Psyllid ID: psy12268

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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-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------410
Protein Sequence
CKNKKEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKKKEKNKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKEEEEKKKEAEEKKKKRTKKKEKNKNKSRKEEEEEEKKKKKKKKKKKRTKKKEEEKRKNEKAVRLTKLSAFGISGYLLQWIRNFLSGWIQIVRVGTSTSEPIHIPSGCIQGGHMSGLLFSLFINDIAEIFPGFNFWLFADDLKVALRVGGQREVDSMQSMLSRLYHWCSINKMELNIGKCMVMTYHRNKSPILASYDINGQALARCEQVRDLGVTFQKTLERQINDLIFIYKLVNNQIFCPDILTYSFTFSQEIGKQAEHNIIVLVEFAIALVTILDQINRESFQRFRLRM
Secondary Structure (PSIPRED)
cccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHcccEEEEEEcccccccccccccccccccHHHHHHHHHHccccccccccccEEEEcccHHEEEcccHHHHHHHHHHHHHHHHHHHHccccccccccEEEEEEccccccccEEEEccccccccccEEEEEEEEEccHHHHHHHHHHHHHHHccccccccccEEEEEEEEccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccc
Secondary Structure Prediction (SSPRO)
ccccHHHHHHHHHHccHHHHcccccccHHHHHHHHHHHHHHcccccccccHHHHHHHHcHHHHHccccccHHHHHHHHHHccHHHHcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHHccccHHHHHHHHHHHcccEEEEEEccccccccEccccccccccHHHHHHHHHHHcHHccccccEEEEEHcccEEEccccccccHHHHHHHHHHHHHHHHHccccccccccEEEEEEccccccccEEEEcccEcccccHHHHcEEEEcccHHHHHHHHHHHHHHHHccEEEccHHHcccEccccccHHHHHHHHHHHHHHHHHHcHHHHHHHHHHHHHcccc
Coil and Loop (DISEMBL)
cknkkeekKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKKKEKNKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKEEEEKKKEAEEKKKKRTKKKEKNKNKSRKEEEEEEKKKKKKKKKKKRTKKKEEEKRKNEKAVRLTKLSAFGISGYLLQWIRNFLSGWIQIVRVgtstsepihipsgciqgghmsgLLFSLFINDIAeifpgfnfwlFADDLKVALRVGGQREVDSMQSMLSRLYHWCSINKMELNIGKCMVMtyhrnkspilasydingQALARCEQVRDLGVTFQKTLERQINDLIFIYKLVNnqifcpdiltysftFSQEIGKQAEHNIIVLVEFAIALVTILDQINRESFQRFRLRM
Flexible Loop (DISEMBL)
cknkkeekkkkkkrrtkkkeknknksrkeeeeekrtkkkeknkknknksrkeeekkkrtkkkeknknknrkeekkkkkkrrtkkkeknknksrkeekkkeaeeekkktknkeknknksrkeeeekkkeaeekkkkrtkkkeknknksrkeeeeeekkkkkkkkkkkrtkkkeeekrknekavrltklsafGISGYLLQWIRNFLSGWIQIVRVGTSTSEPIHIPSGCIQGGHMSGLLFSLFINDIAEIFPGFNFWLFADDLKVALRVGGQREVDSMQSMLSRLYHWCSINKMELNIGKCMVMTYHRNKSPILASYDINGQALARCEQVRDLGVTFQKTLERQINDLIFIYKLVNNQIFCPDILTYSFTFSQEIGKQAEHNIIVLVEFAIALVTILDQINRESFQRFRLRM
Low Complexity Region (SEG)
CknkkeekkkkkkrrtkkkeknknksrkeeeeekrtkkkeknkknknksrkeeekkkrtkkkeknknknrkeekkkkkkrrtkkkeknknksrkeekkkeaeeekkktknkeknknksrkeeeekkkeaeekkkkrtkkkeknknksrkeeeeeekkkkkkkkkkkrtkkkeeekrknekAVRLTKLSAFGISGYLLQWIRNFLSGWIQIVRVGTSTSEPIHIPSGCIQGGHMSGLLFSLFINDIAEIFPGFNFWLFADDLKVALRVGGQREVDSMQSMLSRLYHWCSINKMELNIGKCMVMTYHRNKSPILASYDINGQALARCEQVRDLGVTFQKTLERQINDLIFIYKLVNNQIFCPDILTYSFTFSQEIGKQAEHNIIVLVEFAIALVTILDQINRESFQRFRLRM
Disordered region (IsUnstruct)
*************************************************************************************************************************************************************************************VRLTKLSAFGISGYLLQWIRNFLSGWIQIVRVGTSTSEPIHIPSGCIQGGHMSGLLFSLFINDIAEIFPGFNFWLFADDLKVALRVGGQREVDSMQSMLSRLYHWCSINKMELNIGKCMVMTYHRNKSPILASYDINGQALARCEQVRDLGVTFQKTLERQINDLIFIYKLVNNQIFCPDILTYSFTFSQEIGKQAEHNIIVLVEFAIALVTILDQINRE*********
Disordered Region (DISOPRED)
***************************************************************************************************************************************************************************************LTKLSAFGISGYLLQWIRNFLSGWIQIVRVGTSTSEPIHIPSGCIQGGHMSGLLFSLFINDIAEIFPGFNFWLFADDLKVALRVGGQREVDSMQSMLSRLYHWCSINKMELNIGKCMVMTYHRNKSPILASYDINGQALARCEQVRDLGVTFQKTLERQINDLIFIYKLVNNQIFCPDILTYSFTFSQEIGKQAEHNIIVLVEFAIALVTILDQINRESFQRFRLRM
Disordered Region (DISEMBL)
*************************************************************************************************************************************************************************************VRLTKLSAFGISGYLLQWIRNFLSGWIQIVRVGTSTSEPIHIPSGCIQGGHMSGLLFSLFINDIAEIFPGFNFWLFADDLKVALRVGGQREVDSMQSMLSRLYHWCSINKMELNIGKCMVMTYHRNKSPILASYDINGQALARCEQVRDLGVTFQKTLERQINDLIFIYKLVNNQIFCPDILTYSFTFSQEIGKQAEHNIIVLVEFAIALVTILDQINRESFQRFRLRM
Disordered Region (DISPRO)
CKNKKEEK*KKK**********************************************T************************************EKKKEAEEEKKKTKNKEKNKNKSRKEEEEKKKEAEEKKKKRTKKKEKNKNKSRKEEEEEEKKKKKKKKKKKRTKKKEEEKRKNEKAVRLTKLSAFGISGYLLQWIRNFLSGWIQIVRVGTSTSEPIHIPSGCIQGGHMSGLLFSLFINDIAEIFPGFNFWLFADDLKVALRVGGQREVDSMQSMLSRLYHWCSINKMELNIGKCMVMTYHRNKSPILASYDINGQALARCEQVRDLGVTFQKTLERQINDLIFIYKLVNNQIFCPDILTYSFTFSQEIGKQAEHNIIVLVEFAIALVTILDQINRESFQRFRLR*
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHooooooooooooooooHHHHHHHHHHHHHHHHHHiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxRLTKLSAFGISGYLLQWIRNFLSGWIQIVRVGTSTSEPIHIPSGCIQGGHMSGLLFSLFINDIAEIFPGFNFWLFADDLKVALRVGGQREVDSMQSMLSRLYHWCSINKMELNIGKCMVMTYHRNKSPILASYDINGQALARCEQVRDLGVTFQKTLERQINDLIFIYKLVNNQIFCPDILTYSFTFSQEIGKQAEHNIIVLVEFAIALVTILDQINRESFQRFRLRM
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	410	2.2.26 [Sep-21-2011]
Q4PBP6	1520	Stress response protein N	N/A	N/A	0.373	0.100	0.237	2e-06
F1QBY1	2876	Nipped-B-like protein B O	no	N/A	0.421	0.060	0.340	1e-05
A4R2R1	1311	Stress response protein N	N/A	N/A	0.407	0.127	0.241	2e-05
O01761	8081	Muscle M-line assembly pr	yes	N/A	0.434	0.022	0.328	3e-05
Q2GZN9	1255	Stress response protein N	N/A	N/A	0.407	0.133	0.255	5e-05

>sp|Q4PBP6|NST1_USTMA Stress response protein NST1 OS=Ustilago maydis (strain 521 / FGSC 9021) GN=NST1 PE=3 SV=1

 Score = 54.3 bits (129), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 37/156 (23%), Positives = 93/156 (59%), Gaps = 3/156 (1%)

Query: 29   EEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKKKEKNKNKNRKEEKKKKKKRRTKKKEKN 88
            E+  E R  K+ + KK+K K+++E ++ +R KK ++      +   +++ +R  + K++ 
Sbjct: 853  EKAREARRMKESQKKKDKKKAQREAKEAERLKKDQERAAAEAEVRAQQQAQRDAELKKQE 912

Query: 89   KNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKEEEEKKKEAEEKKKKRTKKKEKNKNKSR 148
            + + +KE ++K  E+EK K   + + +    +E + + +    +K+++ + + + + K++
Sbjct: 913  EIRLKKEAERKAREDEKAKKDEERRRRQAEERERQLEVERKRREKEEKIRLERELQEKAK 972

Query: 149  KEEEEEEKKKKKKKKKKKRTKK---KEEEKRKNEKA 181
            ++ EE ++K K+++++ +R K+   KEE++RK E A
Sbjct: 973  RDREEAQRKAKEEQQRVQRAKELKAKEEQERKAEAA 1008

May act as a negative regulator of salt tolerance.
Ustilago maydis (strain 521 / FGSC 9021) (taxid: 237631)

>sp|F1QBY1|NIPLB_DANRE Nipped-B-like protein B OS=Danio rerio GN=nipblb PE=2 SV=1

 Score = 51.6 bits (122), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 63/185 (34%), Positives = 112/185 (60%), Gaps = 12/185 (6%)

Query: 5   KEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNK-KNKNKSRKEEEKKKRTKKKE 63
           KE +K + K R K +EK++ K R +E E+ R K++ K++ K + K R +E+ K R KK+ 
Sbjct: 700 KELEKGRDKERVKDQEKDQEKGRDKEVEKGRYKERVKDRVKEQEKVRDKEQVKGRDKKRS 759

Query: 64  KNKNKNR-KEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEE--EKKKTKNKEKNKNKSRK 120
           K+  K R K++ K+ +K R K ++K   K R++++ KE E+  EK + K  EK + K + 
Sbjct: 760 KDLEKCREKDQDKELEKDREKNQDKELEKGREKDQDKELEKGREKDRDKEMEKAREKDQD 819

Query: 121 EEEEKKKEAEEKK-------KKRTKKKEKNKNKSR-KEEEEEEKKKKKKKKKKKRTKKKE 172
           +E EK +E ++ K       K R K +EK+++K R K+ ++  +K + K ++K R K +E
Sbjct: 820 KELEKGREKDQDKELEKGQEKDRDKVREKDRDKVRDKDRDKVREKDRDKVREKDRDKLRE 879

Query: 173 EEKRK 177
           +++ K
Sbjct: 880 KDREK 884

Probably plays a structural role in chromatin. Involved in sister chromatid cohesion, possibly by facilitating the cohesin complex loading, and in transcription regulation.

Danio rerio (taxid: 7955)

>sp|A4R2R1|NST1_MAGO7 Stress response protein NST1 OS=Magnaporthe oryzae (strain 70-15 / ATCC MYA-4617 / FGSC 8958) GN=NST1 PE=3 SV=2

 Score = 50.4 bits (119), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 42/174 (24%), Positives = 106/174 (60%), Gaps = 7/174 (4%)

Query: 2   KNKKEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKK 61
           ++++ EK+K KK++  +K ++K   +K+ + E++ +K  +    + +   EE++++  ++
Sbjct: 617 EDRETEKRKAKKQKEAQKRRDKALQKKQAQAEEKARKDAEKAAEEAERLAEEQRRQEEQR 676

Query: 62  KEKNKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEE-------KKKTKNKEKN 114
           ++  + K +KE ++K ++   ++KE  + +  +E+K+++AE++       +K+ K KE+ 
Sbjct: 677 QKNEERKKKKEAQRKAEEEERQRKEAERLRRAQEQKERQAEQDRKAREAKEKEKKAKEEA 736

Query: 115 KNKSRKEEEEKKKEAEEKKKKRTKKKEKNKNKSRKEEEEEEKKKKKKKKKKKRT 168
           K + +   E K++EA E+K+K  K++ + + K + E+E  E ++K ++  +K T
Sbjct: 737 KQREKAARELKEREARERKEKADKERLEKEAKIKAEKEAREAQRKAERASQKAT 790

May act as a negative regulator of salt tolerance.

Magnaporthe oryzae (strain 70-15 / ATCC MYA-4617 / FGSC 8958) (taxid: 242507)

>sp|O01761|UNC89_CAEEL Muscle M-line assembly protein unc-89 OS=Caenorhabditis elegans GN=unc-89 PE=1 SV=3

 Score = 50.1 bits (118), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 70/213 (32%), Positives = 98/213 (46%), Gaps = 35/213 (16%)

Query: 4    KKEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKN---------KKNKNKSR-KEE 53
            K EEK     ++ K  EK  + ++K E E K   KKEK+         K  K KS  K +
Sbjct: 1569 KVEEKPASPTKKEKSPEKPASPTKKSENEVKSPTKKEKSPEKSVVEELKSPKEKSPEKAD 1628

Query: 54   EKKKRTKKKEKNKNKNRKEEKK---KKKKRRTKKKEKNKNKSRKE--------------- 95
            +K K   KKEK+  K+  E+ K   KK+K   K +EK  + ++KE               
Sbjct: 1629 DKPKSPTKKEKSPEKSATEDVKSPTKKEKSPEKVEEKPTSPTKKESSPTKKTDDEVKSPT 1688

Query: 96   --EKKKEAEEEKKKTKN-KEKNKNKSRKEE----EEKKKEAEEKKKKRTKKKEKNKNKSR 148
              EK  +  EEK  +   KEK+  KS  EE    +EK  E  E+K K   KKEK+  KS 
Sbjct: 1689 KKEKSPQTVEEKPASPTKKEKSPEKSVVEEVKSPKEKSPEKAEEKPKSPTKKEKSPEKSA 1748

Query: 149  KEEEEEEKKKKKKKKKKKRTKKKEEEKRKNEKA 181
             EE +   KK+K  +K    K K   K+++   
Sbjct: 1749 AEEVKSPTKKEKSPEKSAEEKPKSPTKKESSPV 1781

Structural component of the muscle M-line. Myofilament lattice assembly begins with positional cues laid down in the basement membrane and muscle cell membrane. UNC-89 responds to these signals, localizes, and then participates in assembling an M-line.

