEKK-EEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKK 241
           Q+ ++    RK+ +  ++     +   +      K +   +E K    +K  +    +  
Sbjct: 823 QKFQRMYVVRKRYQCMRDATIALQALLRGYLVRNKYQMMLREHKSIIIQKHVRGWLARVH 882

Query: 242 KKEKKKKKEEKKKEKKKKKKKKEKKKKKDEGRR 274
                K     +   ++   K+E KK K E R 
Sbjct: 883 YHRTLKAIVYLQCCYRRMMAKRELKKLKIEARS 915

>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic vesicle, membrane, Ca structural protein; 7.94A {Bos taurus} Length = 190

 Score = 55.9 bits (134), Expect = 1e-09
 Identities = 14/74 (18%), Positives = 37/74 (50%)

Query: 191 KRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKE 250
            R  +E E   + +EE++K  ++     K  +++ +EK KK  ++  +++ ++ +K K  
Sbjct: 78  DRLTQEPESIRKWREEQRKRLQELDAASKVMEQEWREKAKKDLEEWNQRQSEQVEKNKIN 137

Query: 251 EKKKEKKKKKKKKE 264
            +  +K   ++   
Sbjct: 138 NRIADKAFYQQPDA 151

>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic vesicle, membrane, Ca structural protein; 7.94A {Bos taurus} Length = 190

 Score = 52.9 bits (126), Expect = 1e-08
 Identities = 13/65 (20%), Positives = 35/65 (53%), Gaps = 2/65 (3%)

Query: 181 RKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKK 240
           RK R  +RKR ++ +     +  ++E +++ KK+ ++  +++ ++ EK K   +  +K  
Sbjct: 88  RKWREEQRKRLQELDAAS--KVMEQEWREKAKKDLEEWNQRQSEQVEKNKINNRIADKAF 145

Query: 241 KKKEK 245
            ++  
Sbjct: 146 YQQPD 150

>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic vesicle, membrane, Ca structural protein; 7.94A {Bos taurus} Length = 190

 Score = 51.7 bits (123), Expect = 3e-08
 Identities = 10/66 (15%), Positives = 34/66 (51%), Gaps = 2/66 (3%)

Query: 186 RKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEK 245
           RK + +++K  +E +     +  +++ +EK K+  ++  +++ ++ +K K   +   K  
Sbjct: 88  RKWREEQRKRLQELDAA--SKVMEQEWREKAKKDLEEWNQRQSEQVEKNKINNRIADKAF 145

Query: 246 KKKKEE 251
            ++ + 
Sbjct: 146 YQQPDA 151

>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic vesicle, membrane, Ca structural protein; 7.94A {Bos taurus} Length = 190

 Score = 47.8 bits (113), Expect = 5e-07
 Identities = 12/61 (19%), Positives = 32/61 (52%)

Query: 177 KKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKK 236
           ++E+RK+ +      +  E+E +E+ KK+ ++  +++ ++ EK K   +   K   ++  
Sbjct: 91  REEQRKRLQELDAASKVMEQEWREKAKKDLEEWNQRQSEQVEKNKINNRIADKAFYQQPD 150

Query: 237 E 237
            
Sbjct: 151 A 151

>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic vesicle, membrane, Ca structural protein; 7.94A {Bos taurus} Length = 190

 Score = 47.8 bits (113), Expect = 6e-07
 Identities = 12/78 (15%), Positives = 40/78 (51%), Gaps = 3/78 (3%)

Query: 195 EEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKKK 254
           + +   +E   E  ++ ++E++K  ++ +   +  +++ ++K KK  ++  +++ E+ +K
Sbjct: 76  QADRLTQE--PESIRKWREEQRKRLQELDAASKVMEQEWREKAKKDLEEWNQRQSEQVEK 133

Query: 255 EKKK-KKKKKEKKKKKDE 271
            K   +   K   ++ D 
Sbjct: 134 NKINNRIADKAFYQQPDA 151

>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic vesicle, membrane, Ca structural protein; 7.94A {Bos taurus} Length = 190

 Score = 39.4 bits (91), Expect = 4e-04
 Identities = 11/64 (17%), Positives = 34/64 (53%), Gaps = 1/64 (1%)

Query: 213 KEKKKEKKKKEKKKEKKKKKKKKKEKK-KKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDE 271
               +E +   K +E+++K+ ++ +   K  +++ ++K +K  E+  +++ ++ +K K  
Sbjct: 78  DRLTQEPESIRKWREEQRKRLQELDAASKVMEQEWREKAKKDLEEWNQRQSEQVEKNKIN 137

Query: 272 GRRR 275
            R  
Sbjct: 138 NRIA 141

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A Length = 1184

 Score = 57.9 bits (140), Expect = 1e-09
 Identities = 22/101 (21%), Positives = 51/101 (50%), Gaps = 2/101 (1%)

Query: 173  YKGGKKERRKQRRRKRKRKRKKEEE--EKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKK 230
                 + R   ++++ +    + E   E+EEE+ ++ + EKKK +++    +E+ +E++ 
Sbjct: 910  EAEEMRVRLAAKKQELEEILHEMEARIEEEEERSQQLQAEKKKMQQQMLDLEEQLEEEEA 969

Query: 231  KKKKKKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDE 271
             ++K + +K     K KK E+     + +  K  K++K  E
Sbjct: 970  ARQKLQLEKVTADGKIKKMEDDILIMEDQNNKLTKERKLLE 1010

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A Length = 1184

 Score = 56.0 bits (135), Expect = 4e-09
 Identities = 17/94 (18%), Positives = 49/94 (52%)

Query: 177 KKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKK 236
           K   +++ + + +   + EE       K+++ +E   E +   +++E++ ++ + +KKK 
Sbjct: 894 KNLLQEKLQAETELYAEAEEMRVRLAAKKQELEEILHEMEARIEEEEERSQQLQAEKKKM 953

Query: 237 EKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKD 270
           +++    E++ ++EE  ++K + +K     K K 
Sbjct: 954 QQQMLDLEEQLEEEEAARQKLQLEKVTADGKIKK 987

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A Length = 1184

 Score = 56.0 bits (135), Expect = 4e-09
 Identities = 15/95 (15%), Positives = 49/95 (51%)

Query: 177 KKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKK 236
            +        + + +   +++E EE   E + + +++E++ ++ + EKKK +++    ++
Sbjct: 903 AETELYAEAEEMRVRLAAKKQELEEILHEMEARIEEEEERSQQLQAEKKKMQQQMLDLEE 962

Query: 237 EKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDE 271
           + ++++  ++K + EK     K KK ++     ++
Sbjct: 963 QLEEEEAARQKLQLEKVTADGKIKKMEDDILIMED 997

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A Length = 1184

 Score = 55.6 bits (134), Expect = 6e-09
 Identities = 13/95 (13%), Positives = 49/95 (51%)

Query: 177 KKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKK 236
           +K   +++ +       + EE +     ++++ E+   + + + ++E+++ ++ + +KKK
Sbjct: 893 EKNLLQEKLQAETELYAEAEEMRVRLAAKKQELEEILHEMEARIEEEEERSQQLQAEKKK 952

Query: 237 EKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDE 271
            +++    +++ +EE+   +K + +K     K  +
Sbjct: 953 MQQQMLDLEEQLEEEEAARQKLQLEKVTADGKIKK 987

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A Length = 1184

 Score = 55.6 bits (134), Expect = 6e-09
 Identities = 14/93 (15%), Positives = 49/93 (52%)

Query: 177 KKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKK 236
           +K + +        + +     K++E +E   + + + +++E++ ++ + EKKK +++  
Sbjct: 899 EKLQAETELYAEAEEMRVRLAAKKQELEEILHEMEARIEEEEERSQQLQAEKKKMQQQML 958

Query: 237 EKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKK 269
           + +++ +E++  +++ + EK     K +K +  
Sbjct: 959 DLEEQLEEEEAARQKLQLEKVTADGKIKKMEDD 991

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A Length = 1184

 Score = 55.6 bits (134), Expect = 6e-09
 Identities = 18/93 (19%), Positives = 48/93 (51%)

Query: 177  KKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKK 236
             K++  +        R +EEEE+ ++ + EKKK +++    E++ +E++  ++K + +K 
Sbjct: 920  AKKQELEEILHEMEARIEEEEERSQQLQAEKKKMQQQMLDLEEQLEEEEAARQKLQLEKV 979

Query: 237  EKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKK 269
                K K+ +      + +  K  K+++  +++
Sbjct: 980  TADGKIKKMEDDILIMEDQNNKLTKERKLLEER 1012

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A Length = 1184

 Score = 54.8 bits (132), Expect = 1e-08
 Identities = 15/95 (15%), Positives = 55/95 (57%)

Query: 177 KKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKK 236
           K+  +K  +   ++   +E+ + E E   E ++ + +   K+++ +E   E + + ++++
Sbjct: 881 KELEQKHTQLCEEKNLLQEKLQAETELYAEAEEMRVRLAAKKQELEEILHEMEARIEEEE 940

Query: 237 EKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDE 271
           E+ ++ + +KKK +++  + +++ +++E  ++K +
Sbjct: 941 ERSQQLQAEKKKMQQQMLDLEEQLEEEEAARQKLQ 975

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A Length = 1184

 Score = 54.5 bits (131), Expect = 1e-08
 Identities = 16/95 (16%), Positives = 49/95 (51%)

Query: 177 KKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKK 236
           +    K   +++ +   +   E EE +     K+++ E+   + +   ++E+++ ++ + 
Sbjct: 889 QLCEEKNLLQEKLQAETELYAEAEEMRVRLAAKKQELEEILHEMEARIEEEEERSQQLQA 948

Query: 237 EKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDE 271
           EKKK +++    +E+ ++E+  ++K + +K   D 
Sbjct: 949 EKKKMQQQMLDLEEQLEEEEAARQKLQLEKVTADG 983

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A Length = 1184

 Score = 53.7 bits (129), Expect = 2e-08
 Identities = 20/105 (19%), Positives = 56/105 (53%), Gaps = 10/105 (9%)

Query: 176 GKKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKK----------KEKK 225
            ++E + +    ++ K ++++ E E ++ E+K  +  +EK   ++K           E+ 
Sbjct: 855 QEEEMQAKDEELQRTKERQQKAEAELKELEQKHTQLCEEKNLLQEKLQAETELYAEAEEM 914

Query: 226 KEKKKKKKKKKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKD 270
           + +   KK++ E+   + E + ++EE++ ++ + +KKK +++  D
Sbjct: 915 RVRLAAKKQELEEILHEMEARIEEEEERSQQLQAEKKKMQQQMLD 959

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A Length = 1184

 Score = 53.3 bits (128), Expect = 3e-08
 Identities = 21/95 (22%), Positives = 46/95 (48%)

Query: 177  KKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKK 236
            ++E R Q+ +  K+K +++  + EE+ +EE+   +K + +K     + KK +      + 
Sbjct: 938  EEEERSQQLQAEKKKMQQQMLDLEEQLEEEEAARQKLQLEKVTADGKIKKMEDDILIMED 997

Query: 237  EKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDE 271
            +  K  KE+K  +E          +++EK K   +
Sbjct: 998  QNNKLTKERKLLEERVSDLTTNLAEEEEKAKNLTK 1032

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A Length = 1184

 Score = 52.1 bits (125), Expect = 8e-08
 Identities = 18/94 (19%), Positives = 47/94 (50%), Gaps = 2/94 (2%)

Query: 177  KKERRKQRRRKRKRKRKKEEE--EKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKK 234
            K+E  +       R  ++EE   + + EKK+ +++    E++ E+++  ++K + +K   
Sbjct: 922  KQELEEILHEMEARIEEEEERSQQLQAEKKKMQQQMLDLEEQLEEEEAARQKLQLEKVTA 981

Query: 235  KKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKK 268
              + KK + +    +++  K  K++K  +E+   
Sbjct: 982  DGKIKKMEDDILIMEDQNNKLTKERKLLEERVSD 1015

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A Length = 1184

 Score = 51.4 bits (123), Expect = 2e-07
 Identities = 11/95 (11%), Positives = 46/95 (48%)

Query: 177  KKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKK 236
             +   +    + + ++ + E++K +++  + +++ ++E+   +K + +K     K KK +
Sbjct: 930  HEMEARIEEEEERSQQLQAEKKKMQQQMLDLEEQLEEEEAARQKLQLEKVTADGKIKKME 989

Query: 237  EKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDE 271
            +     +++  K  +++K  +++         ++E
Sbjct: 990  DDILIMEDQNNKLTKERKLLEERVSDLTTNLAEEE 1024

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A Length = 1184

 Score = 51.0 bits (122), Expect = 2e-07
 Identities = 20/93 (21%), Positives = 44/93 (47%)

Query: 178  KERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKE 237
            +E    R++ +  K   + + K+ E      +++  +  KE+K  E++         ++E
Sbjct: 965  EEEEAARQKLQLEKVTADGKIKKMEDDILIMEDQNNKLTKERKLLEERVSDLTTNLAEEE 1024