Caenorhabditis elegans (taxid: 6239)

>sp|Q2GZN9|NST1_CHAGB Stress response protein NST1 OS=Chaetomium globosum (strain ATCC 6205 / CBS 148.51 / DSM 1962 / NBRC 6347 / NRRL 1970) GN=NST1 PE=3 SV=1

 Score = 49.7 bits (117), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 44/172 (25%), Positives = 103/172 (59%)

Query: 4   KKEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKKKE 63
           +K +K K  +RR  +  K K    +E+   +  K  E+  +   ++RK EE++ + ++K 
Sbjct: 572 RKAKKAKDAQRRKDRAAKKKEAQAEEKARREAEKAAEEAARRAEEARKAEEQRAKAEEKR 631

Query: 64  KNKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKEEE 123
           K K   RK E+++++++  ++  K +++   E K +EA E +KKT+ + + + K  +E++
Sbjct: 632 KKKEAQRKAEEEERQRKEAERLRKIQDREEAERKAREAREREKKTREEARLREKEAREQK 691

Query: 124 EKKKEAEEKKKKRTKKKEKNKNKSRKEEEEEEKKKKKKKKKKKRTKKKEEEK 175
           E+K     ++++R +++++ K K+ +E +E ++ K+ K+ K  + ++K+EE+
Sbjct: 692 ERKDRERREQQERERREKEAKAKAEREAKEAKEAKEAKEGKDTKERRKKEER 743

May act as a negative regulator of salt tolerance.

Chaetomium globosum (strain ATCC 6205 / CBS 148.51 / DSM 1962 / NBRC 6347 / NRRL 1970) (taxid: 306901)

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	410
328716306	1568	PREDICTED: hypothetical protein LOC10057	0.373	0.097	0.372	4e-22
334085159	963	putative reverse transcriptase [Culex qu	0.409	0.174	0.331	8e-21
70907198	820	reverse transcriptase [Aedes aegypti]	0.412	0.206	0.339	3e-20
103015	975	hypothetical protein - African malaria m	0.363	0.152	0.355	1e-19
343481903	897	unknown [Pectinophora gossypiella]	0.478	0.218	0.333	1e-17
270015859	1141	hypothetical protein TcasGA2_TC016102 [T	0.387	0.139	0.327	1e-17
270015858	713	hypothetical protein TcasGA2_TC016101 [T	0.395	0.227	0.333	2e-17
442761621	399	Putative rte ele1 orf1 -h 1e-60 -j 4, pa	0.380	0.390	0.371	1e-16
270003248	737	hypothetical protein TcasGA2_TC002455 [T	0.365	0.203	0.346	1e-13
358386705	1232	hypothetical protein TRIVIDRAFT_30653 [T	0.270	0.090	0.316	1e-10

>gi|328716306|ref|XP_003245892.1| PREDICTED: hypothetical protein LOC100575767 [Acyrthosiphon pisum]

 Score =  112 bits (279), Expect = 4e-22,   Method: Composition-based stats.
 Identities = 57/153 (37%), Positives = 85/153 (55%)

Query: 187 LSAFGISGYLLQWIRNFLSGWIQIVRVGTSTSEPIHIPSGCIQGGHMSGLLFSLFINDIA 246
           L   GI   LL W  ++LS   Q VR+   +S+     SG  QG H+S LLF++FIN + 
Sbjct: 793 LDRLGIGEPLLSWFGSYLSDRRQFVRLFGKSSDFFRASSGVPQGSHLSPLLFNIFINTMC 852

Query: 247 EIFPGFNFWLFADDLKVALRVGGQREVDSMQSMLSRLYHWCSINKMELNIGKCMVMTYHR 306
                    LFADD K+ LR+    +  ++Q+ L +  +WC+   + LNI KC VM++HR
Sbjct: 853 SAISSCRLLLFADDSKIFLRITTNNDCLTLQNTLDKFTNWCNTFNLSLNISKCKVMSFHR 912

Query: 307 NKSPILASYDINGQALARCEQVRDLGVTFQKTL 339
           +KS     Y + G ++ R  QV+DLG+ F  +L
Sbjct: 913 SKSVFSFDYKLGGISIQRVNQVQDLGILFVPSL 945

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|334085159|dbj|BAK26811.1| putative reverse transcriptase [Culex quinquefasciatus]

 Score =  107 bits (268), Expect = 8e-21,   Method: Compositional matrix adjust.
 Identities = 57/172 (33%), Positives = 96/172 (55%), Gaps = 4/172 (2%)

Query: 179 EKAVRLTKLSAFGISGYLLQWIRNFLSGWIQIVRVGTSTSEPIHIPSGCIQGGHMSGLLF 238
           +  + + KL   GI   LL+W++++L+   QIVR     SE IH+ SG  QG H+  LLF
Sbjct: 609 DIPLLIFKLQKIGIQPNLLEWLKSYLTKREQIVRFQNVLSESIHVTSGVPQGSHLGPLLF 668

Query: 239 SLFINDIAEIFPGFNFWLFADDLKVALRVGGQREVDSMQSMLSRLYHWCSINKMELNIGK 298
            L++NDI+ I    N  ++ADD+K+ + +G   +    Q+ ++  Y WCS + ++ N+ K
Sbjct: 669 ILYVNDISFILKKINVLVYADDMKLYMEIGNANDSHVFQNEINLFYTWCSKSLLQFNVNK 728

Query: 299 CMVMTYHR-NKSPILASYDINGQALARCEQVRDLGVTF--QKTLERQINDLI 347
           C  + + R +++P +    +  Q + +C+ VRDLGV    Q T     N +I
Sbjct: 729 CNSIAFSRKHETPNITVL-LGNQPVEKCKVVRDLGVILDSQLTFVEHYNTII 779

Source: Culex quinquefasciatus

Species: Culex quinquefasciatus

Genus: Culex

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|70907198|gb|AAZ15240.1| reverse transcriptase [Aedes aegypti]

 Score =  105 bits (263), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 58/171 (33%), Positives = 94/171 (54%), Gaps = 2/171 (1%)

Query: 179 EKAVRLTKLSAFGISGYLLQWIRNFLSGWIQIVRVGTSTSEPIHIPSGCIQGGHMSGLLF 238
           +  + L KL   G+S   + W  ++L+     V++G++ S      SG  QG ++  LLF
Sbjct: 485 DHGILLQKLRKCGVSDSFIDWFESYLTNRSLCVKIGSNESSSFTNLSGVPQGSNLGPLLF 544

Query: 239 SLFINDIAEIFPGFNFWLFADDLKVALRVGGQREVDSMQSMLSRLYHWCSINKMELNIGK 298
           SLFIND + + P      +ADD KV + V    +   +Q +L+    WCS N M L+I K
Sbjct: 545 SLFINDASLVLPPGTRLFYADDTKVYMIVDSLDDCHHLQRLLNAFEAWCSRNCMTLSIEK 604

Query: 299 CMVMTYHRNKSPILASYDINGQALARCEQVRDLGVTFQK--TLERQINDLI 347
           C V++++R ++PI   Y ++G A+ R ++VRDLGV   +  T     ND++
Sbjct: 605 CQVISFNRKRNPIHFQYTLSGTAIERVQRVRDLGVWLDEEFTFNYHFNDIV 655

Source: Aedes aegypti

Species: Aedes aegypti

Genus: Aedes

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|103015|pir||B34751 hypothetical protein - African malaria mosquito transposon T1-2 (fragment) gi|159644|gb|AAA29367.1| unknown [Anopheles gambiae]

 Score =  103 bits (258), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 53/149 (35%), Positives = 81/149 (54%)

Query: 191 GISGYLLQWIRNFLSGWIQIVRVGTSTSEPIHIPSGCIQGGHMSGLLFSLFINDIAEIFP 250
           G    ++ W+ ++LS     V+ G+  SE     SG  QG  +S LLFSLFIND+  + P
Sbjct: 636 GFGDGIISWLSSYLSNRSCRVKTGSYLSEEFFCTSGVPQGCVLSPLLFSLFINDVCNVLP 695

Query: 251 GFNFWLFADDLKVALRVGGQREVDSMQSMLSRLYHWCSINKMELNIGKCMVMTYHRNKSP 310
                L+ADD+K+ L V    +  S+Q  L+   HWCS N + L   KC V+++  + SP
Sbjct: 696 PDGHLLYADDIKIFLPVSSSSDCMSLQHYLNAFVHWCSSNLLRLCPDKCSVISFSHSLSP 755

Query: 311 ILASYDINGQALARCEQVRDLGVTFQKTL 339
           I  +Y ++  +L+R   +RDLG+     L
Sbjct: 756 ISFNYTLSNSSLSRVLSIRDLGIILDSRL 784

Source: Anopheles gambiae

Species: Anopheles gambiae

Genus: Anopheles

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|343481903|gb|AEM44817.1| unknown [Pectinophora gossypiella]

 Score = 97.4 bits (241), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 69/207 (33%), Positives = 111/207 (53%), Gaps = 11/207 (5%)

Query: 182 VRLTKLSAFGISGYLLQWIRNFLSGWIQIVRVGTSTSEPIHIPSGCIQGGHMSGLLFSLF 241
           + L K++  GI G LL+W  +++    Q V V    S+ IH+ SG  QG  +  LLF +F
Sbjct: 609 LLLEKIAYNGIRGNLLRWFSSYVCNRSQRVVVNGFHSDLIHVTSGVPQGSILGPLLFLIF 668

Query: 242 INDIAEIFPGFNFWLFADDLKVALRVGGQREVDSMQSMLSRLYHWCSINKMELNIGKCMV 301
            NDI   F   +F L+ADDLK+   +    +   +Q+ L+ L H+C INK++L+I KC  
Sbjct: 669 NNDIKNCFRHSHFLLYADDLKIYKSIHSDIDCTLLQNDLNHLTHYCYINKLKLSIPKCHG 728

Query: 302 MTYHRNKSPILASYDINGQALARCEQVRDLGVTFQK--TLERQINDLI---F-IYKLVNN 355
           +++ +NK+ I+ +Y +   +L   + +RDLGV       L+  I+ +I   F +YK V  
Sbjct: 729 ISFTKNKNKIIYNYKLCDNSLTAVDYLRDLGVILDSKLHLDLHIDSIISRGFRMYKFVMR 788

Query: 356 QIFCPD---ILTYSFTFSQEIGKQAEH 379
                D   I TY + ++  I  Q E+
Sbjct: 789 AT--TDFSRISTYLYLYTTLIRPQVEY 813

Source: Pectinophora gossypiella

Species: Pectinophora gossypiella

Genus: Pectinophora

Family: Gelechiidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|270015859|gb|EFA12307.1| hypothetical protein TcasGA2_TC016102 [Tribolium castaneum]

 Score = 97.4 bits (241), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 52/159 (32%), Positives = 89/159 (55%)

Query: 179  EKAVRLTKLSAFGISGYLLQWIRNFLSGWIQIVRVGTSTSEPIHIPSGCIQGGHMSGLLF 238
            +  + L+KL+ FG S  L+   +++L    Q VR     S      SG  QG ++  L+F
Sbjct: 975  DHYILLSKLNTFGFSDSLVSLTKSYLFHRRQRVRYNNFLSNEFITTSGVPQGSNLGPLIF 1034

Query: 239  SLFINDIAEIFPGFNFWLFADDLKVALRVGGQREVDSMQSMLSRLYHWCSINKMELNIGK 298
             L+IND+A++    +  LFADDLK+ + +   ++ + +Q  L  L  WC  N+++LN+ K
Sbjct: 1035 LLYINDLADLLNQCSILLFADDLKLYMEINSFQDSEILQECLKTLNIWCDKNRLQLNLAK 1094

Query: 299  CMVMTYHRNKSPILASYDINGQALARCEQVRDLGVTFQK 337
            C V+++ + ++ I   Y+I+   L R   V+DLG+TF  
Sbjct: 1095 CCVVSFTKKQNIINYPYEISNSVLNRVITVKDLGITFDA 1133

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|270015858|gb|EFA12306.1| hypothetical protein TcasGA2_TC016101 [Tribolium castaneum]

 Score = 96.3 bits (238), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 54/162 (33%), Positives = 91/162 (56%)

Query: 179 EKAVRLTKLSAFGISGYLLQWIRNFLSGWIQIVRVGTSTSEPIHIPSGCIQGGHMSGLLF 238
           +  + L+KL+ FG S  L+  I+++L    Q VR     S      SG  QG ++  L+F
Sbjct: 357 DHYILLSKLNTFGFSDSLVSLIKSYLFHRRQRVRYNNFLSNEFITTSGVPQGSNLGPLIF 416

Query: 239 SLFINDIAEIFPGFNFWLFADDLKVALRVGGQREVDSMQSMLSRLYHWCSINKMELNIGK 298
            L+IND+A++    +  LFADDLK+ + +   ++ + +Q  L  L  WC  N+++LN+ K
Sbjct: 417 LLYINDLADLLNQCSILLFADDLKLYMEINSFQDSEILQECLKTLNIWCDKNRLQLNLAK 476

Query: 299 CMVMTYHRNKSPILASYDINGQALARCEQVRDLGVTFQKTLE 340
           C V+++ + ++ I   Y+I+   L R   V+DLG+TF   L 
Sbjct: 477 CCVVSFTKKQNIINYPYEISNSVLNRVITVKDLGITFDAELS 518

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|442761621|gb|JAA72969.1| Putative rte ele1 orf1 -h 1e-60 -j 4, partial [Ixodes ricinus]

 Score = 94.0 bits (232), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 59/159 (37%), Positives = 88/159 (55%), Gaps = 3/159 (1%)

Query: 182 VRLTKLSAFGISGYLLQWIRNFLSGWIQIVRVGTSTSEPIHIPSGCIQGGHMSGLLFSLF 241
           + L KL +  I+  + +WI+N+LS   Q V +  S S PI + SG  QG  +  LLF ++
Sbjct: 62  LLLKKLVSLNITNNIQKWIKNYLSDREQCVVLNGSKSLPITVSSGVPQGSVLGPLLFLIY 121

Query: 242 INDIA-EIFPGFNFWLFADDLKVALRVGGQREVDSMQSMLSRLYHWCSINKMELNIGKCM 300
           INDI  +I       LFADD  V  ++    +++ +QS L ++ HWC   KM LNIGKC 
Sbjct: 122 INDIVTDIQSPIK--LFADDCVVYRQIYSTMDIEILQSDLDKIEHWCDKWKMSLNIGKCN 179

Query: 301 VMTYHRNKSPILASYDINGQALARCEQVRDLGVTFQKTL 339
            +++ +N S   ASY I    + R    + LGV F ++L
Sbjct: 180 YLSFTKNVSRSPASYTIKNAIIRRVSDCKYLGVNFTQSL 218

Source: Ixodes ricinus

Species: Ixodes ricinus

Genus: Ixodes

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|270003248|gb|EEZ99695.1| hypothetical protein TcasGA2_TC002455 [Tribolium castaneum]

 Score = 84.0 bits (206), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 52/150 (34%), Positives = 80/150 (53%)

Query: 190 FGISGYLLQWIRNFLSGWIQIVRVGTSTSEPIHIPSGCIQGGHMSGLLFSLFINDIAEIF 249
           +G SG LL  I+++L+   Q V+     S+     SG  QG ++  LLF LFINDI    
Sbjct: 403 YGFSGSLLSLIKSYLANREQRVKYRNYISDSYVATSGVPQGSNLGPLLFLLFINDICGSL 462

Query: 250 PGFNFWLFADDLKVALRVGGQREVDSMQSMLSRLYHWCSINKMELNIGKCMVMTYHRNKS 309
                 LFADDLK+   +    +  ++Q+ ++ +  WC+ N++ LN  KC VM+Y + + 
Sbjct: 463 STCAKLLFADDLKIYTEIKSIEDCLTLQNNINAVVKWCNENRLYLNPSKCNVMSYTKKRE 522

Query: 310 PILASYDINGQALARCEQVRDLGVTFQKTL 339
            +   YDI+   L R   ++DLGV F   L
Sbjct: 523 FLEFVYDISSVTLHRTFIIKDLGVIFDTEL 552

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|358386705|gb|EHK24300.1| hypothetical protein TRIVIDRAFT_30653 [Trichoderma virens Gv29-8]

 Score = 73.9 bits (180), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 38/120 (31%), Positives = 71/120 (59%)

Query: 68  KNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKEEEEKKK 127
           K +  E+K+K + + K+KE  K        KKEAE  ++  + KEK     RK  E K++
Sbjct: 585 KKKIAEQKQKAEEKRKQKEAQKKAEEDARLKKEAERLRRIHEQKEKQAESERKAREAKER 644

Query: 128 EAEEKKKKRTKKKEKNKNKSRKEEEEEEKKKKKKKKKKKRTKKKEEEKRKNEKAVRLTKL 187
           E + K ++RT+++E  + K R+ +E +EK+++ K++K+ R  K ++E ++  +A R  +L
Sbjct: 645 EKKLKDEQRTREREAREQKEREAQERKEKQERDKREKEARAAKAQKESQEAAEAAREQQL 704

Source: Trichoderma virens Gv29-8

Species: Trichoderma virens

Genus: Trichoderma

Family: Hypocreaceae

Order: Hypocreales

Class: Sordariomycetes

Phylum: Ascomycota

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	410
FB|FBgn0004852	1307	Ac76E "Adenylyl cyclase 76E" [	0.231	0.072	0.395	4.7e-08
RGD|619966	95	Adcy7 "adenylate cyclase 7" [R	0.097	0.421	0.560	5.3e-05

FB|FBgn0004852 Ac76E "Adenylyl cyclase 76E" [Drosophila melanogaster (taxid:7227)]

 Score = 144 (55.7 bits), Expect = 4.7e-08, Sum P(2) = 4.7e-08
 Identities = 38/96 (39%), Positives = 52/96 (54%)

Query:   316 DINGQALARCEQVRDLGVTFQKTLERQINDLIFIYKLVNNQIFCPDILTYSFTFSQEIGK 375
             D+N Q L     + ++   F K L +     I   K + +   C   L           K
Sbjct:  1127 DVNKQGLECLRLLNEIICDFDKLLLKPKFSGIEKIKTIASTYMCASGLRPGKEDGATDEK 1186

Query:   376 QAE-HNIIVLVEFAIALVTILDQINRESFQRFRLRM 410
             + E HN+++LVEFAIAL++ILD INRESFQRFRLR+
Sbjct:  1187 RTEEHNVVILVEFAIALMSILDSINRESFQRFRLRI 1222

GO:0004016 "adenylate cyclase activity" evidence=ISS;NAS

GO:0009190 "cyclic nucleotide biosynthetic process" evidence=IEA

GO:0035556 "intracellular signal transduction" evidence=IEA

RGD|619966 Adcy7 "adenylate cyclase 7" [Rattus norvegicus (taxid:10116)]

 Score = 100 (40.3 bits), Expect = 5.3e-05, P = 5.3e-05
 Identities = 23/41 (56%), Positives = 31/41 (75%)

Query:   370 SQEIGKQAEHNIIVLVEFAIALVTILDQINRESFQRFRLRM 410
             +QE+ +Q  H I V+VEF+IAL++ LD INR SF  FRLR+
Sbjct:    35 NQELERQHAH-IGVMVEFSIALMSKLDGINRHSFNSFRLRV 74


Parameters:
  V=100
  filter=SEG
  E=0.001

  ctxfactor=1.00

  Query                        -----  As Used  -----    -----  Computed  ----
  Frame  MatID Matrix name     Lambda    K       H      Lambda    K       H
   +0      0   BLOSUM62        0.328   0.141   0.434    same    same    same
               Q=9,R=2         0.244   0.0300  0.180     n/a     n/a     n/a

  Query
  Frame  MatID  Length  Eff.Length     E     S W   T  X   E2     S2
   +0      0      410       231   0.00084  113 3  11 22  0.44    32
                                                     32  0.42    36


Statistics:

  Database:  /share/blast/go-seqdb.fasta
   Title:  go_20130330-seqdb.fasta
   Posted:  5:47:42 AM PDT Apr 1, 2013
   Created:  5:47:42 AM PDT Apr 1, 2013
   Format:  XDF-1
   # of letters in database:  169,044,731
   # of sequences in database:  368,745
   # of database sequences satisfying E:  2
  No. of states in DFA:  599 (64 KB)
  Total size of DFA:  183 KB (2106 KB)
  Time to generate neighborhood:  0.00u 0.00s 0.00t   Elapsed:  00:00:03
  No. of threads or processors used:  24
  Search cpu time:  19.55u 0.10s 19.65t   Elapsed:  00:00:08
  Total cpu time:  19.55u 0.10s 19.65t   Elapsed:  00:00:11
  Start:  Thu Aug 15 16:06:44 2013   End:  Thu Aug 15 16:06:55 2013