Query: 238  KKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKD 270
            +K K   K K K E    + + + KKE+K +++
Sbjct: 1025 EKAKNLTKLKNKHESMISELEVRLKKEEKSRQE 1057

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A Length = 1184

 Score = 49.4 bits (118), Expect = 6e-07
 Identities = 25/108 (23%), Positives = 49/108 (45%), Gaps = 10/108 (9%)

Query: 177  KKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKK----------EKKKKEKKK 226
            +  R+K +  K     K ++ E +    E++  +  KE+K              ++E+K 
Sbjct: 968  EAARQKLQLEKVTADGKIKKMEDDILIMEDQNNKLTKERKLLEERVSDLTTNLAEEEEKA 1027

Query: 227  EKKKKKKKKKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDEGRR 274
            +   K K K E    + E + KKEEK +++ +K K+K + +  D   +
Sbjct: 1028 KNLTKLKNKHESMISELEVRLKKEEKSRQELEKIKRKLEGESSDLHEQ 1075

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A Length = 1184

 Score = 49.4 bits (118), Expect = 6e-07
 Identities = 21/96 (21%), Positives = 44/96 (45%), Gaps = 1/96 (1%)

Query: 177  KKERRKQRRRKRKRKRKKEEEEKEEEK-KEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKK 235
            + E++K +++    + + EEEE   +K + EK     K KK E      + +  K  K++
Sbjct: 947  QAEKKKMQQQMLDLEEQLEEEEAARQKLQLEKVTADGKIKKMEDDILIMEDQNNKLTKER 1006

Query: 236  KEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDE 271
            K  +++  +      E++++ K   K K K +    
Sbjct: 1007 KLLEERVSDLTTNLAEEEEKAKNLTKLKNKHESMIS 1042

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A Length = 1184

 Score = 49.1 bits (117), Expect = 9e-07
 Identities = 13/99 (13%), Positives = 53/99 (53%)

Query: 177 KKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKK 236
           K E   +   ++  +  +E+   +E+ + E +   + E+ + +   +K++ ++   + + 
Sbjct: 875 KAEAELKELEQKHTQLCEEKNLLQEKLQAETELYAEAEEMRVRLAAKKQELEEILHEMEA 934

Query: 237 EKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDEGRRR 275
             +++++  ++ + EKKK +++    +E+ ++++  R++
Sbjct: 935 RIEEEEERSQQLQAEKKKMQQQMLDLEEQLEEEEAARQK 973

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A Length = 1184

 Score = 46.0 bits (109), Expect = 7e-06
 Identities = 22/102 (21%), Positives = 46/102 (45%), Gaps = 7/102 (6%)

Query: 177  KKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEK-------KKEKK 229
              E +  +  K ++  ++   +      EE++K K   K K K +          KKE+K
Sbjct: 994  IMEDQNNKLTKERKLLEERVSDLTTNLAEEEEKAKNLTKLKNKHESMISELEVRLKKEEK 1053

Query: 230  KKKKKKKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDE 271
             +++ +K K+K + E     E+  + + +  + K +  KK+E
Sbjct: 1054 SRQELEKIKRKLEGESSDLHEQIAELQAQIAELKAQLAKKEE 1095

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A Length = 1184

 Score = 45.6 bits (108), Expect = 1e-05
 Identities = 20/91 (21%), Positives = 42/91 (46%)

Query: 178  KERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKE 237
            +E + +   K K K +    E E   K+E+K  ++ EK K K + E     ++  + + +
Sbjct: 1023 EEEKAKNLTKLKNKHESMISELEVRLKKEEKSRQELEKIKRKLEGESSDLHEQIAELQAQ 1082

Query: 238  KKKKKKEKKKKKEEKKKEKKKKKKKKEKKKK 268
              + K +  KK+EE +    + + +  +K  
Sbjct: 1083 IAELKAQLAKKEEELQAALARLEDETSQKNN 1113

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A Length = 1184

 Score = 44.4 bits (105), Expect = 2e-05
 Identities = 18/94 (19%), Positives = 43/94 (45%), Gaps = 1/94 (1%)

Query: 179  ERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEK 238
            E+ K++         ++  E + +  E K +  KKE++ +      + E  +K    K+ 
Sbjct: 1059 EKIKRKLEGESSDLHEQIAELQAQIAELKAQLAKKEEELQAALARLEDETSQKNNALKKI 1118

Query: 239  KKKKKEKKKKKEEKKKEKKKKKK-KKEKKKKKDE 271
            ++ +      +E+ + EK  + K +K+K+   +E
Sbjct: 1119 RELESHISDLQEDLESEKAARNKAEKQKRDLSEE 1152

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A Length = 1184

 Score = 44.1 bits (104), Expect = 4e-05
 Identities = 25/100 (25%), Positives = 47/100 (47%), Gaps = 7/100 (7%)

Query: 178  KERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEK-------KKEKKK 230
            K+  K R+   K KRK E E  +  ++  + + +  E K +  KKE+       + E + 
Sbjct: 1049 KKEEKSRQELEKIKRKLEGESSDLHEQIAELQAQIAELKAQLAKKEEELQAALARLEDET 1108

Query: 231  KKKKKKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKD 270
             +K    KK ++ E      ++  E +K  + K +K+K+D
Sbjct: 1109 SQKNNALKKIRELESHISDLQEDLESEKAARNKAEKQKRD 1148

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A Length = 1184

 Score = 42.1 bits (99), Expect = 1e-04
 Identities = 22/99 (22%), Positives = 47/99 (47%), Gaps = 2/99 (2%)

Query: 177  KKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKK--EKKKKKKK 234
            +++  ++R         +EEE+ +   K + K E    + + + KKE+K   E +K K+K
Sbjct: 1005 ERKLLEERVSDLTTNLAEEEEKAKNLTKLKNKHESMISELEVRLKKEEKSRQELEKIKRK 1064

Query: 235  KKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDEGR 273
             + +     E+  + + +  E K +  KKE++ +    R
Sbjct: 1065 LEGESSDLHEQIAELQAQIAELKAQLAKKEEELQAALAR 1103

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A Length = 1184

 Score = 41.7 bits (98), Expect = 2e-04
 Identities = 15/94 (15%), Positives = 41/94 (43%), Gaps = 1/94 (1%)

Query: 178  KERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKE 237
            K +  ++  + +    + E+E  ++    KK  ++ E      +++ + EK  + K +K+
Sbjct: 1087 KAQLAKKEEELQAALARLEDETSQKNNALKKI-RELESHISDLQEDLESEKAARNKAEKQ 1145

Query: 238  KKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDE 271
            K+   +E +  K E +        ++E +    +
Sbjct: 1146 KRDLSEELEALKTELEDTLDTTATQQELRGSDYK 1179

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A Length = 1184

 Score = 41.4 bits (97), Expect = 2e-04
 Identities = 19/93 (20%), Positives = 40/93 (43%)

Query: 178  KERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKE 237
            K+          +  K  +E K  E++         E++++ K   K K K +    + E
Sbjct: 986  KKMEDDILIMEDQNNKLTKERKLLEERVSDLTTNLAEEEEKAKNLTKLKNKHESMISELE 1045

Query: 238  KKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKD 270
             + KK+EK +++ EK K K + +     ++  +
Sbjct: 1046 VRLKKEEKSRQELEKIKRKLEGESSDLHEQIAE 1078

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A Length = 1184

 Score = 40.2 bits (94), Expect = 5e-04
 Identities = 14/83 (16%), Positives = 37/83 (44%)

Query: 177  KKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKK 236
             +   +  ++    K+ +E E    + +E+ + EK    K EK+K++  +E +  K + +
Sbjct: 1102 ARLEDETSQKNNALKKIRELESHISDLQEDLESEKAARNKAEKQKRDLSEELEALKTELE 1161

Query: 237  EKKKKKKEKKKKKEEKKKEKKKK 259
            +       +++ +    K+   K
Sbjct: 1162 DTLDTTATQQELRGSDYKDDDDK 1184

>4ady_A RPN2, 26S proteasome regulatory subunit RPN2; protein binding, PC repeat; 2.70A {Saccharomyces cerevisiae} Length = 963

 Score = 55.2 bits (132), Expect = 7e-09
 Identities = 21/82 (25%), Positives = 44/82 (53%), Gaps = 5/82 (6%)

Query: 193 KKEEEEKEEEKKEEKKKE-----KKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKK 247
           +  EE   +E ++          + K + K+ KK++   E++KKK+ ++++K+++  KK 
Sbjct: 797 RMYEEASGKEVEKVATAVLSTTARAKARAKKTKKEKGPNEEEKKKEHEEKEKERETNKKG 856

Query: 248 KKEEKKKEKKKKKKKKEKKKKK 269
            KE K+ +++  K K   K  K
Sbjct: 857 IKETKENDEEFYKNKYSSKPYK 878

>4ady_A RPN2, 26S proteasome regulatory subunit RPN2; protein binding, PC repeat; 2.70A {Saccharomyces cerevisiae} Length = 963

 Score = 53.3 bits (127), Expect = 3e-08
 Identities = 21/61 (34%), Positives = 36/61 (59%)

Query: 184 RRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKK 243
           R + R +K KKE+   EEEKK+E ++++K+ +  +K  KE K+  ++  K K   K  K 
Sbjct: 820 RAKARAKKTKKEKGPNEEEKKKEHEEKEKERETNKKGIKETKENDEEFYKNKYSSKPYKV 879

Query: 244 E 244
           +
Sbjct: 880 D 880

>4ady_A RPN2, 26S proteasome regulatory subunit RPN2; protein binding, PC repeat; 2.70A {Saccharomyces cerevisiae} Length = 963

 Score = 52.9 bits (126), Expect = 4e-08
 Identities = 18/85 (21%), Positives = 41/85 (48%), Gaps = 3/85 (3%)

Query: 190 RKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKK 249
            + K   ++ ++EK   ++++KK+ ++KEK+++  KK  K+ K+  +E  K K      K
Sbjct: 819 ARAKARAKKTKKEKGPNEEEKKKEHEEKEKERETNKKGIKETKENDEEFYKNKYS---SK 875

Query: 250 EEKKKEKKKKKKKKEKKKKKDEGRR 274
             K     +   ++ +     +  R
Sbjct: 876 PYKVDNMTRILPQQSRYISFIKDDR 900

>4ady_A RPN2, 26S proteasome regulatory subunit RPN2; protein binding, PC repeat; 2.70A {Saccharomyces cerevisiae} Length = 963

 Score = 51.4 bits (122), Expect = 2e-07
 Identities = 21/73 (28%), Positives = 40/73 (54%)

Query: 199 KEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKKKEKKK 258
           +  E+   K+ EK          + K + KK KK+K   +++KKKE ++K++E++  KK 
Sbjct: 797 RMYEEASGKEVEKVATAVLSTTARAKARAKKTKKEKGPNEEEKKKEHEEKEKERETNKKG 856

Query: 259 KKKKKEKKKKKDE 271
            K+ KE  ++  +
Sbjct: 857 IKETKENDEEFYK 869

>4ady_A RPN2, 26S proteasome regulatory subunit RPN2; protein binding, PC repeat; 2.70A {Saccharomyces cerevisiae} Length = 963

 Score = 49.8 bits (118), Expect = 5e-07
 Identities = 19/74 (25%), Positives = 40/74 (54%)

Query: 202 EKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKKKEKKKKKK 261
             +E   KE +K          + K + KK KK+K   +++K+K+ +++EK++E  KK  
Sbjct: 798 MYEEASGKEVEKVATAVLSTTARAKARAKKTKKEKGPNEEEKKKEHEEKEKERETNKKGI 857

Query: 262 KKEKKKKKDEGRRR 275
           K+ K+  ++  + +
Sbjct: 858 KETKENDEEFYKNK 871

>4ady_A RPN2, 26S proteasome regulatory subunit RPN2; protein binding, PC repeat; 2.70A {Saccharomyces cerevisiae} Length = 963

 Score = 47.9 bits (113), Expect = 2e-06
 Identities = 16/73 (21%), Positives = 40/73 (54%)

Query: 188 RKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKK 247
            + K + ++ +KE+   EE+KK++ +EK+KE++  +K  ++ K+  ++  K K   +  K
Sbjct: 819 ARAKARAKKTKKEKGPNEEEKKKEHEEKEKERETNKKGIKETKENDEEFYKNKYSSKPYK 878

Query: 248 KKEEKKKEKKKKK 260
                +   ++ +
Sbjct: 879 VDNMTRILPQQSR 891

>4ady_A RPN2, 26S proteasome regulatory subunit RPN2; protein binding, PC repeat; 2.70A {Saccharomyces cerevisiae} Length = 963

 Score = 45.6 bits (107), Expect = 1e-05
 Identities = 14/57 (24%), Positives = 29/57 (50%)

Query: 174 KGGKKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKK 230
           +  K ++ K    + K+K  +E+E++ E  K+  K+ K+ +++  K K   K  K  
Sbjct: 824 RAKKTKKEKGPNEEEKKKEHEEKEKERETNKKGIKETKENDEEFYKNKYSSKPYKVD 880