GO:0004016 "adenylate cyclase activity" evidence=ISO;IDA

GO:0006171 "cAMP biosynthetic process" evidence=ISO;IDA

GO:0007165 "signal transduction" evidence=NAS

GO:0016020 "membrane" evidence=IDA

GO:0016021 "integral to membrane" evidence=ISO

GO:0030819 "positive regulation of cAMP biosynthetic process" evidence=ISO;IMP

GO:0060135 "maternal process involved in female pregnancy" evidence=IEP

GO:0071361 "cellular response to ethanol" evidence=ISO

---

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	410
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	1e-16
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	2e-15
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	2e-15
cd01650	220	cd01650, RT_nLTR_like, RT_nLTR: Non-LTR (long term	2e-15
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	2e-14
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	3e-14
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	6e-14
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	7e-14
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	7e-14
PRK05306	746	PRK05306, infB, translation initiation factor IF-2	1e-13
PRK05306	746	PRK05306, infB, translation initiation factor IF-2	2e-13
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	4e-13
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	5e-13
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	5e-13
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	5e-13
TIGR02794	346	TIGR02794, tolA_full, TolA protein	5e-13
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	1e-12
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	1e-12
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	2e-12
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	4e-12
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	4e-12
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	9e-12
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	1e-11
TIGR02794	346	TIGR02794, tolA_full, TolA protein	1e-11
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	2e-11
pfam10243	506	pfam10243, MIP-T3, Microtubule-binding protein MIP	2e-11
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	3e-11
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	4e-11
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	4e-11
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	4e-11
PRK09510	387	PRK09510, tolA, cell envelope integrity inner memb	4e-11
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	5e-11
pfam10243	506	pfam10243, MIP-T3, Microtubule-binding protein MIP	5e-11
PRK09510	387	PRK09510, tolA, cell envelope integrity inner memb	6e-11
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	9e-11
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	2e-10
PRK05901	509	PRK05901, PRK05901, RNA polymerase sigma factor; P	4e-10
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	5e-10
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	6e-10
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	9e-10
COG3064	387	COG3064, TolA, Membrane protein involved in colici	9e-10
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	1e-09
PRK05306	746	PRK05306, infB, translation initiation factor IF-2	1e-09
pfam10243	506	pfam10243, MIP-T3, Microtubule-binding protein MIP	1e-09
PTZ00108	1388	PTZ00108, PTZ00108, DNA topoisomerase 2-like prote	1e-09
PRK05901	509	PRK05901, PRK05901, RNA polymerase sigma factor; P	5e-09
PRK12704	520	PRK12704, PRK12704, phosphodiesterase; Provisional	6e-09
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	8e-09
pfam10243	506	pfam10243, MIP-T3, Microtubule-binding protein MIP	1e-08
pfam10243	506	pfam10243, MIP-T3, Microtubule-binding protein MIP	1e-08
COG3064	387	COG3064, TolA, Membrane protein involved in colici	1e-08
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	1e-08
PTZ00108	1388	PTZ00108, PTZ00108, DNA topoisomerase 2-like prote	2e-08
PTZ00372	413	PTZ00372, PTZ00372, endonuclease 4-like protein; P	2e-08
pfam05262	489	pfam05262, Borrelia_P83, Borrelia P83/100 protein	2e-08
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	4e-08
PTZ00108	1388	PTZ00108, PTZ00108, DNA topoisomerase 2-like prote	5e-08
PRK04195	482	PRK04195, PRK04195, replication factor C large sub	6e-08
PRK04195	482	PRK04195, PRK04195, replication factor C large sub	7e-08
PRK04195	482	PRK04195, PRK04195, replication factor C large sub	7e-08
PRK05901	509	PRK05901, PRK05901, RNA polymerase sigma factor; P	9e-08
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	9e-08
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	1e-07
pfam10243	506	pfam10243, MIP-T3, Microtubule-binding protein MIP	2e-07
COG3064	387	COG3064, TolA, Membrane protein involved in colici	2e-07
pfam09507	427	pfam09507, CDC27, DNA polymerase subunit Cdc27	2e-07
PRK09510	387	PRK09510, tolA, cell envelope integrity inner memb	3e-07
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	3e-07
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	3e-07
COG1293	564	COG1293, COG1293, Predicted RNA-binding protein ho	3e-07
PRK05901	509	PRK05901, PRK05901, RNA polymerase sigma factor; P	4e-07
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	4e-07
pfam05262	489	pfam05262, Borrelia_P83, Borrelia P83/100 protein	4e-07
PRK05901	509	PRK05901, PRK05901, RNA polymerase sigma factor; P	5e-07
PRK05901	509	PRK05901, PRK05901, RNA polymerase sigma factor; P	5e-07
PRK12704	520	PRK12704, PRK12704, phosphodiesterase; Provisional	5e-07
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	6e-07
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	7e-07
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	7e-07
pfam04615	728	pfam04615, Utp14, Utp14 protein	7e-07
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	8e-07
PTZ00372	413	PTZ00372, PTZ00372, endonuclease 4-like protein; P	8e-07
pfam04615	728	pfam04615, Utp14, Utp14 protein	8e-07
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	9e-07
PRK04195	482	PRK04195, PRK04195, replication factor C large sub	9e-07
PTZ00108	1388	PTZ00108, PTZ00108, DNA topoisomerase 2-like prote	1e-06
PRK12704	520	PRK12704, PRK12704, phosphodiesterase; Provisional	1e-06
PRK12704	520	PRK12704, PRK12704, phosphodiesterase; Provisional	1e-06
pfam09507	427	pfam09507, CDC27, DNA polymerase subunit Cdc27	1e-06
PRK00409	782	PRK00409, PRK00409, recombination and DNA strand e	1e-06
PRK05035	695	PRK05035, PRK05035, electron transport complex pro	1e-06
COG0419	908	COG0419, SbcC, ATPase involved in DNA repair [DNA	1e-06
COG3064	387	COG3064, TolA, Membrane protein involved in colici	2e-06
PTZ00108	1388	PTZ00108, PTZ00108, DNA topoisomerase 2-like prote	2e-06
PTZ00108	1388	PTZ00108, PTZ00108, DNA topoisomerase 2-like prote	2e-06
PTZ00108	1388	PTZ00108, PTZ00108, DNA topoisomerase 2-like prote	2e-06
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	2e-06
PTZ00372	413	PTZ00372, PTZ00372, endonuclease 4-like protein; P	2e-06
PRK04195	482	PRK04195, PRK04195, replication factor C large sub	2e-06
TIGR03319	514	TIGR03319, RNase_Y, ribonuclease Y	2e-06
PRK11192	434	PRK11192, PRK11192, ATP-dependent RNA helicase Srm	2e-06
PRK11192	434	PRK11192, PRK11192, ATP-dependent RNA helicase Srm	2e-06
PRK04195	482	PRK04195, PRK04195, replication factor C large sub	3e-06
PRK13808	333	PRK13808, PRK13808, adenylate kinase; Provisional	3e-06
pfam02029	431	pfam02029, Caldesmon, Caldesmon	3e-06
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	4e-06
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	4e-06
TIGR02168	1179	TIGR02168, SMC_prok_B, chromosome segregation prot	4e-06
PTZ00053	470	PTZ00053, PTZ00053, methionine aminopeptidase 2; P	4e-06
pfam13904	261	pfam13904, DUF4207, Domain of unknown function (DU	4e-06
PTZ00108	1388	PTZ00108, PTZ00108, DNA topoisomerase 2-like prote	5e-06
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	5e-06
PTZ00372	413	PTZ00372, PTZ00372, endonuclease 4-like protein; P	5e-06
pfam05262	489	pfam05262, Borrelia_P83, Borrelia P83/100 protein	5e-06
PRK04195	482	PRK04195, PRK04195, replication factor C large sub	5e-06
PRK04195	482	PRK04195, PRK04195, replication factor C large sub	5e-06
COG1293	564	COG1293, COG1293, Predicted RNA-binding protein ho	5e-06
COG1293	564	COG1293, COG1293, Predicted RNA-binding protein ho	5e-06
PLN02967	581	PLN02967, PLN02967, kinase	5e-06
PRK03918	880	PRK03918, PRK03918, chromosome segregation protein	5e-06
TIGR01554	384	TIGR01554, major_cap_HK97, phage major capsid prot	5e-06
PRK04195	482	PRK04195, PRK04195, replication factor C large sub	6e-06
pfam02029	431	pfam02029, Caldesmon, Caldesmon	6e-06
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	7e-06
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	7e-06
PRK13808	333	PRK13808, PRK13808, adenylate kinase; Provisional	7e-06
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	8e-06
PRK12903	925	PRK12903, secA, preprotein translocase subunit Sec	8e-06
PTZ00372	413	PTZ00372, PTZ00372, endonuclease 4-like protein; P	9e-06
PRK13808	333	PRK13808, PRK13808, adenylate kinase; Provisional	9e-06
PRK03918	880	PRK03918, PRK03918, chromosome segregation protein	9e-06
PRK03918	880	PRK03918, PRK03918, chromosome segregation protein	9e-06
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	1e-05
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	1e-05
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	1e-05
PRK04195	482	PRK04195, PRK04195, replication factor C large sub	1e-05
PRK04195	482	PRK04195, PRK04195, replication factor C large sub	1e-05
PRK04195	482	PRK04195, PRK04195, replication factor C large sub	1e-05
pfam04615	728	pfam04615, Utp14, Utp14 protein	1e-05
TIGR02168	1179	TIGR02168, SMC_prok_B, chromosome segregation prot	1e-05
PTZ00053	470	PTZ00053, PTZ00053, methionine aminopeptidase 2; P	1e-05
pfam00078	194	pfam00078, RVT_1, Reverse transcriptase (RNA-depen	1e-05
PRK10811	1068	PRK10811, rne, ribonuclease E; Reviewed	1e-05
PRK00247	429	PRK00247, PRK00247, putative inner membrane protei	1e-05
pfam06375	561	pfam06375, BLVR, Bovine leukaemia virus receptor (	1e-05
PLN03237	1465	PLN03237, PLN03237, DNA topoisomerase 2; Provision	1e-05
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	2e-05
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	2e-05
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	2e-05
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	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
pfam04615	728	pfam04615, Utp14, Utp14 protein	2e-05
pfam06375	561	pfam06375, BLVR, Bovine leukaemia virus receptor (	2e-05
TIGR02169	1164	TIGR02169, SMC_prok_A, chromosome segregation prot	2e-05
CHL00204	1832	CHL00204, ycf1, Ycf1; Provisional	2e-05
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	3e-05
PRK04195	482	PRK04195, PRK04195, replication factor C large sub	3e-05
PRK12903	925	PRK12903, secA, preprotein translocase subunit Sec	3e-05
PRK10811	1068	PRK10811, rne, ribonuclease E; Reviewed	3e-05
PRK00247	429	PRK00247, PRK00247, putative inner membrane protei	3e-05
PRK00247	429	PRK00247, PRK00247, putative inner membrane protei	3e-05
pfam07767	387	pfam07767, Nop53, Nop53 (60S ribosomal biogenesis)	3e-05
pfam04086	272	pfam04086, SRP-alpha_N, Signal recognition particl	3e-05
pfam05793	528	pfam05793, TFIIF_alpha, Transcription initiation f	3e-05
pfam05764	238	pfam05764, YL1, YL1 nuclear protein	3e-05
COG4499	434	COG4499, COG4499, Predicted membrane protein [Func	3e-05
pfam08432	182	pfam08432, DUF1742, Fungal protein of unknown func	3e-05
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	4e-05
PRK13808	333	PRK13808, PRK13808, adenylate kinase; Provisional	4e-05
PRK00448	1437	PRK00448, polC, DNA polymerase III PolC; Validated	4e-05
pfam05087	887	pfam05087, Rota_VP2, Rotavirus VP2 protein	4e-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
PRK04195	482	PRK04195, PRK04195, replication factor C large sub	5e-05
pfam09507	427	pfam09507, CDC27, DNA polymerase subunit Cdc27	5e-05
PLN02967	581	PLN02967, PLN02967, kinase	5e-05
pfam08432	182	pfam08432, DUF1742, Fungal protein of unknown func	5e-05
pfam05262	489	pfam05262, Borrelia_P83, Borrelia P83/100 protein	6e-05
TIGR02168	1179	TIGR02168, SMC_prok_B, chromosome segregation prot	6e-05
PRK10811	1068	PRK10811, rne, ribonuclease E; Reviewed	6e-05
pfam08432	182	pfam08432, DUF1742, Fungal protein of unknown func	6e-05
PRK04195	482	PRK04195, PRK04195, replication factor C large sub	7e-05
PRK00409	782	PRK00409, PRK00409, recombination and DNA strand e	7e-05
CHL00189	742	CHL00189, infB, translation initiation factor 2; P	7e-05
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	8e-05
PTZ00372	413	PTZ00372, PTZ00372, endonuclease 4-like protein; P	8e-05
pfam13904	261	pfam13904, DUF4207, Domain of unknown function (DU	8e-05
CHL00189	742	CHL00189, infB, translation initiation factor 2; P	8e-05
PTZ00108	1388	PTZ00108, PTZ00108, DNA topoisomerase 2-like prote	9e-05
COG0419	908	COG0419, SbcC, ATPase involved in DNA repair [DNA	9e-05
pfam05087	887	pfam05087, Rota_VP2, Rotavirus VP2 protein	9e-05
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	1e-04
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	1e-04
TIGR02794	346	TIGR02794, tolA_full, TolA protein	1e-04
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	1e-04
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	1e-04
PRK05035	695	PRK05035, PRK05035, electron transport complex pro	1e-04
COG0419	908	COG0419, SbcC, ATPase involved in DNA repair [DNA	1e-04
COG0419	908	COG0419, SbcC, ATPase involved in DNA repair [DNA	1e-04
PRK11192	434	PRK11192, PRK11192, ATP-dependent RNA helicase Srm	1e-04
pfam06375	561	pfam06375, BLVR, Bovine leukaemia virus receptor (	1e-04
CHL00204	1832	CHL00204, ycf1, Ycf1; Provisional	1e-04
PRK07735	430	PRK07735, PRK07735, NADH dehydrogenase subunit C;	1e-04
COG3064	387	COG3064, TolA, Membrane protein involved in colici	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
PRK00409	782	PRK00409, PRK00409, recombination and DNA strand e	2e-04
PRK05035	695	PRK05035, PRK05035, electron transport complex pro	2e-04
COG0419	908	COG0419, SbcC, ATPase involved in DNA repair [DNA	2e-04
TIGR03319	514	TIGR03319, RNase_Y, ribonuclease Y	2e-04
PRK11192	434	PRK11192, PRK11192, ATP-dependent RNA helicase Srm	2e-04
PRK13808	333	PRK13808, PRK13808, adenylate kinase; Provisional	2e-04
pfam12569	516	pfam12569, NARP1, NMDA receptor-regulated protein	2e-04
PRK11642	813	PRK11642, PRK11642, exoribonuclease R; Provisional	2e-04
PRK11642	813	PRK11642, PRK11642, exoribonuclease R; Provisional	2e-04
pfam07423	214	pfam07423, DUF1510, Protein of unknown function (D	2e-04
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	3e-04
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	3e-04
PTZ00372	413	PTZ00372, PTZ00372, endonuclease 4-like protein; P	3e-04
PTZ00372	413	PTZ00372, PTZ00372, endonuclease 4-like protein; P	3e-04
PRK04195	482	PRK04195, PRK04195, replication factor C large sub	3e-04
pfam09507	427	pfam09507, CDC27, DNA polymerase subunit Cdc27	3e-04
COG5116	926	COG5116, RPN2, 26S proteasome regulatory complex c	3e-04
pfam10310	436	pfam10310, DUF2413, Protein of unknown function (D	3e-04
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	4e-04
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	4e-04
PRK11192	434	PRK11192, PRK11192, ATP-dependent RNA helicase Srm	4e-04
TIGR02168	1179	TIGR02168, SMC_prok_B, chromosome segregation prot	4e-04
PRK12903	925	PRK12903, secA, preprotein translocase subunit Sec	4e-04
pfam06375	561	pfam06375, BLVR, Bovine leukaemia virus receptor (	4e-04
pfam12569	516	pfam12569, NARP1, NMDA receptor-regulated protein	4e-04
pfam00183	529	pfam00183, HSP90, Hsp90 protein	4e-04
pfam07946	322	pfam07946, DUF1682, Protein of unknown function (D	4e-04
PRK05901	509	PRK05901, PRK05901, RNA polymerase sigma factor; P	5e-04
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	5e-04
PRK04195	482	PRK04195, PRK04195, replication factor C large sub	5e-04
pfam09507	427	pfam09507, CDC27, DNA polymerase subunit Cdc27	5e-04
pfam04615	728	pfam04615, Utp14, Utp14 protein	5e-04
COG0419	908	COG0419, SbcC, ATPase involved in DNA repair [DNA	5e-04
PTZ00053	470	PTZ00053, PTZ00053, methionine aminopeptidase 2; P	5e-04
PRK03918	880	PRK03918, PRK03918, chromosome segregation protein	5e-04
TIGR01554	384	TIGR01554, major_cap_HK97, phage major capsid prot	5e-04
pfam06375	561	pfam06375, BLVR, Bovine leukaemia virus receptor (	5e-04
PRK07735	430	PRK07735, PRK07735, NADH dehydrogenase subunit C;	5e-04
PRK11642	813	PRK11642, PRK11642, exoribonuclease R; Provisional	5e-04
pfam07423	214	pfam07423, DUF1510, Protein of unknown function (D	5e-04
pfam07946	322	pfam07946, DUF1682, Protein of unknown function (D	5e-04
COG1579	239	COG1579, COG1579, Zn-ribbon protein, possibly nucl	5e-04
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	6e-04
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	6e-04
PLN02967	581	PLN02967, PLN02967, kinase	6e-04
PRK00247	429	PRK00247, PRK00247, putative inner membrane protei	6e-04
pfam07767	387	pfam07767, Nop53, Nop53 (60S ribosomal biogenesis)	6e-04
pfam08432	182	pfam08432, DUF1742, Fungal protein of unknown func	6e-04
CHL00189	742	CHL00189, infB, translation initiation factor 2; P	6e-04
pfam07423	214	pfam07423, DUF1510, Protein of unknown function (D	6e-04
TIGR01069	771	TIGR01069, mutS2, MutS2 family protein	6e-04
PTZ00372	413	PTZ00372, PTZ00372, endonuclease 4-like protein; P	7e-04
PRK11192	434	PRK11192, PRK11192, ATP-dependent RNA helicase Srm	7e-04
PRK13808	333	PRK13808, PRK13808, adenylate kinase; Provisional	7e-04
TIGR02169	1164	TIGR02169, SMC_prok_A, chromosome segregation prot	7e-04
pfam05793	528	pfam05793, TFIIF_alpha, Transcription initiation f	7e-04
COG4499	434	COG4499, COG4499, Predicted membrane protein [Func	7e-04
PRK11642	813	PRK11642, PRK11642, exoribonuclease R; Provisional	7e-04
COG0810	244	COG0810, TonB, Periplasmic protein TonB, links inn	7e-04
PTZ00108	1388	PTZ00108, PTZ00108, DNA topoisomerase 2-like prote	8e-04
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	8e-04
PRK04195	482	PRK04195, PRK04195, replication factor C large sub	8e-04
PRK11192	434	PRK11192, PRK11192, ATP-dependent RNA helicase Srm	8e-04
PRK11192	434	PRK11192, PRK11192, ATP-dependent RNA helicase Srm	8e-04
PLN02967	581	PLN02967, PLN02967, kinase	8e-04
TIGR02169	1164	TIGR02169, SMC_prok_A, chromosome segregation prot	8e-04
pfam12569	516	pfam12569, NARP1, NMDA receptor-regulated protein	8e-04
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	9e-04
TIGR02169	1164	TIGR02169, SMC_prok_A, chromosome segregation prot	9e-04
PRK11642	813	PRK11642, PRK11642, exoribonuclease R; Provisional	9e-04
TIGR01069	771	TIGR01069, mutS2, MutS2 family protein	9e-04
pfam03154	979	pfam03154, Atrophin-1, Atrophin-1 family	9e-04
pfam10243	506	pfam10243, MIP-T3, Microtubule-binding protein MIP	0.001
PTZ00108	1388	PTZ00108, PTZ00108, DNA topoisomerase 2-like prote	0.001
PRK05035	695	PRK05035, PRK05035, electron transport complex pro	0.001
COG0419	908	COG0419, SbcC, ATPase involved in DNA repair [DNA	0.001
COG0419	908	COG0419, SbcC, ATPase involved in DNA repair [DNA	0.001
TIGR03319	514	TIGR03319, RNase_Y, ribonuclease Y	0.001
PRK11192	434	PRK11192, PRK11192, ATP-dependent RNA helicase Srm	0.001
PTZ00053	470	PTZ00053, PTZ00053, methionine aminopeptidase 2; P	0.001
pfam13904	261	pfam13904, DUF4207, Domain of unknown function (DU	0.001
TIGR02169	1164	TIGR02169, SMC_prok_A, chromosome segregation prot	0.001
pfam05087	887	pfam05087, Rota_VP2, Rotavirus VP2 protein	0.001
CHL00189	742	CHL00189, infB, translation initiation factor 2; P	0.001
pfam12569	516	pfam12569, NARP1, NMDA receptor-regulated protein	0.001
pfam07423	214	pfam07423, DUF1510, Protein of unknown function (D	0.001
TIGR01069	771	TIGR01069, mutS2, MutS2 family protein	0.001
TIGR00927	1096	TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger	0.001
TIGR00927	1096	TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger	0.001
COG5269	379	COG5269, ZUO1, Ribosome-associated chaperone zuoti	0.001
pfam03343	603	pfam03343, SART-1, SART-1 family	0.001
pfam03343	603	pfam03343, SART-1, SART-1 family	0.001
PLN02381	1066	PLN02381, PLN02381, valyl-tRNA synthetase	0.001
PLN02381	1066	PLN02381, PLN02381, valyl-tRNA synthetase	0.001
PRK13735	942	PRK13735, PRK13735, conjugal transfer mating pair	0.001
COG5182	429	COG5182, CUS1, Splicing factor 3b, subunit 2 [RNA	0.001
pfam10243	506	pfam10243, MIP-T3, Microtubule-binding protein MIP	0.002
COG3064	387	COG3064, TolA, Membrane protein involved in colici	0.002
PTZ00108	1388	PTZ00108, PTZ00108, DNA topoisomerase 2-like prote	0.002
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	0.002
COG0419	908	COG0419, SbcC, ATPase involved in DNA repair [DNA	0.002
PTZ00053	470	PTZ00053, PTZ00053, methionine aminopeptidase 2; P	0.002
PLN03237	1465	PLN03237, PLN03237, DNA topoisomerase 2; Provision	0.002
TIGR02169	1164	TIGR02169, SMC_prok_A, chromosome segregation prot	0.002
PRK11642	813	PRK11642, PRK11642, exoribonuclease R; Provisional	0.002
pfam07946	322	pfam07946, DUF1682, Protein of unknown function (D	0.002
TIGR01069	771	TIGR01069, mutS2, MutS2 family protein	0.002
pfam03154	979	pfam03154, Atrophin-1, Atrophin-1 family	0.002
pfam03154	979	pfam03154, Atrophin-1, Atrophin-1 family	0.002
pfam03154	979	pfam03154, Atrophin-1, Atrophin-1 family	0.002
COG5269	379	COG5269, ZUO1, Ribosome-associated chaperone zuoti	0.002
pfam08208	193	pfam08208, RNA_polI_A34, DNA-directed RNA polymera	0.002
TIGR01642	509	TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, la	0.002
pfam14181	155	pfam14181, YqfQ, YqfQ-like protein	0.002
pfam13476	204	pfam13476, AAA_23, AAA domain	0.002
smart00435	391	smart00435, TOPEUc, DNA Topoisomerase I (eukaryota	0.002
pfam05758	832	pfam05758, Ycf1, Ycf1	0.002
pfam10243	506	pfam10243, MIP-T3, Microtubule-binding protein MIP	0.003
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	0.003
PRK00409	782	PRK00409, PRK00409, recombination and DNA strand e	0.003
COG0419	908	COG0419, SbcC, ATPase involved in DNA repair [DNA	0.003
PRK11192	434	PRK11192, PRK11192, ATP-dependent RNA helicase Srm	0.003
PRK03918	880	PRK03918, PRK03918, chromosome segregation protein	0.003
TIGR01554	384	TIGR01554, major_cap_HK97, phage major capsid prot	0.003
CHL00204	1832	CHL00204, ycf1, Ycf1; Provisional	0.003
PRK07735	430	PRK07735, PRK07735, NADH dehydrogenase subunit C;	0.003
PRK11642	813	PRK11642, PRK11642, exoribonuclease R; Provisional	0.003
TIGR00927	1096	TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger	0.003
pfam03343	603	pfam03343, SART-1, SART-1 family	0.003
pfam08208	193	pfam08208, RNA_polI_A34, DNA-directed RNA polymera	0.003
COG4942	420	COG4942, COG4942, Membrane-bound metallopeptidase	0.003
COG4487	438	COG4487, COG4487, Uncharacterized protein conserve	0.003
pfam13166	713	pfam13166, AAA_13, AAA domain	0.003
PTZ00399	651	PTZ00399, PTZ00399, cysteinyl-tRNA-synthetase; Pro	0.003
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	0.004
COG0419	908	COG0419, SbcC, ATPase involved in DNA repair [DNA	0.004
TIGR03319	514	TIGR03319, RNase_Y, ribonuclease Y	0.004
COG4499	434	COG4499, COG4499, Predicted membrane protein [Func	0.004
pfam12569	516	pfam12569, NARP1, NMDA receptor-regulated protein	0.004
COG0810	244	COG0810, TonB, Periplasmic protein TonB, links inn	0.004
PLN02381	1066	PLN02381, PLN02381, valyl-tRNA synthetase	0.004
PLN02381	1066	PLN02381, PLN02381, valyl-tRNA synthetase	0.004
pfam14181	155	pfam14181, YqfQ, YqfQ-like protein	0.004
COG4487	438	COG4487, COG4487, Uncharacterized protein conserve	0.004
pfam13166	713	pfam13166, AAA_13, AAA domain	0.004
PRK05771	646	PRK05771, PRK05771, V-type ATP synthase subunit I;	0.004

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

 Score = 82.1 bits (202), Expect = 1e-16
 Identities = 62/182 (34%), Positives = 95/182 (52%), Gaps = 3/182 (1%)

Query: 4    KKEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKKKE 63
            KK E+KKK     K +EK K    K++ EE +   + K K  + K + +  KKK  + K+
Sbjct: 1284 KKAEEKKKADEAKKAEEKKKADEAKKKAEEAKKADEAKKKAEEAKKKADAAKKKAEEAKK 1343

Query: 64   KNKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKEEE 123
              +    + E    +    ++K +   + +KEE KK+A+  KKK + K+K     +K EE
Sbjct: 1344 AAEAAKAEAEAAADEAEAAEEKAE-AAEKKKEEAKKKADAAKKKAEEKKKADEAKKKAEE 1402

Query: 124  EKKKEAEEKKKKRTKKK--EKNKNKSRKEEEEEEKKKKKKKKKKKRTKKKEEEKRKNEKA 181
            +KKK  E KK    KKK  E  K    K++ +E KKK ++ KK    KKK EE +K E+A
Sbjct: 1403 DKKKADELKKAAAAKKKADEAKKKAEEKKKADEAKKKAEEAKKADEAKKKAEEAKKAEEA 1462

Query: 182  VR 183
             +
Sbjct: 1463 KK 1464

Length = 2084

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

 Score = 78.3 bits (192), Expect = 2e-15
 Identities = 64/180 (35%), Positives = 97/180 (53%), Gaps = 2/180 (1%)

Query: 2    KNKKEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKK 61
            K K+E KKK    + K +EK K    K++ EE + K  E  K    K + +E KKK  +K
Sbjct: 1371 KKKEEAKKKADAAKKKAEEKKKADEAKKKAEEDKKKADELKKAAAAKKKADEAKKKAEEK 1430

Query: 62   KEKNKNKNRKEEKKKKKKRRTKKKEKNK--NKSRKEEKKKEAEEEKKKTKNKEKNKNKSR 119
            K+ ++ K + EE KK  + + K +E  K     +K E+ K+A+E KKK +  +K     +
Sbjct: 1431 KKADEAKKKAEEAKKADEAKKKAEEAKKAEEAKKKAEEAKKADEAKKKAEEAKKADEAKK 1490

Query: 120  KEEEEKKKEAEEKKKKRTKKKEKNKNKSRKEEEEEEKKKKKKKKKKKRTKKKEEEKRKNE 179
            K EE KKK  E KK    KKK     K+ + ++ +E KK ++ KK    KK EE+K+ +E
Sbjct: 1491 KAEEAKKKADEAKKAAEAKKKADEAKKAEEAKKADEAKKAEEAKKADEAKKAEEKKKADE 1550

Length = 2084

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

 Score = 78.3 bits (192), Expect = 2e-15
 Identities = 59/180 (32%), Positives = 91/180 (50%), Gaps = 3/180 (1%)

Query: 4    KKEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKKKE 63
            K EEKKK  + + K +E  K    K++ EE + K     KK +   +  E  K   +   
Sbjct: 1297 KAEEKKKADEAKKKAEEAKKADEAKKKAEEAKKKADAAKKKAEEAKKAAEAAKAEAEAAA 1356

Query: 64   KNKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKEEE 123
                   ++ +  +KK+   KK+ +  K + EEKKK A+E KKK +  +K  ++ +K   
Sbjct: 1357 DEAEAAEEKAEAAEKKKEEAKKKADAAKKKAEEKKK-ADEAKKKAEEDKKKADELKKAAA 1415

Query: 124  EKKKEAEEKKKKRTKKK--EKNKNKSRKEEEEEEKKKKKKKKKKKRTKKKEEEKRKNEKA 181
             KKK  E KKK   KKK  E  K     ++ +E KKK ++ KK +  KKK EE +K ++A
Sbjct: 1416 AKKKADEAKKKAEEKKKADEAKKKAEEAKKADEAKKKAEEAKKAEEAKKKAEEAKKADEA 1475

Length = 2084

>gnl|CDD|238827 cd01650, RT_nLTR_like, RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT)

 Score = 74.6 bits (184), Expect = 2e-15
 Identities = 33/120 (27%), Positives = 52/120 (43%), Gaps = 15/120 (12%)

Query: 226 GCIQGGHMSGLLFSLFINDIAEI----------FPGFNFWLFADDLKVALRVGGQREVDS 275
           G  QG  +S LLF+L ++D+  +           PG     +ADD+ +      +     
Sbjct: 106 GVRQGDPLSPLLFNLALDDLLRLLNKEEEIKLGGPGITHLAYADDIVLFSEGKSR----K 161

Query: 276 MQSMLSRLYHWCSINKMELNIGKCMVMTYHRNKSPILASYDINGQALARCEQVRDLGVTF 335
           +Q +L RL  W   + +++N  K  VM    NK   L    +NG  +   E  + LGVT 
Sbjct: 162 LQELLQRLQEWSKESGLKINPSKSKVMLI-GNKKKRLKDITLNGTPIEAVETFKYLGVTI 220

This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities. Length = 220

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

 Score = 74.8 bits (183), Expect = 2e-14
 Identities = 57/181 (31%), Positives = 95/181 (52%), Gaps = 1/181 (0%)

Query: 2    KNKKEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKK 61
            K K EE KK  + + K +E  K     +++ E+  K  E  K     +  E E  +   +
Sbjct: 1308 KKKAEEAKKADEAKKKAEEAKKKADAAKKKAEEAKKAAEAAKAEAEAAADEAEAAEEKAE 1367

Query: 62   KEKNKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKE 121
              + K +  K++    KK+  +KK+ ++ K + EE KK+A+E KK    K+K     +K 
Sbjct: 1368 AAEKKKEEAKKKADAAKKKAEEKKKADEAKKKAEEDKKKADELKKAAAAKKKADEAKKKA 1427

Query: 122  EEEKKKEAEEKKKKRTKKKEKNKNKS-RKEEEEEEKKKKKKKKKKKRTKKKEEEKRKNEK 180
            EE+KK +  +KK +  KK ++ K K+   ++ EE KKK ++ KK    KKK EE +K ++
Sbjct: 1428 EEKKKADEAKKKAEEAKKADEAKKKAEEAKKAEEAKKKAEEAKKADEAKKKAEEAKKADE 1487

Query: 181  A 181
            A
Sbjct: 1488 A 1488

Length = 2084

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

 Score = 74.8 bits (183), Expect = 3e-14
 Identities = 57/185 (30%), Positives = 101/185 (54%), Gaps = 7/185 (3%)

Query: 4    KKEEKKKKKKRRTKKKEKNKNKSRKEEEEEK----RTKKKEKNKKNKNKSRKEEEKKK-- 57
            K E +    +    +++    + +KEE ++K    + K +EK K ++ K + EE+KKK  
Sbjct: 1349 KAEAEAAADEAEAAEEKAEAAEKKKEEAKKKADAAKKKAEEKKKADEAKKKAEEDKKKAD 1408