>4ady_A RPN2, 26S proteasome regulatory subunit RPN2; protein binding, PC repeat; 2.70A {Saccharomyces cerevisiae} Length = 963

 Score = 45.2 bits (106), Expect = 1e-05
 Identities = 16/64 (25%), Positives = 34/64 (53%)

Query: 209 KEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKK 268
           +  ++   KE +K          + K + KK KK++   ++E+KK+ ++K+K+++  KK 
Sbjct: 797 RMYEEASGKEVEKVATAVLSTTARAKARAKKTKKEKGPNEEEKKKEHEEKEKERETNKKG 856

Query: 269 KDEG 272
             E 
Sbjct: 857 IKET 860

>4ady_A RPN2, 26S proteasome regulatory subunit RPN2; protein binding, PC repeat; 2.70A {Saccharomyces cerevisiae} Length = 963

 Score = 41.3 bits (96), Expect = 2e-04
 Identities = 16/66 (24%), Positives = 35/66 (53%), Gaps = 1/66 (1%)

Query: 207 KKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKK 266
           +  E+   K+ EK           + K + +K KK+K   +++++K+ E+K+K+++  KK
Sbjct: 797 RMYEEASGKEVEKVAT-AVLSTTARAKARAKKTKKEKGPNEEEKKKEHEEKEKERETNKK 855

Query: 267 KKKDEG 272
             K+  
Sbjct: 856 GIKETK 861

>1b6a_A Methionine aminopeptidase; angiogenesis inhibitor; HET: TN4; 1.60A {Homo sapiens} SCOP: a.4.5.25 d.127.1.1 PDB: 1qzy_A* 1boa_A* 1kq0_A 1kq9_A 1bn5_A* 1b59_A* 1yw9_A* 1r5g_A* 1r5h_A* 1r58_A* 1yw8_A* 1yw7_A* 2adu_A* 2ea2_A* 2ea4_A* 2ga2_A* 2oaz_A* Length = 478

 Score = 51.8 bits (124), Expect = 8e-08
 Identities = 19/103 (18%), Positives = 41/103 (39%), Gaps = 4/103 (3%)

Query: 174 KGGKKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEK----KKEKKKKEKKKEKK 229
           +                + +      EE  K++++K+KK +      +++  KE      
Sbjct: 6   EVAASGSHLNGDLDPDDREEGAASTAEEAAKKKRRKKKKSKGPSAAGEQEPDKESGASVD 65

Query: 230 KKKKKKKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDEG 272
           +  ++ +    + KE+ +  E+   +      KK+KKKKK  G
Sbjct: 66  EVARQLERSALEDKERDEDDEDGDGDGDGATGKKKKKKKKKRG 108

>1b6a_A Methionine aminopeptidase; angiogenesis inhibitor; HET: TN4; 1.60A {Homo sapiens} SCOP: a.4.5.25 d.127.1.1 PDB: 1qzy_A* 1boa_A* 1kq0_A 1kq9_A 1bn5_A* 1b59_A* 1yw9_A* 1r5g_A* 1r5h_A* 1r58_A* 1yw8_A* 1yw7_A* 2adu_A* 2ea2_A* 2ea4_A* 2ga2_A* 2oaz_A* Length = 478

 Score = 48.4 bits (115), Expect = 1e-06
 Identities = 20/79 (25%), Positives = 40/79 (50%)

Query: 177 KKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKK 236
           KK+RRK+++ K      ++E +KE     ++   + +    E K++++  E         
Sbjct: 36  KKKRRKKKKSKGPSAAGEQEPDKESGASVDEVARQLERSALEDKERDEDDEDGDGDGDGA 95

Query: 237 EKKKKKKEKKKKKEEKKKE 255
             KKKKK+KKK+  + + +
Sbjct: 96  TGKKKKKKKKKRGPKVQTD 114

>1b6a_A Methionine aminopeptidase; angiogenesis inhibitor; HET: TN4; 1.60A {Homo sapiens} SCOP: a.4.5.25 d.127.1.1 PDB: 1qzy_A* 1boa_A* 1kq0_A 1kq9_A 1bn5_A* 1b59_A* 1yw9_A* 1r5g_A* 1r5h_A* 1r58_A* 1yw8_A* 1yw7_A* 2adu_A* 2ea2_A* 2ea4_A* 2ga2_A* 2oaz_A* Length = 478

 Score = 48.0 bits (114), Expect = 2e-06
 Identities = 18/76 (23%), Positives = 38/76 (50%)

Query: 187 KRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKK 246
           K+KR++KK+ +      ++E  KE      +  ++ E+   + K++ +  E      +  
Sbjct: 36  KKKRRKKKKSKGPSAAGEQEPDKESGASVDEVARQLERSALEDKERDEDDEDGDGDGDGA 95

Query: 247 KKKEEKKKEKKKKKKK 262
             K++KKK+KK+  K 
Sbjct: 96  TGKKKKKKKKKRGPKV 111

>1b6a_A Methionine aminopeptidase; angiogenesis inhibitor; HET: TN4; 1.60A {Homo sapiens} SCOP: a.4.5.25 d.127.1.1 PDB: 1qzy_A* 1boa_A* 1kq0_A 1kq9_A 1bn5_A* 1b59_A* 1yw9_A* 1r5g_A* 1r5h_A* 1r58_A* 1yw8_A* 1yw7_A* 2adu_A* 2ea2_A* 2ea4_A* 2ga2_A* 2oaz_A* Length = 478

 Score = 47.2 bits (112), Expect = 2e-06
 Identities = 18/90 (20%), Positives = 43/90 (47%)

Query: 167 DNLEYGYKGGKKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKK 226
           D  E      ++  +K+RR+K+K K      E+E +K+     ++   + +    ++K++
Sbjct: 22  DREEGAASTAEEAAKKKRRKKKKSKGPSAAGEQEPDKESGASVDEVARQLERSALEDKER 81

Query: 227 EKKKKKKKKKEKKKKKKEKKKKKEEKKKEK 256
           ++  +           K+KKKKK+++  + 
Sbjct: 82  DEDDEDGDGDGDGATGKKKKKKKKKRGPKV 111

>1b6a_A Methionine aminopeptidase; angiogenesis inhibitor; HET: TN4; 1.60A {Homo sapiens} SCOP: a.4.5.25 d.127.1.1 PDB: 1qzy_A* 1boa_A* 1kq0_A 1kq9_A 1bn5_A* 1b59_A* 1yw9_A* 1r5g_A* 1r5h_A* 1r58_A* 1yw8_A* 1yw7_A* 2adu_A* 2ea2_A* 2ea4_A* 2ga2_A* 2oaz_A* Length = 478

 Score = 46.8 bits (111), Expect = 3e-06
 Identities = 18/82 (21%), Positives = 38/82 (46%)

Query: 177 KKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKK 236
             E   +++R++K+K K      E+E  +E      +  ++ ++   + KE+ +  +   
Sbjct: 30  TAEEAAKKKRRKKKKSKGPSAAGEQEPDKESGASVDEVARQLERSALEDKERDEDDEDGD 89

Query: 237 EKKKKKKEKKKKKEEKKKEKKK 258
                   KKKKK++KK+  K 
Sbjct: 90  GDGDGATGKKKKKKKKKRGPKV 111

>1b6a_A Methionine aminopeptidase; angiogenesis inhibitor; HET: TN4; 1.60A {Homo sapiens} SCOP: a.4.5.25 d.127.1.1 PDB: 1qzy_A* 1boa_A* 1kq0_A 1kq9_A 1bn5_A* 1b59_A* 1yw9_A* 1r5g_A* 1r5h_A* 1r58_A* 1yw8_A* 1yw7_A* 2adu_A* 2ea2_A* 2ea4_A* 2ga2_A* 2oaz_A* Length = 478

 Score = 41.1 bits (96), Expect = 2e-04
 Identities = 13/78 (16%), Positives = 31/78 (39%)

Query: 195 EEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKKK 254
           EE                +E+      +E  K+K++KKKK K      +++  K+     
Sbjct: 5   EEVAASGSHLNGDLDPDDREEGAASTAEEAAKKKRRKKKKSKGPSAAGEQEPDKESGASV 64

Query: 255 EKKKKKKKKEKKKKKDEG 272
           ++  ++ ++   + K+  
Sbjct: 65  DEVARQLERSALEDKERD 82

>1f5n_A Interferon-induced guanylate-binding protein 1; GBP, GTP hydrolysis, GDP, GMP, dynamin related, large GTPase family. GMPPNP, GPPNHP.; HET: GNP; 1.70A {Homo sapiens} SCOP: a.114.1.1 c.37.1.8 PDB: 1dg3_A* 2b8w_A* 2b92_A* 2bc9_A* 2d4h_A* Length = 592

 Score = 51.1 bits (121), Expect = 2e-07
 Identities = 14/93 (15%), Positives = 49/93 (52%)

Query: 177 KKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKK 236
           K E  +   +     ++K E+  E++++  ++  K+  +K E  + +  KE+++    K 
Sbjct: 495 KAESAQASAKMLHEMQRKNEQMMEQKERSYQEHLKQLTEKMENDRVQLLKEQERTLALKL 554

Query: 237 EKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKK 269
           +++++  ++  +KE +  + + +  + + +++K
Sbjct: 555 QEQEQLLKEGFQKESRIMKNEIQDLQTKMRRRK 587

>1f5n_A Interferon-induced guanylate-binding protein 1; GBP, GTP hydrolysis, GDP, GMP, dynamin related, large GTPase family. GMPPNP, GPPNHP.; HET: GNP; 1.70A {Homo sapiens} SCOP: a.114.1.1 c.37.1.8 PDB: 1dg3_A* 2b8w_A* 2b92_A* 2bc9_A* 2d4h_A* Length = 592

 Score = 48.0 bits (113), Expect = 2e-06
 Identities = 21/104 (20%), Positives = 47/104 (45%), Gaps = 2/104 (1%)

Query: 170 EYGYKGGKKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKK--E 227
           E   KG + E   Q   K K        + ++   E++K+ + +  K E  +   K   E
Sbjct: 449 EEPRKGIQAEEILQTYLKSKESMTDAILQTDQTLTEKEKEIEVERVKAESAQASAKMLHE 508

Query: 228 KKKKKKKKKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDE 271
            ++K ++  E+K++  ++  K+  +K E  + +  KE+++    
Sbjct: 509 MQRKNEQMMEQKERSYQEHLKQLTEKMENDRVQLLKEQERTLAL 552

>1f5n_A Interferon-induced guanylate-binding protein 1; GBP, GTP hydrolysis, GDP, GMP, dynamin related, large GTPase family. GMPPNP, GPPNHP.; HET: GNP; 1.70A {Homo sapiens} SCOP: a.114.1.1 c.37.1.8 PDB: 1dg3_A* 2b8w_A* 2b92_A* 2bc9_A* 2d4h_A* Length = 592

 Score = 41.1 bits (95), Expect = 3e-04
 Identities = 18/109 (16%), Positives = 49/109 (44%)

Query: 161 LWGGCGDNLEYGYKGGKKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKK 220
           ++    + ++ G        R   ++ +  K+K  EE ++  + EE  +   K K+    
Sbjct: 414 IFSPLEEEVKAGIYSKPGGYRLFVQKLQDLKKKYYEEPRKGIQAEEILQTYLKSKESMTD 473

Query: 221 KKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKK 269
              +  +   +K+K+ E ++ K E  +   +   E ++K ++  ++K++
Sbjct: 474 AILQTDQTLTEKEKEIEVERVKAESAQASAKMLHEMQRKNEQMMEQKER 522

>2zkr_c 60S ribosomal protein L4; protein-RNA complex, 60S ribosomal subunit, ribosomal protein/RNA complex; 8.70A {Canis familiaris} Length = 421

 Score = 47.9 bits (113), Expect = 1e-06
 Identities = 24/84 (28%), Positives = 36/84 (42%)

Query: 187 KRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKK 246
           K  R+     + K  + + +K     + K +EK    KK  +KK KK    KK KK    
Sbjct: 333 KTMRRNTILRQAKNHKLRMDKAAAALEAKSEEKGVPGKKPRRKKGKKTVGVKKPKKPVVG 392

Query: 247 KKKEEKKKEKKKKKKKKEKKKKKD 270
           KK    KK    KK  ++K   ++
Sbjct: 393 KKAAATKKPAADKKPAEKKPTTEE 416

>2zkr_c 60S ribosomal protein L4; protein-RNA complex, 60S ribosomal subunit, ribosomal protein/RNA complex; 8.70A {Canis familiaris} Length = 421

 Score = 45.6 bits (107), Expect = 9e-06
 Identities = 22/86 (25%), Positives = 39/86 (45%)

Query: 182 KQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKK 241
           K  RR    ++ K  + + ++     + + +++    KK + KK +K    KK K+    
Sbjct: 333 KTMRRNTILRQAKNHKLRMDKAAAALEAKSEEKGVPGKKPRRKKGKKTVGVKKPKKPVVG 392