Query: 58   RTKKKEKNKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNK 117
              KK    K K  + +KK ++K++  + +K   +++K ++ K+  EE KK +  +K   +
Sbjct: 1409 ELKKAAAAKKKADEAKKKAEEKKKADEAKKKAEEAKKADEAKKKAEEAKKAEEAKKKAEE 1468

Query: 118  SRKEEEEKKKEAEEKKKKRTKKK-EKNKNKSRKEEEEEEKKKKKKKKKKKRTKKKEEEKR 176
            ++K +E KKK  E KK    KKK E+ K K+ + ++  E KKK  + KK    KK +E +
Sbjct: 1469 AKKADEAKKKAEEAKKADEAKKKAEEAKKKADEAKKAAEAKKKADEAKKAEEAKKADEAK 1528

Query: 177  KNEKA 181
            K E+A
Sbjct: 1529 KAEEA 1533

Length = 2084

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

 Score = 73.6 bits (180), Expect = 6e-14
 Identities = 68/191 (35%), Positives = 96/191 (50%), Gaps = 14/191 (7%)

Query: 2    KNKKEEKKKKKKRRTKKKEKNKNK---SRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKR 58
            K K EE KKK     KK E+ K     ++ E E      +  + K    + +KEE KKK 
Sbjct: 1321 KKKAEEAKKKADAAKKKAEEAKKAAEAAKAEAEAAADEAEAAEEKAEAAEKKKEEAKKKA 1380

Query: 59   TKKKEKNKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKS 118
               K+K + K + +E KKK +   KK ++ K   +    KK+A+E KKK + K+K     
Sbjct: 1381 DAAKKKAEEKKKADEAKKKAEEDKKKADELK---KAAAAKKKADEAKKKAEEKKKADEAK 1437

Query: 119  RKEEEEKK-----KEAEEKKKKRTKKK---EKNKNKSRKEEEEEEKKKKKKKKKKKRTKK 170
            +K EE KK     K+AEE KK    KK   E  K    K++ EE KK  + KKK +  KK
Sbjct: 1438 KKAEEAKKADEAKKKAEEAKKAEEAKKKAEEAKKADEAKKKAEEAKKADEAKKKAEEAKK 1497

Query: 171  KEEEKRKNEKA 181
            K +E +K  +A
Sbjct: 1498 KADEAKKAAEA 1508

Length = 2084

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

 Score = 73.6 bits (180), Expect = 7e-14
 Identities = 64/187 (34%), Positives = 105/187 (56%), Gaps = 7/187 (3%)

Query: 4    KKEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKKKE 63
            KK E+KKK     KK E++K K+ + ++     KK ++ KK   + +K +E KK+ ++ +
Sbjct: 1385 KKAEEKKKADEAKKKAEEDKKKADELKKAAAAKKKADEAKKKAEEKKKADEAKKKAEEAK 1444

Query: 64   KNKNKNRKEEKKKKKKRRTKKKEKNKNKS---RKEEKKKEAEEEKKKTKNKEKNKNKSRK 120
            K     +K E+ KK +   KK E+ K      +K E+ K+A+E KKK +  +K  ++++K
Sbjct: 1445 KADEAKKKAEEAKKAEEAKKKAEEAKKADEAKKKAEEAKKADEAKKKAEEAKKKADEAKK 1504

Query: 121  EEEEKKKEAEEKKKKRTKKKEKNKNKSRKEEEEEEKKKKKKKK----KKKRTKKKEEEKR 176
              E KKK  E KK +  KK ++ K     ++ +E KK ++KKK    KK    KK EEK+
Sbjct: 1505 AAEAKKKADEAKKAEEAKKADEAKKAEEAKKADEAKKAEEKKKADELKKAEELKKAEEKK 1564

Query: 177  KNEKAVR 183
            K E+A +
Sbjct: 1565 KAEEAKK 1571

Length = 2084

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

 Score = 73.6 bits (180), Expect = 7e-14
 Identities = 66/188 (35%), Positives = 99/188 (52%), Gaps = 9/188 (4%)

Query: 2    KNKKEEKKKK---KKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKR 58
            K K EE KK     K   +        + ++ E  ++ K++ K K +  K + EE+KK  
Sbjct: 1335 KKKAEEAKKAAEAAKAEAEAAADEAEAAEEKAEAAEKKKEEAKKKADAAKKKAEEKKKAD 1394

Query: 59   TKKKEKNKNKNRKEEKKKK---KKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNK 115
              KK+  ++K + +E KK    KK+  + K+K + K + +E KK+AEE KK  + K+K +
Sbjct: 1395 EAKKKAEEDKKKADELKKAAAAKKKADEAKKKAEEKKKADEAKKKAEEAKKADEAKKKAE 1454

Query: 116  NKSRKEEEEKKKEAEEKKKKRTKKK--EKNKNKSRKEEEEEEKKKKKKKKKKKRTKKKEE 173
               +K EE KKK  E KK    KKK  E  K    K++ EE KKK  + KK    KKK +
Sbjct: 1455 EA-KKAEEAKKKAEEAKKADEAKKKAEEAKKADEAKKKAEEAKKKADEAKKAAEAKKKAD 1513

Query: 174  EKRKNEKA 181
            E +K E+A
Sbjct: 1514 EAKKAEEA 1521

Length = 2084

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

 Score = 72.6 bits (179), Expect = 1e-13
 Identities = 36/176 (20%), Positives = 74/176 (42%), Gaps = 11/176 (6%)

Query: 2   KNKKEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKK 61
           K      K+  ++  +   + K+ S   EEEE R ++            K E +++   +
Sbjct: 11  KELGVSSKELLEKLKELGIEVKSHSSTVEEEEARKEEA-----------KREAEEEAKAE 59

Query: 62  KEKNKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKE 121
            E+      +EE K +       +E  +  +  E   + AE+E  +       + K++K 
Sbjct: 60  AEEAAAAEAEEEAKAEAAAAAPAEEAAEAAAAAEAAARPAEDEAARPAEAAARRPKAKKA 119

Query: 122 EEEKKKEAEEKKKKRTKKKEKNKNKSRKEEEEEEKKKKKKKKKKKRTKKKEEEKRK 177
            ++KK    +KKK + K     K     +     + +++++KKKK+ K  E+  R+
Sbjct: 120 AKKKKGPKPKKKKPKRKAARGGKRGKGGKGRRRRRGRRRRRKKKKKQKPTEKIPRE 175

Length = 746

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

 Score = 71.8 bits (177), Expect = 2e-13
 Identities = 33/175 (18%), Positives = 75/175 (42%), Gaps = 2/175 (1%)

Query: 12  KKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKKKEKNKNKNRK 71
            K R  +  K    S KE  E  + K+     K+ + + +EEE +K   K+E  +    +
Sbjct: 2   SKVRVYELAKELGVSSKELLE--KLKELGIEVKSHSSTVEEEEARKEEAKREAEEEAKAE 59

Query: 72  EEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKEEEEKKKEAEE 131
            E+    +   + K +    +  EE  + A   +   +  E    +  +    + K  + 
Sbjct: 60  AEEAAAAEAEEEAKAEAAAAAPAEEAAEAAAAAEAAARPAEDEAARPAEAAARRPKAKKA 119

Query: 132 KKKKRTKKKEKNKNKSRKEEEEEEKKKKKKKKKKKRTKKKEEEKRKNEKAVRLTK 186
            KKK+  K +K K K +     +  K  K +++++  +++ ++K+K +   ++ +
Sbjct: 120 AKKKKGPKPKKKKPKRKAARGGKRGKGGKGRRRRRGRRRRRKKKKKQKPTEKIPR 174

Length = 746

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

 Score = 71.3 bits (174), Expect = 4e-13
 Identities = 64/188 (34%), Positives = 103/188 (54%), Gaps = 9/188 (4%)

Query: 2    KNKKEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKK 61
            + +  E+K +   + K++ K K  + K++ EEK+   + K K  ++K + +E KK    K
Sbjct: 1358 EAEAAEEKAEAAEKKKEEAKKKADAAKKKAEEKKKADEAKKKAEEDKKKADELKKAAAAK 1417

Query: 62   KEKNKNKNRKEEKKKKKKRRTKKKEKNKNKS--RKEEKKKEAEEEKKKTKNKEKNKNKSR 119
            K+ ++ K + EEKKK  + + K +E  K     +K E+ K+AEE KKK +  +K     +
Sbjct: 1418 KKADEAKKKAEEKKKADEAKKKAEEAKKADEAKKKAEEAKKAEEAKKKAEEAKKADEAKK 1477

Query: 120  KEEEEKK-----KEAEEKKKK--RTKKKEKNKNKSRKEEEEEEKKKKKKKKKKKRTKKKE 172
            K EE KK     K+AEE KKK    KK  + K K+ + ++ EE KK  + KK +  KK +
Sbjct: 1478 KAEEAKKADEAKKKAEEAKKKADEAKKAAEAKKKADEAKKAEEAKKADEAKKAEEAKKAD 1537

Query: 173  EEKRKNEK 180
            E K+  EK
Sbjct: 1538 EAKKAEEK 1545

Length = 2084

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

 Score = 70.9 bits (173), Expect = 5e-13
 Identities = 62/179 (34%), Positives = 103/179 (57%), Gaps = 7/179 (3%)

Query: 4    KKEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKKKE 63
            KK E+ KKK    KK    K K+ + +++ +  KK ++ KK   +++K +E KK+ ++ +
Sbjct: 1398 KKAEEDKKKADELKKAAAAKKKADEAKKKAEEKKKADEAKKKAEEAKKADEAKKKAEEAK 1457

Query: 64   KNKNKNRKEEKKKK----KKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSR 119
            K +   +K E+ KK    KK+  + K+ ++ K + EE KK+A+E KK  + K+K     +
Sbjct: 1458 KAEEAKKKAEEAKKADEAKKKAEEAKKADEAKKKAEEAKKKADEAKKAAEAKKKADEAKK 1517

Query: 120  KEEEEKKKE---AEEKKKKRTKKKEKNKNKSRKEEEEEEKKKKKKKKKKKRTKKKEEEK 175
             EE +K  E   AEE KK    KK + K K+ + ++ EE KK ++KKK +  KK EE+K
Sbjct: 1518 AEEAKKADEAKKAEEAKKADEAKKAEEKKKADELKKAEELKKAEEKKKAEEAKKAEEDK 1576

Length = 2084

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

 Score = 70.9 bits (173), Expect = 5e-13
 Identities = 57/180 (31%), Positives = 93/180 (51%), Gaps = 2/180 (1%)

Query: 6    EEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKKKEKN 65
            EE +K ++ R     + +   + EE  +    KK + KK  ++++K EEKKK  + K+K 
Sbjct: 1252 EEIRKFEEARMAHFARRQAAIKAEEARKADELKKAEEKKKADEAKKAEEKKKADEAKKKA 1311

Query: 66   KNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKEEEEK 125
            +   + +E KKK +   KK +  K K+ + +K  EA + + +    E    + + E  EK
Sbjct: 1312 EEAKKADEAKKKAEEAKKKADAAKKKAEEAKKAAEAAKAEAEAAADEAEAAEEKAEAAEK 1371

Query: 126  KKEAEEKKKKRTKKK--EKNKNKSRKEEEEEEKKKKKKKKKKKRTKKKEEEKRKNEKAVR 183
            KKE  +KK    KKK  EK K    K++ EE+KKK  + KK    KKK +E +K  +  +
Sbjct: 1372 KKEEAKKKADAAKKKAEEKKKADEAKKKAEEDKKKADELKKAAAAKKKADEAKKKAEEKK 1431

Length = 2084

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

 Score = 70.9 bits (173), Expect = 5e-13
 Identities = 58/186 (31%), Positives = 106/186 (56%), Gaps = 3/186 (1%)

Query: 4    KKEEKKKKKKRRTKKKEKNKNKS---RKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTK 60
            KK E+ K K    KK E+ K K    +K+E EEK+  ++ K  + +NK +  EE KK  +
Sbjct: 1613 KKAEEAKIKAEELKKAEEEKKKVEQLKKKEAEEKKKAEELKKAEEENKIKAAEEAKKAEE 1672

Query: 61   KKEKNKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRK 120
             K+K +   + EE +KK     KK+ +   K+ + +KK+  E++K +   K + +NK + 
Sbjct: 1673 DKKKAEEAKKAEEDEKKAAEALKKEAEEAKKAEELKKKEAEEKKKAEELKKAEEENKIKA 1732

Query: 121  EEEEKKKEAEEKKKKRTKKKEKNKNKSRKEEEEEEKKKKKKKKKKKRTKKKEEEKRKNEK 180
            EE +K+ E ++KK +  KK E+ K K    ++EEEKK ++ +K+K+   ++E ++   ++
Sbjct: 1733 EEAKKEAEEDKKKAEEAKKDEEEKKKIAHLKKEEEKKAEEIRKEKEAVIEEELDEEDEKR 1792

Query: 181  AVRLTK 186
             + + K
Sbjct: 1793 RMEVDK 1798

Length = 2084

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

 Score = 69.1 bits (169), Expect = 5e-13
 Identities = 51/193 (26%), Positives = 85/193 (44%), Gaps = 6/193 (3%)

Query: 2   KNKKEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKK 61
           + +K+   KK++ R KK E+   ++ K+   E+  +K+ + +    K+ K+ E+  +  +
Sbjct: 56  QQQKKPAAKKEQERQKKLEQQAEEAEKQRAAEQARQKELEQRAAAEKAAKQAEQAAKQAE 115

Query: 62  KEKNKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKE 121
           +++   K  +E K K+      K E    K  KEE KK+AEEE K    K   + K +  
Sbjct: 116 EKQ---KQAEEAKAKQAAEAKAKAEAEAEKKAKEEAKKQAEEEAKA---KAAAEAKKKAA 169