Query: 242 KKEKKKKKEEKKKEKKKKKKKKEKKK 267
           KK    KK    K+  +KK   E+KK
Sbjct: 393 KKAAATKKPAADKKPAEKKPTTEEKK 418

>2zkr_c 60S ribosomal protein L4; protein-RNA complex, 60S ribosomal subunit, ribosomal protein/RNA complex; 8.70A {Canis familiaris} Length = 421

 Score = 44.9 bits (105), Expect = 2e-05
 Identities = 25/98 (25%), Positives = 42/98 (42%)

Query: 168 NLEYGYKGGKKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKE 227
           NL    K     +  +R    ++ +  +    +     E K E+K    K+ ++K+ KK 
Sbjct: 321 NLRIMLKLNPYAKTMRRNTILRQAKNHKLRMDKAAAALEAKSEEKGVPGKKPRRKKGKKT 380

Query: 228 KKKKKKKKKEKKKKKKEKKKKKEEKKKEKKKKKKKKEK 265
              KK KK    KK    KK   +KK  +KK   +++K
Sbjct: 381 VGVKKPKKPVVGKKAAATKKPAADKKPAEKKPTTEEKK 418

>2zkr_c 60S ribosomal protein L4; protein-RNA complex, 60S ribosomal subunit, ribosomal protein/RNA complex; 8.70A {Canis familiaris} Length = 421

 Score = 44.9 bits (105), Expect = 2e-05
 Identities = 21/100 (21%), Positives = 39/100 (39%)

Query: 174 KGGKKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKK 233
           K   +   K+   K  R   K     +  ++    ++ K  K +  K     + K ++K 
Sbjct: 307 KKIHRRVLKKNPLKNLRIMLKLNPYAKTMRRNTILRQAKNHKLRMDKAAAALEAKSEEKG 366

Query: 234 KKKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDEGR 273
              +K ++KK KK    +K K+    KK    KK   + +
Sbjct: 367 VPGKKPRRKKGKKTVGVKKPKKPVVGKKAAATKKPAADKK 406

>2zkr_c 60S ribosomal protein L4; protein-RNA complex, 60S ribosomal subunit, ribosomal protein/RNA complex; 8.70A {Canis familiaris} Length = 421

 Score = 44.1 bits (103), Expect = 3e-05
 Identities = 22/86 (25%), Positives = 38/86 (44%)

Query: 183 QRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKK 242
           +  R+    R+ +  +   +K     + K +EK    KK  +KK KK    KK +K    
Sbjct: 333 KTMRRNTILRQAKNHKLRMDKAAAALEAKSEEKGVPGKKPRRKKGKKTVGVKKPKKPVVG 392

Query: 243 KEKKKKKEEKKKEKKKKKKKKEKKKK 268
           K+    K+    +K  +KK   ++KK
Sbjct: 393 KKAAATKKPAADKKPAEKKPTTEEKK 418

>2zkr_c 60S ribosomal protein L4; protein-RNA complex, 60S ribosomal subunit, ribosomal protein/RNA complex; 8.70A {Canis familiaris} Length = 421

 Score = 43.7 bits (102), Expect = 3e-05
 Identities = 21/95 (22%), Positives = 38/95 (40%)

Query: 177 KKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKK 236
           KK   K  R   K     +   +    ++ K  + + +K     + + +++    KK ++
Sbjct: 315 KKNPLKNLRIMLKLNPYAKTMRRNTILRQAKNHKLRMDKAAAALEAKSEEKGVPGKKPRR 374

Query: 237 EKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDE 271
           +K KK    KK K+    +K    KK    KK  E
Sbjct: 375 KKGKKTVGVKKPKKPVVGKKAAATKKPAADKKPAE 409

>2zkr_c 60S ribosomal protein L4; protein-RNA complex, 60S ribosomal subunit, ribosomal protein/RNA complex; 8.70A {Canis familiaris} Length = 421

 Score = 40.2 bits (93), Expect = 5e-04
 Identities = 22/96 (22%), Positives = 38/96 (39%)

Query: 180 RRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKK 239
           R+K  RR  K+   K      +     K   +    ++ K  K +  +     + K E+K
Sbjct: 306 RKKIHRRVLKKNPLKNLRIMLKLNPYAKTMRRNTILRQAKNHKLRMDKAAAALEAKSEEK 365

Query: 240 KKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDEGRRR 275
               +K ++K+ KK    KK KK    KK    ++ 
Sbjct: 366 GVPGKKPRRKKGKKTVGVKKPKKPVVGKKAAATKKP 401

>2qag_B Septin-6, protein NEDD5; cell cycle, cell division, GTP-binding, nucleotide-binding, phosphorylation, acetylation, alternative splicing, coiled coil; HET: GDP GTP; 4.00A {Homo sapiens} Length = 427

 Score = 46.3 bits (109), Expect = 5e-06
 Identities = 22/84 (26%), Positives = 41/84 (48%)

Query: 179 ERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEK 238
            +   +R K K    KE E++  EK +  KK  + EKKK + KK+   ++    K++K  
Sbjct: 343 RQMFVQRVKEKEAELKEAEKELHEKFDRLKKLHQDEKKKLEDKKKSLDDEVNAFKQRKTA 402

Query: 239 KKKKKEKKKKKEEKKKEKKKKKKK 262
            +  + +  +    +  K+ K+KK
Sbjct: 403 AELLQSQGSQAGGSQTLKRDKEKK 426

>2qag_B Septin-6, protein NEDD5; cell cycle, cell division, GTP-binding, nucleotide-binding, phosphorylation, acetylation, alternative splicing, coiled coil; HET: GDP GTP; 4.00A {Homo sapiens} Length = 427

 Score = 46.3 bits (109), Expect = 5e-06
 Identities = 25/90 (27%), Positives = 45/90 (50%)

Query: 177 KKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKK 236
           KKE   ++   ++ K K+ E ++ E++  EK    KK  + EKKK E KK+    +    
Sbjct: 337 KKEEEMRQMFVQRVKEKEAELKEAEKELHEKFDRLKKLHQDEKKKLEDKKKSLDDEVNAF 396

Query: 237 EKKKKKKEKKKKKEEKKKEKKKKKKKKEKK 266
           +++K   E  + +  +    +  K+ KEKK
Sbjct: 397 KQRKTAAELLQSQGSQAGGSQTLKRDKEKK 426

>2qag_B Septin-6, protein NEDD5; cell cycle, cell division, GTP-binding, nucleotide-binding, phosphorylation, acetylation, alternative splicing, coiled coil; HET: GDP GTP; 4.00A {Homo sapiens} Length = 427

 Score = 45.9 bits (108), Expect = 7e-06
 Identities = 27/107 (25%), Positives = 52/107 (48%)

Query: 169 LEYGYKGGKKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEK 228
           LE           K    +   + K+ E   E +KKEE+ ++   ++ KEK+ + K+ EK
Sbjct: 303 LEEMGFKDTDPDSKPFSLQETYEAKRNEFLGELQKKEEEMRQMFVQRVKEKEAELKEAEK 362

Query: 229 KKKKKKKKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDEGRRR 275
           +  +K  + KK  + EKKK +++KK    +    K++K   +  + +
Sbjct: 363 ELHEKFDRLKKLHQDEKKKLEDKKKSLDDEVNAFKQRKTAAELLQSQ 409

>2qag_B Septin-6, protein NEDD5; cell cycle, cell division, GTP-binding, nucleotide-binding, phosphorylation, acetylation, alternative splicing, coiled coil; HET: GDP GTP; 4.00A {Homo sapiens} Length = 427

 Score = 45.5 bits (107), Expect = 9e-06
 Identities = 20/95 (21%), Positives = 51/95 (53%)

Query: 177 KKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKK 236
               ++    KR     + ++++EE ++   ++ K+KE + ++ +KE  ++  + KK  +
Sbjct: 317 PFSLQETYEAKRNEFLGELQKKEEEMRQMFVQRVKEKEAELKEAEKELHEKFDRLKKLHQ 376

Query: 237 EKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDE 271
           ++KKK ++KKK  +++    K++K   E  + +  
Sbjct: 377 DEKKKLEDKKKSLDDEVNAFKQRKTAAELLQSQGS 411

>2qag_B Septin-6, protein NEDD5; cell cycle, cell division, GTP-binding, nucleotide-binding, phosphorylation, acetylation, alternative splicing, coiled coil; HET: GDP GTP; 4.00A {Homo sapiens} Length = 427

 Score = 45.1 bits (106), Expect = 1e-05
 Identities = 23/103 (22%), Positives = 51/103 (49%)

Query: 173 YKGGKKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKK 232
           Y+  K E    +      K    +E  E ++ E   + +KKE++  +   ++ KEK+ + 
Sbjct: 298 YRRCKLEEMGFKDTDPDSKPFSLQETYEAKRNEFLGELQKKEEEMRQMFVQRVKEKEAEL 357

Query: 233 KKKKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDEGRRR 275
           K+ +++  +K ++ KK  + +K+K + KKK    +     +R+
Sbjct: 358 KEAEKELHEKFDRLKKLHQDEKKKLEDKKKSLDDEVNAFKQRK 400

>2qag_B Septin-6, protein NEDD5; cell cycle, cell division, GTP-binding, nucleotide-binding, phosphorylation, acetylation, alternative splicing, coiled coil; HET: GDP GTP; 4.00A {Homo sapiens} Length = 427

 Score = 44.7 bits (105), Expect = 2e-05
 Identities = 21/94 (22%), Positives = 49/94 (52%), Gaps = 2/94 (2%)

Query: 177 KKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKK--KK 234
            + ++K+   ++   ++ +E+E E ++ E++  EK    KK  + ++KK E KKK    +
Sbjct: 333 GELQKKEEEMRQMFVQRVKEKEAELKEAEKELHEKFDRLKKLHQDEKKKLEDKKKSLDDE 392

Query: 235 KKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKK 268
               K++K   +  + +  +    +  K++K+KK
Sbjct: 393 VNAFKQRKTAAELLQSQGSQAGGSQTLKRDKEKK 426

>2qag_B Septin-6, protein NEDD5; cell cycle, cell division, GTP-binding, nucleotide-binding, phosphorylation, acetylation, alternative splicing, coiled coil; HET: GDP GTP; 4.00A {Homo sapiens} Length = 427

 Score = 40.1 bits (93), Expect = 5e-04
 Identities = 14/75 (18%), Positives = 36/75 (48%)

Query: 170 EYGYKGGKKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKK 229
           E   +  + E+    +  R +K  ++E++K E+KK+    E    K+++   +  + +  
Sbjct: 352 EKEAELKEAEKELHEKFDRLKKLHQDEKKKLEDKKKSLDDEVNAFKQRKTAAELLQSQGS 411

Query: 230 KKKKKKKEKKKKKKE 244
           +    +  K+ K+K+
Sbjct: 412 QAGGSQTLKRDKEKK 426

>3kio_B Ribonuclease H2 subunit B; aicardi-goutieres syndrome, RNAse H2, protein complex, autoimmune disease, endonuclease, hydrolase, metal-binding; 2.90A {Mus musculus} PDB: 3p5j_B 3puf_B 3p56_B Length = 332

 Score = 45.2 bits (106), Expect = 9e-06
 Identities = 19/82 (23%), Positives = 27/82 (32%), Gaps = 6/82 (7%)

Query: 194 KEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKK 253
            +  +  E          KK K  ++  + K+   K   K  K  KK  K    +K   K
Sbjct: 250 SKFLKLPEPPASLPNPPSKKLKLSDEPVEAKEDYTKFNTKDLKTGKKNSKMTAAQKALAK 309

Query: 254 KEKKKKK------KKKEKKKKK 269
            +K   K        K KK  K
Sbjct: 310 VDKSGMKSIDAFFGAKNKKTGK 331

>3kio_B Ribonuclease H2 subunit B; aicardi-goutieres syndrome, RNAse H2, protein complex, autoimmune disease, endonuclease, hydrolase, metal-binding; 2.90A {Mus musculus} PDB: 3p5j_B 3puf_B 3p56_B Length = 332

 Score = 44.4 bits (104), Expect = 2e-05
 Identities = 18/82 (21%), Positives = 26/82 (31%), Gaps = 2/82 (2%)

Query: 187 KRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKK 246
            +  K  +          ++ K   +  + KE   K   K+ K  KK  K    +K   K
Sbjct: 250 SKFLKLPEPPASLPNPPSKKLKLSDEPVEAKEDYTKFNTKDLKTGKKNSKMTAAQKALAK 309

Query: 247 KKKEEKKKEKK--KKKKKKEKK 266
             K   K        K KK  K
Sbjct: 310 VDKSGMKSIDAFFGAKNKKTGK 331

>3kio_B Ribonuclease H2 subunit B; aicardi-goutieres syndrome, RNAse H2, protein complex, autoimmune disease, endonuclease, hydrolase, metal-binding; 2.90A {Mus musculus} PDB: 3p5j_B 3puf_B 3p56_B Length = 332

 Score = 42.1 bits (98), Expect = 9e-05
 Identities = 22/97 (22%), Positives = 33/97 (34%), Gaps = 5/97 (5%)

Query: 155 DLKREWLWGGCGDNLEYGYKGGKKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKE 214
            L  +++     D+L    K  +          +K K   E  E +E+  +   K+ K  
Sbjct: 235 GLISDYIPKELSDDLSKFLKLPEPPASLPNPPSKKLKLSDEPVEAKEDYTKFNTKDLKTG 294

Query: 215 KKKEKKKKEKKKEKKKKKKKKKE-----KKKKKKEKK 246
           KK  K    +K   K  K   K        K KK  K
Sbjct: 295 KKNSKMTAAQKALAKVDKSGMKSIDAFFGAKNKKTGK 331

>3kio_B Ribonuclease H2 subunit B; aicardi-goutieres syndrome, RNAse H2, protein complex, autoimmune disease, endonuclease, hydrolase, metal-binding; 2.90A {Mus musculus} PDB: 3p5j_B 3puf_B 3p56_B Length = 332

 Score = 41.4 bits (96), Expect = 2e-04
 Identities = 14/82 (17%), Positives = 28/82 (34%), Gaps = 3/82 (3%)

Query: 182 KQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKK 241
            +  +  +          ++ K  ++  E K++  K   K  K  +K  K    ++   K
Sbjct: 250 SKFLKLPEPPASLPNPPSKKLKLSDEPVEAKEDYTKFNTKDLKTGKKNSKMTAAQKALAK 309

Query: 242 KKEKKKKKEE---KKKEKKKKK 260
             +   K  +     K KK  K
Sbjct: 310 VDKSGMKSIDAFFGAKNKKTGK 331

>3kio_B Ribonuclease H2 subunit B; aicardi-goutieres syndrome, RNAse H2, protein complex, autoimmune disease, endonuclease, hydrolase, metal-binding; 2.90A {Mus musculus} PDB: 3p5j_B 3puf_B 3p56_B Length = 332

 Score = 39.4 bits (91), Expect = 7e-04
 Identities = 18/74 (24%), Positives = 27/74 (36%)

Query: 196 EEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKKKE 255
           +E  ++  K  K  E          KK K  ++  + K+   K   K  K  KK  K   
Sbjct: 243 KELSDDLSKFLKLPEPPASLPNPPSKKLKLSDEPVEAKEDYTKFNTKDLKTGKKNSKMTA 302

Query: 256 KKKKKKKKEKKKKK 269
            +K   K +K   K
Sbjct: 303 AQKALAKVDKSGMK 316

>2qag_C Septin-7; cell cycle, cell division, GTP-binding, nucleotide-binding, phosphorylation, acetylation, alternative splicing, coiled coil; HET: GDP GTP; 4.00A {Homo sapiens} Length = 418

 Score = 45.2 bits (106), Expect = 1e-05
 Identities = 21/97 (21%), Positives = 56/97 (57%)

Query: 177 KKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKK 236
            +E R++   K K+   + E+  E + KE+ +K K  E + +++ ++ KK  + + K+ +
Sbjct: 320 MEEERREHVAKMKKMEMEMEQVFEMKVKEKVQKLKDSEAELQRRHEQMKKNLEAQHKELE 379

Query: 237 EKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDEGR 273
           EK+++ +++K   E +++  +++   +  +K K +G+
Sbjct: 380 EKRRQFEDEKANWEAQQRILEQQNSSRTLEKNKKKGK 416

>2qag_C Septin-7; cell cycle, cell division, GTP-binding, nucleotide-binding, phosphorylation, acetylation, alternative splicing, coiled coil; HET: GDP GTP; 4.00A {Homo sapiens} Length = 418

 Score = 41.0 bits (95), Expect = 3e-04
 Identities = 27/93 (29%), Positives = 52/93 (55%), Gaps = 1/93 (1%)

Query: 184 RRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKK-KKKKKEKKKKK 242
             + + +  K    + EEE++E   K KK E + E+  + K KEK +K K  + E +++ 
Sbjct: 305 NNKNKGQLTKSPLAQMEEERREHVAKMKKMEMEMEQVFEMKVKEKVQKLKDSEAELQRRH 364

Query: 243 KEKKKKKEEKKKEKKKKKKKKEKKKKKDEGRRR 275
           ++ KK  E + KE ++K+++ E +K   E ++R
Sbjct: 365 EQMKKNLEAQHKELEEKRRQFEDEKANWEAQQR 397

>3lvh_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic vesicle, membrane, Ca structural protein; 9.00A {Bos taurus} Length = 205

 Score = 44.1 bits (103), Expect = 1e-05
 Identities = 14/74 (18%), Positives = 37/74 (50%)

Query: 191 KRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKE 250
            R  +E E   + +EE++K  ++     K  +++ +EK KK  ++  +++ ++ +K K  
Sbjct: 93  DRLTQEPESIRKWREEQRKRLQELDAASKVMEQEWREKAKKDLEEWNQRQSEQVEKNKIN 152

Query: 251 EKKKEKKKKKKKKE 264
            +  +K   ++   
Sbjct: 153 NRIADKAFYQQPDA 166

>3lvh_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic vesicle, membrane, Ca structural protein; 9.00A {Bos taurus} Length = 205

 Score = 43.0 bits (100), Expect = 3e-05
 Identities = 12/57 (21%), Positives = 34/57 (59%)

Query: 183 QRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKK 239
           ++ R+ +RKR +E +   +  ++E +++ KK+ ++  +++ ++ EK K   +  +K 
Sbjct: 103 RKWREEQRKRLQELDAASKVMEQEWREKAKKDLEEWNQRQSEQVEKNKINNRIADKA 159

>3lvh_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic vesicle, membrane, Ca structural protein; 9.00A {Bos taurus} Length = 205

 Score = 41.8 bits (97), Expect = 8e-05
 Identities = 13/76 (17%), Positives = 38/76 (50%)

Query: 195 EEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKKK 254
            +   +E +   K +E+++++ +E     K  E++ ++K KK+ ++  + + ++ E+ K 
Sbjct: 92  ADRLTQEPESIRKWREEQRKRLQELDAASKVMEQEWREKAKKDLEEWNQRQSEQVEKNKI 151

Query: 255 EKKKKKKKKEKKKKKD 270
             +   K   ++   D
Sbjct: 152 NNRIADKAFYQQPDAD 167

>3lvh_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic vesicle, membrane, Ca structural protein; 9.00A {Bos taurus} Length = 205

 Score = 39.9 bits (92), Expect = 3e-04
 Identities = 11/86 (12%), Positives = 37/86 (43%)

Query: 166 GDNLEYGYKGGKKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKK 225
           G    Y          ++    RK + ++ +  +E +   +  +++ +EK K+  ++  +
Sbjct: 81  GPADGYAAIAQADRLTQEPESIRKWREEQRKRLQELDAASKVMEQEWREKAKKDLEEWNQ 140

Query: 226 KEKKKKKKKKKEKKKKKKEKKKKKEE 251
           ++ ++ +K K   +   K   ++ + 
Sbjct: 141 RQSEQVEKNKINNRIADKAFYQQPDA 166

>3lvh_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic vesicle, membrane, Ca structural protein; 9.00A {Bos taurus} Length = 205

 Score = 39.9 bits (92), Expect = 4e-04
 Identities = 10/71 (14%), Positives = 37/71 (52%), Gaps = 1/71 (1%)

Query: 196 EEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKKKE 255
            +     ++ E  ++ ++E++K  ++ +    K  +++ +++ KK  +E  +++ E+ ++
Sbjct: 90  AQADRLTQEPESIRKWREEQRKRLQELDAA-SKVMEQEWREKAKKDLEEWNQRQSEQVEK 148

Query: 256 KKKKKKKKEKK 266
            K   +  +K 
Sbjct: 149 NKINNRIADKA 159

>2zjr_S 50S ribosomal protein L25; ribosome, large ribosomal subunit, ribonucleoprotein, RNA-binding, rRNA-binding, tRNA-binding, methylation; 2.91A {Deinococcus radiodurans} SCOP: b.53.1.1 PDB: 1njm_T* 1nwx_T* 1njp_T* 1xbp_T* 2zjp_S* 2zjq_S 1nwy_T 3cf5_S* 3dll_S* 3pio_S* 3pip_S* 1nkw_T 1sm1_T* 1yl3_V 2b66_Z 2b9n_Z 2b9p_Z 1pnu_T 1pny_T 1vor_W ... Length = 237

 Score = 44.0 bits (104), Expect = 2e-05
 Identities = 5/56 (8%), Positives = 18/56 (32%)

Query: 194 KEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKK 249
           + E +  +        E  +E  +   + +   E+ K +  +       ++    +
Sbjct: 182 EAEVQAAQVAGLVAAGELSEEAAEAVLEGDASLEEVKAEASEDNAGTDSEDNSDAQ 237

>2zjr_S 50S ribosomal protein L25; ribosome, large ribosomal subunit, ribonucleoprotein, RNA-binding, rRNA-binding, tRNA-binding, methylation; 2.91A {Deinococcus radiodurans} SCOP: b.53.1.1 PDB: 1njm_T* 1nwx_T* 1njp_T* 1xbp_T* 2zjp_S* 2zjq_S 1nwy_T 3cf5_S* 3dll_S* 3pio_S* 3pip_S* 1nkw_T 1sm1_T* 1yl3_V 2b66_Z 2b9n_Z 2b9p_Z 1pnu_T 1pny_T 1vor_W ... Length = 237

 Score = 44.0 bits (104), Expect = 2e-05
 Identities = 7/60 (11%), Positives = 20/60 (33%)

Query: 194 KEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKK 253
            EE E E +  +        E  +E  +   + +   ++ K +  +       +   + +
Sbjct: 178 AEELEAEVQAAQVAGLVAAGELSEEAAEAVLEGDASLEEVKAEASEDNAGTDSEDNSDAQ 237

>2zjr_S 50S ribosomal protein L25; ribosome, large ribosomal subunit, ribonucleoprotein, RNA-binding, rRNA-binding, tRNA-binding, methylation; 2.91A {Deinococcus radiodurans} SCOP: b.53.1.1 PDB: 1njm_T* 1nwx_T* 1njp_T* 1xbp_T* 2zjp_S* 2zjq_S 1nwy_T 3cf5_S* 3dll_S* 3pio_S* 3pip_S* 1nkw_T 1sm1_T* 1yl3_V 2b66_Z 2b9n_Z 2b9p_Z 1pnu_T 1pny_T 1vor_W ... Length = 237

 Score = 43.2 bits (102), Expect = 3e-05
 Identities = 7/63 (11%), Positives = 19/63 (30%)

Query: 188 RKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKK 247
           R    + E E +  +        +  E+  E   +     ++ K +  ++      E   
Sbjct: 175 RLTAEELEAEVQAAQVAGLVAAGELSEEAAEAVLEGDASLEEVKAEASEDNAGTDSEDNS 234

Query: 248 KKE 250
             +
Sbjct: 235 DAQ 237

>2zjr_S 50S ribosomal protein L25; ribosome, large ribosomal subunit, ribonucleoprotein, RNA-binding, rRNA-binding, tRNA-binding, methylation; 2.91A {Deinococcus radiodurans} SCOP: b.53.1.1 PDB: 1njm_T* 1nwx_T* 1njp_T* 1xbp_T* 2zjp_S* 2zjq_S 1nwy_T 3cf5_S* 3dll_S* 3pio_S* 3pip_S* 1nkw_T 1sm1_T* 1yl3_V 2b66_Z 2b9n_Z 2b9p_Z 1pnu_T 1pny_T 1vor_W ... Length = 237

 Score = 43.2 bits (102), Expect = 3e-05
 Identities = 7/63 (11%), Positives = 19/63 (30%)

Query: 192 RKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEE 251
           R   EE + E +  +        +  E+  +   +     ++ K E  +       +   
Sbjct: 175 RLTAEELEAEVQAAQVAGLVAAGELSEEAAEAVLEGDASLEEVKAEASEDNAGTDSEDNS 234

Query: 252 KKK 254
             +
Sbjct: 235 DAQ 237

>2zjr_S 50S ribosomal protein L25; ribosome, large ribosomal subunit, ribonucleoprotein, RNA-binding, rRNA-binding, tRNA-binding, methylation; 2.91A {Deinococcus radiodurans} SCOP: b.53.1.1 PDB: 1njm_T* 1nwx_T* 1njp_T* 1xbp_T* 2zjp_S* 2zjq_S 1nwy_T 3cf5_S* 3dll_S* 3pio_S* 3pip_S* 1nkw_T 1sm1_T* 1yl3_V 2b66_Z 2b9n_Z 2b9p_Z 1pnu_T 1pny_T 1vor_W ... Length = 237

 Score = 42.4 bits (100), Expect = 6e-05
 Identities = 4/63 (6%), Positives = 21/63 (33%)