Query: 122 EEEKKKEAEEKKKKRTKKKEKNKNKSRKEEEEEEKKKKKKKKKKKRTKKKEEEKRKNEKA 181
           E +KK EAE K K   K K K +    K E  + K   +   K +             KA
Sbjct: 170 EAKKKAEAEAKAKAEAKAKAKAEEAKAKAEAAKAKAAAEAAAKAEAEAAAAAAAEAERKA 229

Query: 182 VRLTKLSAFGISG 194
                   FG++ 
Sbjct: 230 DEAELGDIFGLAS 242

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 = 69.8 bits (170), Expect = 1e-12
 Identities = 66/186 (35%), Positives = 105/186 (56%), Gaps = 9/186 (4%)

Query: 2    KNKKEEKKKKKKRRT---KKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKR 58
              K EE K    R+    KK E+ + +   +  EE++  K E+ KK +    K EE KK 
Sbjct: 1569 AKKAEEDKNMALRKAEEAKKAEEARIEEVMKLYEEEKKMKAEEAKKAEEAKIKAEELKKA 1628

Query: 59   TKKKEKNKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKS 118
             ++K+K +   +KE ++KKK    KK E+ +NK +  E+ K+AEE+KKK +  +K +   
Sbjct: 1629 EEEKKKVEQLKKKEAEEKKKAEELKKAEE-ENKIKAAEEAKKAEEDKKKAEEAKKAEEDE 1687

Query: 119  RKEEEEKKKEAEEKKK-----KRTKKKEKNKNKSRKEEEEEEKKKKKKKKKKKRTKKKEE 173
            +K  E  KKEAEE KK     K+  +++K   + +K EEE + K ++ KK+ +  KKK E
Sbjct: 1688 KKAAEALKKEAEEAKKAEELKKKEAEEKKKAEELKKAEEENKIKAEEAKKEAEEDKKKAE 1747

Query: 174  EKRKNE 179
            E +K+E
Sbjct: 1748 EAKKDE 1753

Length = 2084

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

 Score = 69.8 bits (170), Expect = 1e-12
 Identities = 62/181 (34%), Positives = 107/181 (59%), Gaps = 4/181 (2%)

Query: 4    KKEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKKKE 63
            KK E+ + ++     +E+ K K+ + ++ E+   K E+ KK + + +K E+ KK+  +++
Sbjct: 1587 KKAEEARIEEVMKLYEEEKKMKAEEAKKAEEAKIKAEELKKAEEEKKKVEQLKKKEAEEK 1646

Query: 64   KNKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKEEE 123
            K   + +K E++ K K   + K+  ++K + EE KK  E+EKK  +  +K   +++K EE
Sbjct: 1647 KKAEELKKAEEENKIKAAEEAKKAEEDKKKAEEAKKAEEDEKKAAEALKKEAEEAKKAEE 1706

Query: 124  EKKKEAEEKKKKRTKKKEKNKNKSR----KEEEEEEKKKKKKKKKKKRTKKKEEEKRKNE 179
             KKKEAEEKKK    KK + +NK +    K+E EE+KKK ++ KK +  KKK    +K E
Sbjct: 1707 LKKKEAEEKKKAEELKKAEEENKIKAEEAKKEAEEDKKKAEEAKKDEEEKKKIAHLKKEE 1766

Query: 180  K 180
            +
Sbjct: 1767 E 1767

Length = 2084

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

 Score = 69.0 bits (168), Expect = 2e-12
 Identities = 54/179 (30%), Positives = 102/179 (56%), Gaps = 3/179 (1%)

Query: 2    KNKKEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKK 61
            K K +E KK ++ +  +++K   +++K EE++    +K +  K   ++R EE  K   ++
Sbjct: 1545 KKKADELKKAEELKKAEEKKKAEEAKKAEEDKNMALRKAEEAKKAEEARIEEVMKLYEEE 1604

Query: 62   KEKNKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKE 121
            K+    + +K E+ K K    KK E+ K K  + +KK+  E++K +   K + +NK +  
Sbjct: 1605 KKMKAEEAKKAEEAKIKAEELKKAEEEKKKVEQLKKKEAEEKKKAEELKKAEEENKIKAA 1664

Query: 122  EEEKKKEAEEKKKKRTKKKEKNKNKSRKEEEEEEKKKKKKKKKKKRTKKKEEEKRKNEK 180
            EE KK E ++KK +  KK E+++   +K  E  +K+ ++ KK ++  KK+ EEK+K E+
Sbjct: 1665 EEAKKAEEDKKKAEEAKKAEEDE---KKAAEALKKEAEEAKKAEELKKKEAEEKKKAEE 1720

Length = 2084

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

 Score = 68.2 bits (166), Expect = 4e-12
 Identities = 48/178 (26%), Positives = 96/178 (53%), Gaps = 1/178 (0%)

Query: 4    KKEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKKKE 63
            K EE++K ++ R  +  K     +K EE +K  ++ +K ++ +N     + ++ R     
Sbjct: 1207 KAEEERKAEEARKAEDAKKAEAVKKAEEAKKDAEEAKKAEEERNNEEIRKFEEARMAHFA 1266

Query: 64   KNKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKEEE 123
            + +   + EE +K  + +  +++K  ++++K E+KK+A+E KKK +  +K     +K EE
Sbjct: 1267 RRQAAIKAEEARKADELKKAEEKKKADEAKKAEEKKKADEAKKKAEEAKKADEAKKKAEE 1326

Query: 124  EKKKEAEEKKKKRTKKKEKNKNKSRKEEEEEEKKKKKKKKKKKRTKKKEEEKRKNEKA 181
             KKK A+  KKK  + K+  +    + E   ++ +  ++K +   KKKEE K+K + A
Sbjct: 1327 AKKK-ADAAKKKAEEAKKAAEAAKAEAEAAADEAEAAEEKAEAAEKKKEEAKKKADAA 1383

Length = 2084

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

 Score = 67.9 bits (165), Expect = 4e-12
 Identities = 44/177 (24%), Positives = 91/177 (51%)

Query: 4    KKEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKKKE 63
            K EE +K +  +  +  K   +++K+ EE K+ +++  N++ +           R +   
Sbjct: 1213 KAEEARKAEDAKKAEAVKKAEEAKKDAEEAKKAEEERNNEEIRKFEEARMAHFARRQAAI 1272

Query: 64   KNKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKEEE 123
            K +   + +E KK ++++   + K   + +K ++ K+  EE KK    +K   +++K+ +
Sbjct: 1273 KAEEARKADELKKAEEKKKADEAKKAEEKKKADEAKKKAEEAKKADEAKKKAEEAKKKAD 1332

Query: 124  EKKKEAEEKKKKRTKKKEKNKNKSRKEEEEEEKKKKKKKKKKKRTKKKEEEKRKNEK 180
              KK+AEE KK     K + +  + + E  EEK +  +KKK++  KK +  K+K E+
Sbjct: 1333 AAKKKAEEAKKAAEAAKAEAEAAADEAEAAEEKAEAAEKKKEEAKKKADAAKKKAEE 1389

Length = 2084

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

 Score = 67.1 bits (163), Expect = 9e-12
 Identities = 68/180 (37%), Positives = 106/180 (58%), Gaps = 2/180 (1%)

Query: 4    KKEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKKKE 63
            ++E+K K ++ +  ++ K K +  K+ EEEK+  ++ K K+ + K + EE KK   + K 
Sbjct: 1602 EEEKKMKAEEAKKAEEAKIKAEELKKAEEEKKKVEQLKKKEAEEKKKAEELKKAEEENKI 1661

Query: 64   KNKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKEEE 123
            K   + +K E+ KKK    KK E+++ K   E  KKEAEE KK  + K+K   + +K EE
Sbjct: 1662 KAAEEAKKAEEDKKKAEEAKKAEEDEKK-AAEALKKEAEEAKKAEELKKKEAEEKKKAEE 1720

Query: 124  EKKKEAEEKKKKRTKKKEKNKNKSRKEE-EEEEKKKKKKKKKKKRTKKKEEEKRKNEKAV 182
             KK E E K K    KKE  ++K + EE +++E++KKK    KK  +KK EE RK ++AV
Sbjct: 1721 LKKAEEENKIKAEEAKKEAEEDKKKAEEAKKDEEEKKKIAHLKKEEEKKAEEIRKEKEAV 1780

Length = 2084

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

 Score = 66.3 bits (161), Expect = 1e-11
 Identities = 54/183 (29%), Positives = 106/183 (57%), Gaps = 3/183 (1%)

Query: 4    KKEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKKKE 63
            KK ++ KK + + K  E  K +  K+ EE+K+ ++ +K +++KN + ++ E+ K+ ++  
Sbjct: 1534 KKADEAKKAEEKKKADELKKAEELKKAEEKKKAEEAKKAEEDKNMALRKAEEAKKAEEAR 1593

Query: 64   KNKNKNRKEEKKKKKKRRTKKKEKNKNKS---RKEEKKKEAEEEKKKTKNKEKNKNKSRK 120
              +     EE+KK K    KK E+ K K+   +K E++K+  E+ KK + +EK K +  K
Sbjct: 1594 IEEVMKLYEEEKKMKAEEAKKAEEAKIKAEELKKAEEEKKKVEQLKKKEAEEKKKAEELK 1653

Query: 121  EEEEKKKEAEEKKKKRTKKKEKNKNKSRKEEEEEEKKKKKKKKKKKRTKKKEEEKRKNEK 180
            + EE+ K    ++ K+ ++ +K   +++K EE+E+K  +  KK+ +  KK EE K+K  +
Sbjct: 1654 KAEEENKIKAAEEAKKAEEDKKKAEEAKKAEEDEKKAAEALKKEAEEAKKAEELKKKEAE 1713

Query: 181  AVR 183
              +
Sbjct: 1714 EKK 1716

Length = 2084

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

 Score = 64.9 bits (158), Expect = 1e-11
 Identities = 39/162 (24%), Positives = 82/162 (50%), Gaps = 4/162 (2%)

Query: 24  NKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKKKEKNKNKNRKEEKKKKKKRRTK 83
           +     ++  +  ++K+   K + + +K+ E++    +K++   + R++E +++      
Sbjct: 44  DPGAVAQQANRIQQQKKPAAKKEQERQKKLEQQAEEAEKQRAAEQARQKELEQRAAAEKA 103

Query: 84  KKEKNKNKSRKEEKKKEAEEEKKKT----KNKEKNKNKSRKEEEEKKKEAEEKKKKRTKK 139
            K+  +   + EEK+K+AEE K K     K K + + + + +EE KK+  EE K K   +
Sbjct: 104 AKQAEQAAKQAEEKQKQAEEAKAKQAAEAKAKAEAEAEKKAKEEAKKQAEEEAKAKAAAE 163

Query: 140 KEKNKNKSRKEEEEEEKKKKKKKKKKKRTKKKEEEKRKNEKA 181
            +K   +++K+ E E K K + K K K  + K + +    KA
Sbjct: 164 AKKKAAEAKKKAEAEAKAKAEAKAKAKAEEAKAKAEAAKAKA 205

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 = 65.5 bits (159), Expect = 2e-11
 Identities = 62/195 (31%), Positives = 107/195 (54%), Gaps = 15/195 (7%)

Query: 2    KNKKEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKK 61
            K   E KKK  + +  ++ K  ++++K EE +K  + K+  +K K    K+ E+ K+ ++
Sbjct: 1503 KKAAEAKKKADEAKKAEEAKKADEAKKAEEAKKADEAKKAEEKKKADELKKAEELKKAEE 1562

Query: 62   KEKNKNKNRKEEKKKKKKRRTKKKEK-------------NKNKSRKEEKKKEAEEEKKKT 108
            K+K +   + EE K    R+ ++ +K              + K  K E+ K+AEE K K 
Sbjct: 1563 KKKAEEAKKAEEDKNMALRKAEEAKKAEEARIEEVMKLYEEEKKMKAEEAKKAEEAKIKA 1622

Query: 109  KNKEKNKNKSRKEEEEKKKEAEEKKKKRTKKKEKNKNKSRKEEEEEEKKKKKKKKKKKRT 168
            +  +K + + +K E+ KKKEAEEKKK    KK + +NK +    EE KK ++ KKK +  
Sbjct: 1623 EELKKAEEEKKKVEQLKKKEAEEKKKAEELKKAEEENKIKA--AEEAKKAEEDKKKAEEA 1680

Query: 169  KKKEEEKRKNEKAVR 183
            KK EE+++K  +A++
Sbjct: 1681 KKAEEDEKKAAEALK 1695

Length = 2084

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

 Score = 64.9 bits (158), Expect = 2e-11
 Identities = 45/180 (25%), Positives = 100/180 (55%), Gaps = 3/180 (1%)

Query: 4   KKEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKKKE 63
           K+ EK   K    K K   + K+   +EEEK  ++ ++ KK K +  KEE K ++ K++ 
Sbjct: 78  KRVEKGGSKGPAAKTKPAKEPKNESGKEEEKEKEQVKEEKKKKKEKPKEEPKDRKPKEEA 137

Query: 64  KNKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKEEE 123
           K K   +++EK+K+KK    ++ +++ + +K E+ +     KK  K K  NK K   EEE
Sbjct: 138 KEKRPPKEKEKEKEKK---VEEPRDREEEKKRERVRAKSRPKKPPKKKPPNKKKEPPEEE 194

Query: 124 EKKKEAEEKKKKRTKKKEKNKNKSRKEEEEEEKKKKKKKKKKKRTKKKEEEKRKNEKAVR 183
           ++++ A E  K + ++ + N+ + ++E++ ++++      ++  +++  E  R++  +++
Sbjct: 195 KQRQAAREAVKGKPEEPDVNEEREKEEDDGKDRETTTSPMEEDESRQSSEISRRSSSSLK 254