Query: 190 RKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKK 249
           R   +E E + +  +        +  ++  +   +     ++ K +  +     + +   
Sbjct: 175 RLTAEELEAEVQAAQVAGLVAAGELSEEAAEAVLEGDASLEEVKAEASEDNAGTDSEDNS 234

Query: 250 EEK 252
           + +
Sbjct: 235 DAQ 237

>2zjr_S 50S ribosomal protein L25; ribosome, large ribosomal subunit, ribonucleoprotein, RNA-binding, rRNA-binding, tRNA-binding, methylation; 2.91A {Deinococcus radiodurans} SCOP: b.53.1.1 PDB: 1njm_T* 1nwx_T* 1njp_T* 1xbp_T* 2zjp_S* 2zjq_S 1nwy_T 3cf5_S* 3dll_S* 3pio_S* 3pip_S* 1nkw_T 1sm1_T* 1yl3_V 2b66_Z 2b9n_Z 2b9p_Z 1pnu_T 1pny_T 1vor_W ... Length = 237

 Score = 42.0 bits (99), Expect = 8e-05
 Identities = 7/63 (11%), Positives = 20/63 (31%)

Query: 193 KKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEK 252
           +   EE E E +  +        +  ++  E   E     ++ K +  +       ++  
Sbjct: 175 RLTAEELEAEVQAAQVAGLVAAGELSEEAAEAVLEGDASLEEVKAEASEDNAGTDSEDNS 234

Query: 253 KKE 255
             +
Sbjct: 235 DAQ 237

>2zjr_S 50S ribosomal protein L25; ribosome, large ribosomal subunit, ribonucleoprotein, RNA-binding, rRNA-binding, tRNA-binding, methylation; 2.91A {Deinococcus radiodurans} SCOP: b.53.1.1 PDB: 1njm_T* 1nwx_T* 1njp_T* 1xbp_T* 2zjp_S* 2zjq_S 1nwy_T 3cf5_S* 3dll_S* 3pio_S* 3pip_S* 1nkw_T 1sm1_T* 1yl3_V 2b66_Z 2b9n_Z 2b9p_Z 1pnu_T 1pny_T 1vor_W ... Length = 237

 Score = 40.1 bits (94), Expect = 3e-04
 Identities = 7/61 (11%), Positives = 19/61 (31%)

Query: 198 EKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKKKEKK 257
             EE + E +  +        +  +E  +   +     +E K +  E     + +     
Sbjct: 177 TAEELEAEVQAAQVAGLVAAGELSEEAAEAVLEGDASLEEVKAEASEDNAGTDSEDNSDA 236

Query: 258 K 258
           +
Sbjct: 237 Q 237

>1qy5_A Endoplasmin; GRP94, NECA, HSP90, chaperone; HET: NEC; 1.75A {Canis lupus familiaris} SCOP: d.122.1.1 PDB: 1qy8_A* 1qye_A* 1u0y_A* 1yt2_A* Length = 269

 Score = 44.1 bits (105), Expect = 2e-05
 Identities = 16/47 (34%), Positives = 28/47 (59%)

Query: 193 KKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKK 239
             + E  EE  +EE+  +++KE   ++   E+++E+KK K KK EK 
Sbjct: 215 SSKTETVEEPMEEEEAAKEEKEDSDDEAAVEEEEEEKKPKTKKVEKT 261

>1qy5_A Endoplasmin; GRP94, NECA, HSP90, chaperone; HET: NEC; 1.75A {Canis lupus familiaris} SCOP: d.122.1.1 PDB: 1qy8_A* 1qye_A* 1u0y_A* 1yt2_A* Length = 269

 Score = 43.7 bits (104), Expect = 2e-05
 Identities = 15/49 (30%), Positives = 28/49 (57%)

Query: 189 KRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKE 237
            +    EE  +EEE  +E+K++   E   E++++EKK + KK +K   +
Sbjct: 216 SKTETVEEPMEEEEAAKEEKEDSDDEAAVEEEEEEKKPKTKKVEKTVWD 264

>1qy5_A Endoplasmin; GRP94, NECA, HSP90, chaperone; HET: NEC; 1.75A {Canis lupus familiaris} SCOP: d.122.1.1 PDB: 1qy8_A* 1qye_A* 1u0y_A* 1yt2_A* Length = 269

 Score = 42.6 bits (101), Expect = 5e-05
 Identities = 14/46 (30%), Positives = 27/46 (58%)

Query: 198 EKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKK 243
            K E  +E  ++E+  +++KE    E   E+++++KK K KK +K 
Sbjct: 216 SKTETVEEPMEEEEAAKEEKEDSDDEAAVEEEEEEKKPKTKKVEKT 261

>1qy5_A Endoplasmin; GRP94, NECA, HSP90, chaperone; HET: NEC; 1.75A {Canis lupus familiaris} SCOP: d.122.1.1 PDB: 1qy8_A* 1qye_A* 1u0y_A* 1yt2_A* Length = 269

 Score = 41.8 bits (99), Expect = 1e-04
 Identities = 11/49 (22%), Positives = 28/49 (57%)

Query: 196 EEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKE 244
            + +  E+  E+++  K+EK+    +   ++E+++KK K K+ +K   +
Sbjct: 216 SKTETVEEPMEEEEAAKEEKEDSDDEAAVEEEEEEKKPKTKKVEKTVWD 264

>1qy5_A Endoplasmin; GRP94, NECA, HSP90, chaperone; HET: NEC; 1.75A {Canis lupus familiaris} SCOP: d.122.1.1 PDB: 1qy8_A* 1qye_A* 1u0y_A* 1yt2_A* Length = 269

 Score = 41.0 bits (97), Expect = 2e-04
 Identities = 9/47 (19%), Positives = 28/47 (59%)

Query: 213 KEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKKKEKKKK 259
             K +  ++  +++E  K++K+  + +   +E++++K+ K K+ +K 
Sbjct: 215 SSKTETVEEPMEEEEAAKEEKEDSDDEAAVEEEEEEKKPKTKKVEKT 261

>1qy5_A Endoplasmin; GRP94, NECA, HSP90, chaperone; HET: NEC; 1.75A {Canis lupus familiaris} SCOP: d.122.1.1 PDB: 1qy8_A* 1qye_A* 1u0y_A* 1yt2_A* Length = 269

 Score = 41.0 bits (97), Expect = 2e-04
 Identities = 13/49 (26%), Positives = 29/49 (59%)

Query: 203 KKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEE 251
            K E  +E  +E++  K++KE   ++   +++++EKK K K+ +K   +
Sbjct: 216 SKTETVEEPMEEEEAAKEEKEDSDDEAAVEEEEEEKKPKTKKVEKTVWD 264

>1qy5_A Endoplasmin; GRP94, NECA, HSP90, chaperone; HET: NEC; 1.75A {Canis lupus familiaris} SCOP: d.122.1.1 PDB: 1qy8_A* 1qye_A* 1u0y_A* 1yt2_A* Length = 269

 Score = 40.7 bits (96), Expect = 2e-04
 Identities = 10/49 (20%), Positives = 29/49 (59%)

Query: 202 EKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKE 250
            K E  ++  ++E+  +++K++   E   +++++++K K KK +K   +
Sbjct: 216 SKTETVEEPMEEEEAAKEEKEDSDDEAAVEEEEEEKKPKTKKVEKTVWD 264

>1qy5_A Endoplasmin; GRP94, NECA, HSP90, chaperone; HET: NEC; 1.75A {Canis lupus familiaris} SCOP: d.122.1.1 PDB: 1qy8_A* 1qye_A* 1u0y_A* 1yt2_A* Length = 269

 Score = 40.3 bits (95), Expect = 4e-04
 Identities = 11/45 (24%), Positives = 27/45 (60%)

Query: 187 KRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKK 231
           K +   +  EEE+  ++++E   ++   +++E++KK K K+ +K 
Sbjct: 217 KTETVEEPMEEEEAAKEEKEDSDDEAAVEEEEEEKKPKTKKVEKT 261

>1qy5_A Endoplasmin; GRP94, NECA, HSP90, chaperone; HET: NEC; 1.75A {Canis lupus familiaris} SCOP: d.122.1.1 PDB: 1qy8_A* 1qye_A* 1u0y_A* 1yt2_A* Length = 269

 Score = 39.9 bits (94), Expect = 4e-04
 Identities = 15/45 (33%), Positives = 26/45 (57%)

Query: 186 RKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKK 230
           +    +   EEEE  +E+KE+   E   E+++E+KK + KK +K 
Sbjct: 217 KTETVEEPMEEEEAAKEEKEDSDDEAAVEEEEEEKKPKTKKVEKT 261

>1qy5_A Endoplasmin; GRP94, NECA, HSP90, chaperone; HET: NEC; 1.75A {Canis lupus familiaris} SCOP: d.122.1.1 PDB: 1qy8_A* 1qye_A* 1u0y_A* 1yt2_A* Length = 269

 Score = 39.5 bits (93), Expect = 5e-04
 Identities = 13/47 (27%), Positives = 28/47 (59%)

Query: 220 KKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKK 266
             K +  E+  ++++  +++K+  + +   EE+++EKK K KK EK 
Sbjct: 215 SSKTETVEEPMEEEEAAKEEKEDSDDEAAVEEEEEEKKPKTKKVEKT 261

>1qy5_A Endoplasmin; GRP94, NECA, HSP90, chaperone; HET: NEC; 1.75A {Canis lupus familiaris} SCOP: d.122.1.1 PDB: 1qy8_A* 1qye_A* 1u0y_A* 1yt2_A* Length = 269

 Score = 39.5 bits (93), Expect = 6e-04
 Identities = 9/47 (19%), Positives = 28/47 (59%)

Query: 222 KEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKK 268
             K +  ++  ++++  K++K++   +   +++E++KK K K+ +K 
Sbjct: 215 SSKTETVEEPMEEEEAAKEEKEDSDDEAAVEEEEEEKKPKTKKVEKT 261

>1a31_A Protein (topoisomerase I); topoisomerase I/DNA, DNA, isomerase/DNA complex; HET: DNA 5IU PTR; 2.10A {Homo sapiens} SCOP: d.163.1.2 e.15.1.1 PDB: 1k4t_A* 1k4s_A* 1sc7_A* 1t8i_A* 1tl8_A* 1seu_A* 1a35_A* 1a36_A* 1r49_A* 1rrj_A* 1nh3_A* 1lpq_A* 1rr8_C* 1ej9_A* Length = 591

 Score = 44.0 bits (103), Expect = 3e-05
 Identities = 18/86 (20%), Positives = 40/86 (46%)

Query: 186 RKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEK 245
            +R   +  E+     + K + KKE+  + +++ K  +   +  K  K KK  + KKK  
Sbjct: 458 HQRAPPKTFEKSMMNLQTKIDAKKEQLADARRDLKSAKADAKVMKDAKTKKVVESKKKAV 517

Query: 246 KKKKEEKKKEKKKKKKKKEKKKKKDE 271
           ++ +E+  K + +   ++E K+    
Sbjct: 518 QRLEEQLMKLEVQATDREENKQIALG 543

>1a31_A Protein (topoisomerase I); topoisomerase I/DNA, DNA, isomerase/DNA complex; HET: DNA 5IU PTR; 2.10A {Homo sapiens} SCOP: d.163.1.2 e.15.1.1 PDB: 1k4t_A* 1k4s_A* 1sc7_A* 1t8i_A* 1tl8_A* 1seu_A* 1a35_A* 1a36_A* 1r49_A* 1rrj_A* 1nh3_A* 1lpq_A* 1rr8_C* 1ej9_A* Length = 591

 Score = 43.2 bits (101), Expect = 5e-05
 Identities = 15/87 (17%), Positives = 39/87 (44%)

Query: 182 KQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKK 241
           ++     + K   ++E+  + +++ K  +   +  K+ K K+  + KKK  ++ +E+  K
Sbjct: 467 EKSMMNLQTKIDAKKEQLADARRDLKSAKADAKVMKDAKTKKVVESKKKAVQRLEEQLMK 526

Query: 242 KKEKKKKKEEKKKEKKKKKKKKEKKKK 268
            + +   +EE K+      K      +
Sbjct: 527 LEVQATDREENKQIALGTSKLNYLDPR 553

>1a31_A Protein (topoisomerase I); topoisomerase I/DNA, DNA, isomerase/DNA complex; HET: DNA 5IU PTR; 2.10A {Homo sapiens} SCOP: d.163.1.2 e.15.1.1 PDB: 1k4t_A* 1k4s_A* 1sc7_A* 1t8i_A* 1tl8_A* 1seu_A* 1a35_A* 1a36_A* 1r49_A* 1rrj_A* 1nh3_A* 1lpq_A* 1rr8_C* 1ej9_A* Length = 591

 Score = 42.0 bits (98), Expect = 1e-04
 Identities = 14/75 (18%), Positives = 34/75 (45%)

Query: 197 EEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKKKEK 256
           + K+E+  + ++  K  +   +  K  K K+  + KKK  ++ +++  K + +   ++E 
Sbjct: 478 DAKKEQLADARRDLKSAKADAKVMKDAKTKKVVESKKKAVQRLEEQLMKLEVQATDREEN 537

Query: 257 KKKKKKKEKKKKKDE 271
           K+      K    D 
Sbjct: 538 KQIALGTSKLNYLDP 552

>1a31_A Protein (topoisomerase I); topoisomerase I/DNA, DNA, isomerase/DNA complex; HET: DNA 5IU PTR; 2.10A {Homo sapiens} SCOP: d.163.1.2 e.15.1.1 PDB: 1k4t_A* 1k4s_A* 1sc7_A* 1t8i_A* 1tl8_A* 1seu_A* 1a35_A* 1a36_A* 1r49_A* 1rrj_A* 1nh3_A* 1lpq_A* 1rr8_C* 1ej9_A* Length = 591

 Score = 41.7 bits (97), Expect = 2e-04
 Identities = 19/83 (22%), Positives = 36/83 (43%)

Query: 187 KRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKK 246
           K   K     + K + KKE+    ++  K  +   K  K  K KK  + K+K  ++ E++
Sbjct: 464 KTFEKSMMNLQTKIDAKKEQLADARRDLKSAKADAKVMKDAKTKKVVESKKKAVQRLEEQ 523

Query: 247 KKKEEKKKEKKKKKKKKEKKKKK 269
             K E +   +++ K+      K
Sbjct: 524 LMKLEVQATDREENKQIALGTSK 546

>1a31_A Protein (topoisomerase I); topoisomerase I/DNA, DNA, isomerase/DNA complex; HET: DNA 5IU PTR; 2.10A {Homo sapiens} SCOP: d.163.1.2 e.15.1.1 PDB: 1k4t_A* 1k4s_A* 1sc7_A* 1t8i_A* 1tl8_A* 1seu_A* 1a35_A* 1a36_A* 1r49_A* 1rrj_A* 1nh3_A* 1lpq_A* 1rr8_C* 1ej9_A* Length = 591

 Score = 41.3 bits (96), Expect = 3e-04
 Identities = 16/85 (18%), Positives = 36/85 (42%)

Query: 178 KERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKE 237
             +  ++     + +   ++E+  + + + K  K   K  +  K +K  E KKK  ++ E
Sbjct: 462 PPKTFEKSMMNLQTKIDAKKEQLADARRDLKSAKADAKVMKDAKTKKVVESKKKAVQRLE 521

Query: 238 KKKKKKEKKKKKEEKKKEKKKKKKK 262
           ++  K E +    E+ K+      K
Sbjct: 522 EQLMKLEVQATDREENKQIALGTSK 546

>1a31_A Protein (topoisomerase I); topoisomerase I/DNA, DNA, isomerase/DNA complex; HET: DNA 5IU PTR; 2.10A {Homo sapiens} SCOP: d.163.1.2 e.15.1.1 PDB: 1k4t_A* 1k4s_A* 1sc7_A* 1t8i_A* 1tl8_A* 1seu_A* 1a35_A* 1a36_A* 1r49_A* 1rrj_A* 1nh3_A* 1lpq_A* 1rr8_C* 1ej9_A* Length = 591

 Score = 40.5 bits (94), Expect = 4e-04
 Identities = 16/95 (16%), Positives = 44/95 (46%)

Query: 179 ERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEK 238
           +R   +  ++     + + + ++E+  + +++ K  K   K  K+ K +K  + KKK  +
Sbjct: 459 QRAPPKTFEKSMMNLQTKIDAKKEQLADARRDLKSAKADAKVMKDAKTKKVVESKKKAVQ 518

Query: 239 KKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDEGR 273
           + +++  K + +   +E+ K+      K    + R
Sbjct: 519 RLEEQLMKLEVQATDREENKQIALGTSKLNYLDPR 553

>2p4f_A Similar to SP|P32453 saccharomyces cerevisiae YNL ATP11; half barrel, chaperone; HET: P6G; 1.40A {Candida glabrata cbs 138} Length = 299

 Score = 42.0 bits (98), Expect = 1e-04
 Identities = 24/85 (28%), Positives = 37/85 (43%), Gaps = 1/85 (1%)

Query: 185 RRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKE 244
           + K  +K K E  E  EE K ++  ++ +EKKKE  K +  +E ++           K+ 
Sbjct: 18  KEKLLQKAKAEGVESIEELK-KRLADQIEEKKKELNKIDPLRELEQHLNAGSRIHTNKEH 76

Query: 245 KKKKKEEKKKEKKKKKKKKEKKKKK 269
           K  K   K  EK      K+K  K 
Sbjct: 77  KTTKMSNKSNEKSGNVLPKDKPYKT 101

>2y9y_A Imitation switch protein 1 (DEL_ATPase); transcription, nuclear protein complex, chromatin remodeling nucleosome remodeling; 3.25A {Saccharomyces cerevisiae} PDB: 2y9z_A Length = 374

 Score = 41.3 bits (96), Expect = 2e-04
 Identities = 9/81 (11%), Positives = 32/81 (39%)

Query: 191 KRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKE 250
           +++       ++  +++ K++ +  K+ +++   +   +K+     E KK K E      
Sbjct: 293 EKEFNAGIVLDDATKDRMKKEDENGKRIREEFADQTANEKENVDGVESKKAKIEDTSNVG 352

Query: 251 EKKKEKKKKKKKKEKKKKKDE 271
            ++   +K  + +        
Sbjct: 353 TEQLVAEKIPENETTHHHHHH 373

>2y9y_A Imitation switch protein 1 (DEL_ATPase); transcription, nuclear protein complex, chromatin remodeling nucleosome remodeling; 3.25A {Saccharomyces cerevisiae} PDB: 2y9z_A Length = 374

 Score = 39.8 bits (92), Expect = 6e-04
 Identities = 14/97 (14%), Positives = 35/97 (36%)

Query: 178 KERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKE 237
           + R      +R     +  E++           K + KK+++  K  ++E   +   +KE
Sbjct: 274 RSRTPVELARRGNTLLQCLEKEFNAGIVLDDATKDRMKKEDENGKRIREEFADQTANEKE 333

Query: 238 KKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDEGRR 274
                + KK K E+      ++   ++  + +     
Sbjct: 334 NVDGVESKKAKIEDTSNVGTEQLVAEKIPENETTHHH 370

>2efk_A CDC42-interacting protein 4; EFC domain, structural genomics, NPPSFA, national project on structural and functional analyses; 2.30A {Homo sapiens} SCOP: a.238.1.4 Length = 301

 Score = 40.9 bits (95), Expect = 2e-04
 Identities = 15/89 (16%), Positives = 41/89 (46%), Gaps = 2/89 (2%)

Query: 182 KQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKK 241
            +  ++ K++RK   +E    + +++ +   K+ +  K+K E+   + +K  +  E+  +
Sbjct: 101 TKYSQEMKQERKMHFQE--GRRAQQQLENGFKQLENSKRKFERDCREAEKAAQTAERLDQ 158

Query: 242 KKEKKKKKEEKKKEKKKKKKKKEKKKKKD 270
                K   EK K++   +    ++ K +
Sbjct: 159 DINATKADVEKAKQQAHLRSHMAEESKNE 187

>2efk_A CDC42-interacting protein 4; EFC domain, structural genomics, NPPSFA, national project on structural and functional analyses; 2.30A {Homo sapiens} SCOP: a.238.1.4 Length = 301

 Score = 40.9 bits (95), Expect = 3e-04
 Identities = 15/87 (17%), Positives = 40/87 (45%), Gaps = 3/87 (3%)

Query: 180 RRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKK---EKKKKEKKKEKKKKKKKKK 236
            +  +  K++RK   +E  + +++ E   K+ +  K+K   + ++ EK  +  ++  +  
Sbjct: 101 TKYSQEMKQERKMHFQEGRRAQQQLENGFKQLENSKRKFERDCREAEKAAQTAERLDQDI 160

Query: 237 EKKKKKKEKKKKKEEKKKEKKKKKKKK 263
              K   EK K++   +    ++ K +
Sbjct: 161 NATKADVEKAKQQAHLRSHMAEESKNE 187

>3auy_A DNA double-strand break repair RAD50 ATPase; DNA repair, ABC transporter ATPase domain-like; HET: DNA ADP; 2.70A {Methanocaldococcus jannaschii} PDB: 3aux_A* 3av0_B* Length = 371

 Score = 41.0 bits (96), Expect = 3e-04
 Identities = 11/93 (11%), Positives = 32/93 (34%)

Query: 176 GKKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKK 235
           G+   +++  + R ++    E+EKE+  K  +  +K +        +   +EK     +K
Sbjct: 184 GELNYKEESLKARLKEMSNLEKEKEKLTKFVEYLDKVRRIFGRNGFQAYLREKYVPLIQK 243

Query: 236 KEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKK 268
              +   +        +  +  + +        
Sbjct: 244 YLNEAFSEFDLPYSFVELTKDFEVRVHAPNGVL 276

>3auy_A DNA double-strand break repair RAD50 ATPase; DNA repair, ABC transporter ATPase domain-like; HET: DNA ADP; 2.70A {Methanocaldococcus jannaschii} PDB: 3aux_A* 3av0_B* Length = 371

 Score = 40.6 bits (95), Expect = 3e-04
 Identities = 17/86 (19%), Positives = 39/86 (45%)

Query: 190 RKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKK 249
            ++ +   +     + EK  +K  E  KE +K+ ++ E +   K++  K + K+    +K
Sbjct: 146 SEKLETVAKLLGIDEFEKCYQKMGEIVKEYEKRLERIEGELNYKEESLKARLKEMSNLEK 205

Query: 250 EEKKKEKKKKKKKKEKKKKKDEGRRR 275
           E++K  K  +   K ++     G + 
Sbjct: 206 EKEKLTKFVEYLDKVRRIFGRNGFQA 231

>3vkg_A Dynein heavy chain, cytoplasmic; AAA+ protein, molecular motor, microtubles, motor protein; HET: ADP SPM; 2.81A {Dictyostelium discoideum} PDB: 3vkh_A* 3vkh_C* Length = 3245

 Score = 41.0 bits (96), Expect = 4e-04
 Identities = 15/107 (14%), Positives = 38/107 (35%), Gaps = 21/107 (19%)

Query: 184  RRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKK---------------------EKKKK 222
             + ++  + K+++  + + + + + KE   +K K                     E    
Sbjct: 1965 VQDQQAAEIKQKDARELQVQLDVRNKEIAVQKVKAYADLEKAEPTGPLREEVEQLENAAN 2024

Query: 223  EKKKEKKKKKKKKKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKK 269
            E K ++ +        +K     K++     +E ++ K +  K K K
Sbjct: 2025 ELKLKQDEIVATITALEKSIATYKEEYATLIRETEQIKTESSKVKNK 2071

>1kxf_A Sindbis virus capsid protein; chymotrypsin-like serine proteinase, wild type, viral protein; 2.38A {Sindbis virus} SCOP: b.47.1.3 PDB: 1ld4_A 3j0f_A Length = 264

 Score = 40.2 bits (93), Expect = 4e-04
 Identities = 16/88 (18%), Positives = 38/88 (43%)

Query: 180 RRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKK 239
               R R+R++            + ++           +  + +  + +   ++KK+  K
Sbjct: 18  TAMWRPRRRRQAAPMPARNGLASQIQQLTTAVSALVIGQATRPQNPRPRPPPRQKKQAPK 77

Query: 240 KKKKEKKKKKEEKKKEKKKKKKKKEKKK 267
           +  K KK K +EKKK++  K K  ++++
Sbjct: 78  QPPKPKKPKPQEKKKKQPAKTKPGKRQR 105

>2efl_A Formin-binding protein 1; EFC domain, structural genomics, NPPSFA, national project on structural and functional analyses; 2.61A {Homo sapiens} SCOP: a.238.1.4 Length = 305

 Score = 40.1 bits (93), Expect = 5e-04
 Identities = 14/89 (15%), Positives = 40/89 (44%), Gaps = 2/89 (2%)

Query: 182 KQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKK 241
            +  ++ K++RK      +  K ++  +   K+ +  K++ E+  ++  + ++  EK   
Sbjct: 108 ARYVQELKQERKSNFH--DGRKAQQHIETCWKQLESSKRRFERDCKEADRAQQYFEKMDA 165

Query: 242 KKEKKKKKEEKKKEKKKKKKKKEKKKKKD 270
                K   EK +++ + + +  +  K D
Sbjct: 166 DINVTKADVEKARQQAQIRHQMAEDSKAD 194

>4a17_C RPL4, ribosomal protein L3; eukaryotic ribosome, ribosome, eukaryotic initiation factor 60S, translation, large ribosomal subunit; 3.52A {Tetrahymena thermophila} PDB: 4a1a_C 4a1c_C 4a1e_C Length = 410

 Score = 40.2 bits (93), Expect = 5e-04
 Identities = 11/67 (16%), Positives = 29/67 (43%)

Query: 203 KKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKKKEKKKKKKK 262
           K++ KK  +  + K++   K  +K  K  KK  +       +  ++   K +++      
Sbjct: 341 KEQAKKAAEASKAKRQATLKANRKAAKTHKKGSQAWIAAFNKANEEAIAKARQEDADFIA 400

Query: 263 KEKKKKK 269
           + ++ K+
Sbjct: 401 QGQEIKE 407

>2v0o_A FCHO2, FCH domain only protein 2; lipid-binding protein, EFC domain, vesicle trafficking, membrane curvature, endocytosis, exocytosis, F-BAR domain; 2.30A {Homo sapiens} Length = 276

 Score = 39.7 bits (92), Expect = 5e-04
 Identities = 16/88 (18%), Positives = 39/88 (44%)

Query: 183 QRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKK 242
           +   ++ +  KK +EE     +  +  +   +  ++ K+    K  ++++ KK+   +++
Sbjct: 105 KYGEEQVKSHKKTKEEVAGTLEAVQTIQSITQALQKSKENYNAKCVEQERLKKEGATQRE 164

Query: 243 KEKKKKKEEKKKEKKKKKKKKEKKKKKD 270
            EK   K +K  +  K   +K    K D
Sbjct: 165 IEKAAVKSKKATDTYKLYVEKYALAKAD 192

>2ycu_A Non muscle myosin 2C, alpha-actinin; motor protein; HET: AOV; 2.25A {Homo sapiens} PDB: 1br1_A* 1br4_A* 1br2_A* Length = 995

 Score = 39.6 bits (93), Expect = 8e-04
 Identities = 18/129 (13%), Positives = 34/129 (26%), Gaps = 29/129 (22%)

Query: 176 GKKERRKQRRRKR-----------KRKRKKEEE------------------EKEEEKKEE 206
            K+   + R                ++ KK E+                   K    K E
Sbjct: 776 DKQASLESRDFGDSIESVQSFMNAHKEYKKTEKPPKGQEVSELEAIYNSLQTKLRLIKRE 835

Query: 207 KKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKK 266
                      E        EK +++  +  + + K++KK     +K  +  KK +    
Sbjct: 836 PFVAPAGLTPNEIDSTWSALEKAEQEHAEALRIELKRQKKIAVLLQKYNRILKKLENWAT 895

Query: 267 KKKDEGRRR 275
            K       
Sbjct: 896 TKSVYLGSN 904

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	275
4f0a_B	316	Protein WNT-8, XWNT-8; WNT signaling, ligand-recep	100.0

>4f0a_B Protein WNT-8, XWNT-8; WNT signaling, ligand-receptor complex, frizzled, fatty acylation, glycosylation, signaling protein; HET: NAG BMA MAN FUC PAM; 3.25A {Xenopus laevis}

Probab=100.00  E-value=2e-44  Score=336.69  Aligned_cols=121  Identities=35%  Similarity=0.697  Sum_probs=107.8

Q ss_pred             hhhhHHHHHHHHHHHHHHHHHHhhccCcccCCCCCCCCCCCCCCCCCCCCCCCCCCc-ccccCCchhHHHHHHHHHHHHH
Q psy17095         53 LFADHMASVGRGAAESIAECQHQFRHHRWNCSSGGPGAGGGGGGKSESTTAPSVLPP-TLHIGSREAAFTHAIATAGVVY  131 (275)
Q Consensus        53 ~~p~lm~sV~~GaklAI~ECQ~QFr~~RWNCSs~~~~~~~~~~~k~~~~~~~~~fg~-iL~~GTREtAFV~AItSAGVv~  131 (275)
                      +||++|++|++|+++||+|||+||+++|||||+.                ..++|++ +|..||||+||||||+||||+|
T Consensus        14 ~~~~~~~~v~~Ga~~~i~ECq~QFr~~RWNCs~~----------------~~~~~~~~~l~~g~REtAFv~AissAgv~~   77 (316)
T 4f0a_B           14 AYLTYSASVAVGAQNGIEECKYQFAWERWNCPES----------------TLQLATHNGLRSATRETSFVHAISSAGVMY   77 (316)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTTTSSSCCCCC----------------TTHHHHCTTCCSCCHHHHHHHHHHHHHHHH
T ss_pred             cChHHHHHHHHHHHHHHHHHHHHhcCCCcCCCCC----------------ccccCCcccccCCCHHHHHHHHHHHHHHHH
Confidence            5789999999999999999999999999999965                2345666 6889999999999999999999


Q ss_pred             HHHhhhcCCCCCCccCcCCCCCCCCCCCcccCCCCcchhhhhhhhhhhhhhhHHhHHH
Q psy17095        132 AVARSCKDGSLPSCGCSRTARPKDLKREWLWGGCGDNLEYGYKGGKKERRKQRRRKRK  189 (275)
Q Consensus       132 aVTRACS~G~L~~CgCd~~~~~~~~~~~w~WGGCSDNI~fG~~fSr~FlDa~er~~~~  189 (275)
                      +||+|||.|.|..||||...++.+..++|+||||||||.||+.||+.|||+++++++-
T Consensus        78 avtraCs~G~l~~C~Cd~~~~~~~~~~~w~WgGCsdnv~~G~~fsr~F~D~~e~~~d~  135 (316)
T 4f0a_B           78 TLTRNCSMGDFDNCGCDDSRNGRIGGRGWVWGGCSDNAEFGERISKLFVDGLETGQDA  135 (316)
T ss_dssp             HHHHHHHTTTCSSCCCCCTTTTSEEETTEEECSCCCCHHHHHHHHHHHHHHHCCSSSH
T ss_pred             HHHHHHhCCCCCCCCCCCCCCCCCcccCceeCCccchhHHHHHHHHHHhccccccccH
Confidence            9999999999999999987765433578999999999999999999999998866443

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

ID	Length	Definition	E-value
Query	275
d1zroa1	275	a.264.1.1 (A:8-282) Erythrocyte binding antigen re	3e-04
d1zroa1	275	a.264.1.1 (A:8-282) Erythrocyte binding antigen re	0.001
d1f5na1	300	a.114.1.1 (A:284-583) Interferon-induced guanylate	4e-04
d1f5na1	300	a.114.1.1 (A:284-583) Interferon-induced guanylate	5e-04
d1zroa2	314	a.264.1.1 (A:283-596) Erythrocyte binding antigen	6e-04
d1zroa2	314	a.264.1.1 (A:283-596) Erythrocyte binding antigen	8e-04
d1zroa2	314	a.264.1.1 (A:283-596) Erythrocyte binding antigen	0.001
d2c6ja1	294	a.264.1.1 (A:15-308) Duffy receptor, alpha form {P	9e-04
d2efla1	288	a.238.1.4 (A:1-288) Formin-binding protein 1, FNBP	0.002
d1sa0e_	138	a.137.10.1 (E:) Stathmin 4 {Rat (Rattus norvegicus	0.003
d1sa0e_	138	a.137.10.1 (E:) Stathmin 4 {Rat (Rattus norvegicus	0.004
d2efka1	279	a.238.1.4 (A:10-288) CDC42-interacting protein 4,	0.003

>d1f5na1 a.114.1.1 (A:284-583) Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 300

class: All alpha proteins
fold: Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain
superfamily: Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain
family: Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain
domain: Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 39.0 bits (90), Expect = 4e-04
 Identities = 10/99 (10%), Positives = 48/99 (48%)

Query: 177 KKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKK 236
            ++ ++    + K +  +   +   E + + ++  +++++  ++  ++  EK +  + + 
Sbjct: 200 TEKEKEIEVERVKAESAQASAKMLHEMQRKNEQMMEQKERSYQEHLKQLTEKMENDRVQL 259

Query: 237 EKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDEGRRR 275
            K++++    K +E+++  K+  +K+    K + +  + 
Sbjct: 260 LKEQERTLALKLQEQEQLLKEGFQKESRIMKNEIQDLQT 298

>d1f5na1 a.114.1.1 (A:284-583) Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 300

class: All alpha proteins
fold: Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain
superfamily: Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain
family: Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain
domain: Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 38.6 bits (89), Expect = 5e-04
 Identities = 15/75 (20%), Positives = 41/75 (54%)

Query: 177 KKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKK 236
           + +R+ ++  ++K +  +E  ++  EK E  + +  KE+++    K +++E+  K+  +K
Sbjct: 225 EMQRKNEQMMEQKERSYQEHLKQLTEKMENDRVQLLKEQERTLALKLQEQEQLLKEGFQK 284

Query: 237 EKKKKKKEKKKKKEE 251
           E +  K E +  + +
Sbjct: 285 ESRIMKNEIQDLQTK 299

>d2efla1 a.238.1.4 (A:1-288) Formin-binding protein 1, FNBP1 {Human (Homo sapiens) [TaxId: 9606]} Length = 288

class: All alpha proteins
fold: BAR/IMD domain-like
superfamily: BAR/IMD domain-like
family: FCH domain
domain: Formin-binding protein 1, FNBP1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 36.7 bits (84), Expect = 0.002
 Identities = 10/87 (11%), Positives = 40/87 (45%)

Query: 182 KQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKKKK 241
            +  ++ K++RK    +  + ++  +   K+ E  K + +++ K+  + ++  +K     
Sbjct: 103 ARYVQELKQERKSNFHDGRKAQQHIETCWKQLESSKRRFERDCKEADRAQQYFEKMDADI 162

Query: 242 KKEKKKKKEEKKKEKKKKKKKKEKKKK 268
              K   ++ +++ + + +  ++ K  
Sbjct: 163 NVTKADVEKARQQAQIRHQMAEDSKAD 189

>d1sa0e_ a.137.10.1 (E:) Stathmin 4 {Rat (Rattus norvegicus) [TaxId: 10116]} Length = 138

class: All alpha proteins
fold: Non-globular all-alpha subunits of globular proteins
superfamily: Stathmin
family: Stathmin
domain: Stathmin 4
species: Rat (Rattus norvegicus) [TaxId: 10116]

 Score = 34.9 bits (80), Expect = 0.003
 Identities = 19/96 (19%), Positives = 47/96 (48%)

Query: 180 RRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKKEKK 239
           RR+    +  +K+ +  EE+ + ++ E  K   ++++ E++  +K  E+     K  ++K
Sbjct: 38  RRRDPSLEEIQKKLEAAEERRKYQEAELLKHLAEKREHEREVIQKAIEENNNFIKMAKEK 97

Query: 240 KKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDEGRRR 275
             +K +  K+  +       ++ +EK K  +E R+ 
Sbjct: 98  LAQKMESNKENREAHLAAMLERLQEKDKHAEEVRKN 133

>d1sa0e_ a.137.10.1 (E:) Stathmin 4 {Rat (Rattus norvegicus) [TaxId: 10116]} Length = 138

class: All alpha proteins
fold: Non-globular all-alpha subunits of globular proteins
superfamily: Stathmin
family: Stathmin
domain: Stathmin 4
species: Rat (Rattus norvegicus) [TaxId: 10116]

 Score = 34.5 bits (79), Expect = 0.004
 Identities = 19/92 (20%), Positives = 45/92 (48%)

Query: 177 KKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKKKEKKKKEKKKEKKKKKKKKK 236
             E  +++    + +RK +E E  +   E+++ E++  +K  ++     K  K+K  +K 
Sbjct: 43  SLEEIQKKLEAAEERRKYQEAELLKHLAEKREHEREVIQKAIEENNNFIKMAKEKLAQKM 102

Query: 237 EKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKK 268
           E  K+ +E       ++ ++K K  ++ +K K
Sbjct: 103 ESNKENREAHLAAMLERLQEKDKHAEEVRKNK 134

>d2efka1 a.238.1.4 (A:10-288) CDC42-interacting protein 4, CIP4 {Human (Homo sapiens) [TaxId: 9606]} Length = 279

class: All alpha proteins
fold: BAR/IMD domain-like
superfamily: BAR/IMD domain-like
family: FCH domain
domain: CDC42-interacting protein 4, CIP4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 36.0 bits (82), Expect = 0.003
 Identities = 15/102 (14%), Positives = 45/102 (44%), Gaps = 3/102 (2%)

Query: 177 KKERRKQRRRKRKRKRKKEEEEKEEEKKEEKKKEKKKEKK---KEKKKKEKKKEKKKKKK 233
            +  +  +  K++RK   +E  + +++ E   K+ +  K+   ++ ++ EK  +  ++  
Sbjct: 91  LELTKYSQEMKQERKMHFQEGRRAQQQLENGFKQLENSKRKFERDCREAEKAAQTAERLD 150

Query: 234 KKKEKKKKKKEKKKKKEEKKKEKKKKKKKKEKKKKKDEGRRR 275
           +     K   EK K++   +    ++ K +   + +   R +
Sbjct: 151 QDINATKADVEKAKQQAHLRSHMAEESKNEYAAQLQRFNRDQ 192

Homologous Domains Detected by HHsearch

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

No hit with probability above 80.00