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|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 65.5 bits (159), Expect = 3e-11
 Identities = 58/175 (33%), Positives = 99/175 (56%), Gaps = 8/175 (4%)

Query: 4    KKEEKKKKKKRRTKKKEKNKNKS---RKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTK 60
            K EE+KKK ++  KK+ + K K+   +K EEE K    +E  K  ++K + EE KK    
Sbjct: 1627 KAEEEKKKVEQLKKKEAEEKKKAEELKKAEEENKIKAAEEAKKAEEDKKKAEEAKKAEED 1686

Query: 61   KKEKNKNKNRKEEKKKKKKRRTKKKEKNKNKSRK-----EEKKKEAEEEKKKTKNKEKNK 115
            +K+  +   ++ E+ KK +   KK+ + K K+ +     EE K +AEE KK+ +  +K  
Sbjct: 1687 EKKAAEALKKEAEEAKKAEELKKKEAEEKKKAEELKKAEEENKIKAEEAKKEAEEDKKKA 1746

Query: 116  NKSRKEEEEKKKEAEEKKKKRTKKKEKNKNKSRKEEEEEEKKKKKKKKKKKRTKK 170
             +++K+EEEKKK A  KK++  K +E  K K    EEE +++ +K++ +  +  K
Sbjct: 1747 EEAKKDEEEKKKIAHLKKEEEKKAEEIRKEKEAVIEEELDEEDEKRRMEVDKKIK 1801

Length = 2084

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

 Score = 65.2 bits (158), Expect = 4e-11
 Identities = 60/187 (32%), Positives = 101/187 (54%), Gaps = 4/187 (2%)

Query: 2    KNKKEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKK 61
            K K EEKKK  + + K +E  K    K++ EE +  K E+ KK   +++K +E KK+ ++
Sbjct: 1424 KKKAEEKKKADEAKKKAEEAKKADEAKKKAEEAK--KAEEAKKKAEEAKKADEAKKKAEE 1481

Query: 62   KEKNKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKE 121
             +K     +K E+ KKK    KK  + K K+ + +K +EA++  +  K +E  K    K+
Sbjct: 1482 AKKADEAKKKAEEAKKKADEAKKAAEAKKKADEAKKAEEAKKADEAKKAEEAKKADEAKK 1541

Query: 122  EEEKKKEAEEKKKKRTKKKEKNKN--KSRKEEEEEEKKKKKKKKKKKRTKKKEEEKRKNE 179
             EEKKK  E KK +  KK E+ K   +++K EE++    +K ++ KK  + + EE  K  
Sbjct: 1542 AEEKKKADELKKAEELKKAEEKKKAEEAKKAEEDKNMALRKAEEAKKAEEARIEEVMKLY 1601

Query: 180  KAVRLTK 186
            +  +  K
Sbjct: 1602 EEEKKMK 1608

Length = 2084

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

 Score = 64.8 bits (157), Expect = 4e-11
 Identities = 54/172 (31%), Positives = 99/172 (57%)

Query: 2    KNKKEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKK 61
            K ++E+KK ++ ++ + +EK K +  K+ EEE + K  E+ KK +   +K EE KK  + 
Sbjct: 1627 KAEEEKKKVEQLKKKEAEEKKKAEELKKAEEENKIKAAEEAKKAEEDKKKAEEAKKAEED 1686

Query: 62   KEKNKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKE 121
            ++K     +KE ++ KK    KKKE  + K  +E KK E E + K  + K++ +   +K 
Sbjct: 1687 EKKAAEALKKEAEEAKKAEELKKKEAEEKKKAEELKKAEEENKIKAEEAKKEAEEDKKKA 1746

Query: 122  EEEKKKEAEEKKKKRTKKKEKNKNKSRKEEEEEEKKKKKKKKKKKRTKKKEE 173
            EE KK E E+KK    KK+E+ K +  ++E+E   +++  ++ +KR  + ++
Sbjct: 1747 EEAKKDEEEKKKIAHLKKEEEKKAEEIRKEKEAVIEEELDEEDEKRRMEVDK 1798

Length = 2084

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

 Score = 64.8 bits (157), Expect = 4e-11
 Identities = 58/178 (32%), Positives = 101/178 (56%), Gaps = 3/178 (1%)

Query: 4    KKEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKKKE 63
            KK ++ KKK    KK ++ K K+ + ++ ++  KK E+ KK +   +K EE KK  + K+
Sbjct: 1418 KKADEAKKKAEEKKKADEAKKKAEEAKKADEAKKKAEEAKKAEEAKKKAEEAKKADEAKK 1477

Query: 64   KNKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKEEE 123
            K +   + +E KKK +   KK ++ K  +  ++K  EA++ ++  K  E  K +  K+ +
Sbjct: 1478 KAEEAKKADEAKKKAEEAKKKADEAKKAAEAKKKADEAKKAEEAKKADEAKKAEEAKKAD 1537

Query: 124  EKKKEAEEKKKKRTKKKEKNKNKSRKEEEEEEKKKKKKKKKKKRTKKKEEEKRKNEKA 181
            E KK AEEKKK    KK +   K+  EE+++ ++ KK ++ K    +K EE +K E+A
Sbjct: 1538 EAKK-AEEKKKADELKKAEELKKA--EEKKKAEEAKKAEEDKNMALRKAEEAKKAEEA 1592

Length = 2084

>gnl|CDD|236545 PRK09510, tolA, cell envelope integrity inner membrane protein TolA; Provisional

 Score = 63.7 bits (155), Expect = 4e-11
 Identities = 40/183 (21%), Positives = 83/183 (45%), Gaps = 5/183 (2%)

Query: 2   KNKKEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRT-- 59
             ++ +KK++++    ++++   + R ++ E++R   +E+ K+ +  +++   K+K+   
Sbjct: 77  AEEQRKKKEQQQAEELQQKQAAEQERLKQLEKERLAAQEQKKQAEEAAKQAALKQKQAEE 136

Query: 60  -KKKEKNKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKS 118
              K     K + E + K+     KK      K  + E  K+A  E KK K + +   K+
Sbjct: 137 AAAKAAAAAKAKAEAEAKRAAAAAKKAAAEAKKKAEAEAAKKAAAEAKK-KAEAEAAAKA 195

Query: 119 RKEEEEKKKEAEEKKKKRTKKKEKNKNKSRKEEEEEEKKKKKKKKKKKRTKKKEEEKRKN 178
              E +KK EAE KKK   + K+K   +++    +   + K   +K    K  E+     
Sbjct: 196 -AAEAKKKAEAEAKKKAAAEAKKKAAAEAKAAAAKAAAEAKAAAEKAAAAKAAEKAAAAK 254

Query: 179 EKA 181
             A
Sbjct: 255 AAA 257

Length = 387

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

 Score = 64.4 bits (156), Expect = 5e-11
 Identities = 61/182 (33%), Positives = 98/182 (53%), Gaps = 4/182 (2%)

Query: 2    KNKKEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKK 61
            K K EE KK ++ + K +E  K    K++ EE + K  E  KK +   +K +E KK  + 
Sbjct: 1450 KKKAEEAKKAEEAKKKAEEAKKADEAKKKAEEAK-KADEAKKKAEEAKKKADEAKKAAEA 1508

Query: 62   KEKNKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKT---KNKEKNKNKS 118
            K+K     + EE KK  + +  ++ K  ++++K E+KK+A+E KK     K +EK K + 
Sbjct: 1509 KKKADEAKKAEEAKKADEAKKAEEAKKADEAKKAEEKKKADELKKAEELKKAEEKKKAEE 1568

Query: 119  RKEEEEKKKEAEEKKKKRTKKKEKNKNKSRKEEEEEEKKKKKKKKKKKRTKKKEEEKRKN 178
             K+ EE K  A  K ++  K +E    +  K  EEE+K K ++ KK +  K K EE +K 
Sbjct: 1569 AKKAEEDKNMALRKAEEAKKAEEARIEEVMKLYEEEKKMKAEEAKKAEEAKIKAEELKKA 1628

Query: 179  EK 180
            E+
Sbjct: 1629 EE 1630

Length = 2084

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

 Score = 64.1 bits (156), Expect = 5e-11
 Identities = 44/180 (24%), Positives = 91/180 (50%), Gaps = 1/180 (0%)

Query: 2   KNKKEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKN-KNKSRKEEEKKKRTK 60
           K  KE K +  K   K+KE+ K + +K++E+ K   K  K K+  K K   +E++K++ K
Sbjct: 93  KPAKEPKNESGKEEEKEKEQVKEEKKKKKEKPKEEPKDRKPKEEAKEKRPPKEKEKEKEK 152

Query: 61  KKEKNKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRK 120
           K E+ +++  ++++++ + +   KK   K    K+++  E E++++  +   K K +   
Sbjct: 153 KVEEPRDREEEKKRERVRAKSRPKKPPKKKPPNKKKEPPEEEKQRQAAREAVKGKPEEPD 212

Query: 121 EEEEKKKEAEEKKKKRTKKKEKNKNKSRKEEEEEEKKKKKKKKKKKRTKKKEEEKRKNEK 180
             EE++KE ++ K + T      +++SR+  E   +     KK          E R++ K
Sbjct: 213 VNEEREKEEDDGKDRETTTSPMEEDESRQSSEISRRSSSSLKKPDPSPSMASPETRESSK 272

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|236545 PRK09510, tolA, cell envelope integrity inner membrane protein TolA; Provisional

 Score = 63.3 bits (154), Expect = 6e-11
 Identities = 48/181 (26%), Positives = 90/181 (49%), Gaps = 6/181 (3%)

Query: 3   NKKEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKK-NKNKSRKEEEKKKRTKK 61
           N++++++K  KR  ++++K K + + EE ++K+  ++E+ K+  K +   +E+KK+  + 
Sbjct: 65  NRQQQQQKSAKRAEEQRKK-KEQQQAEELQQKQAAEQERLKQLEKERLAAQEQKKQAEEA 123

Query: 62  KEKNKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKE 121
            ++   K ++ E+   K     K +      R     K+A  E KK   K + +   +  
Sbjct: 124 AKQAALKQKQAEEAAAKAAAAAKAKAEAEAKRAAAAAKKAAAEAKK---KAEAEAAKKAA 180

Query: 122 EEEKKK-EAEEKKKKRTKKKEKNKNKSRKEEEEEEKKKKKKKKKKKRTKKKEEEKRKNEK 180
            E KKK EAE   K   + K+K + +++K+   E KKK   + K    K   E K   EK
Sbjct: 181 AEAKKKAEAEAAAKAAAEAKKKAEAEAKKKAAAEAKKKAAAEAKAAAAKAAAEAKAAAEK 240

Query: 181 A 181
           A
Sbjct: 241 A 241

Length = 387

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

 Score = 63.6 bits (154), Expect = 9e-11
 Identities = 64/191 (33%), Positives = 103/191 (53%), Gaps = 14/191 (7%)

Query: 4    KKEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKKKE 63
            KK E+ KK     K +E  K    K+ EE+K+  + +K ++ K    K++ ++ +  +++
Sbjct: 1516 KKAEEAKKADEAKKAEEAKKADEAKKAEEKKKADELKKAEELKKAEEKKKAEEAKKAEED 1575

Query: 64   KNKNKNRKEEKKKKKKRRTKKKEK--NKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKE 121
            KN    + EE KK ++ R ++  K   + K  K E+ K+AEE K K +  +K + + +K 
Sbjct: 1576 KNMALRKAEEAKKAEEARIEEVMKLYEEEKKMKAEEAKKAEEAKIKAEELKKAEEEKKKV 1635

Query: 122  EEEKKKEAEEKKKKRTKKKEKNKNKSRKEEE---EEEKKKK---------KKKKKKKRTK 169
            E+ KKKEAEEKKK    KK + +NK +  EE    EE KKK          +KK  +  K
Sbjct: 1636 EQLKKKEAEEKKKAEELKKAEEENKIKAAEEAKKAEEDKKKAEEAKKAEEDEKKAAEALK 1695

Query: 170  KKEEEKRKNEK 180
            K+ EE +K E+
Sbjct: 1696 KEAEEAKKAEE 1706

Length = 2084

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

 Score = 62.9 bits (152), Expect = 2e-10
 Identities = 61/187 (32%), Positives = 103/187 (55%), Gaps = 8/187 (4%)

Query: 5    KEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKKKEK 64
            K+ ++KKK    KK E++KN + ++ EE K+ ++    +  K    +++ K +  KK E+
Sbjct: 1558 KKAEEKKKAEEAKKAEEDKNMALRKAEEAKKAEEARIEEVMKLYEEEKKMKAEEAKKAEE 1617

Query: 65   NKNKN---RKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKE 121
             K K    +K E++KKK  + KKKE  + K  +E KK E E + K  +  +K +   +K 
Sbjct: 1618 AKIKAEELKKAEEEKKKVEQLKKKEAEEKKKAEELKKAEEENKIKAAEEAKKAEEDKKKA 1677

Query: 122  EEEKKKEAEEKKKKRTKKKEKNKNKS-----RKEEEEEEKKKKKKKKKKKRTKKKEEEKR 176
            EE KK E +EKK     KKE  + K      +KE EE++K ++ KK +++   K EE K+
Sbjct: 1678 EEAKKAEEDEKKAAEALKKEAEEAKKAEELKKKEAEEKKKAEELKKAEEENKIKAEEAKK 1737

Query: 177  KNEKAVR 183
            + E+  +
Sbjct: 1738 EAEEDKK 1744

Length = 2084

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

 Score = 61.2 bits (149), Expect = 4e-10
 Identities = 30/179 (16%), Positives = 62/179 (34%), Gaps = 4/179 (2%)

Query: 2   KNKKEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKK 61
           +   EE+ KKK ++   K K+K    KEE +E    KK+  ++            K T  
Sbjct: 9   ELAAEEEAKKKLKKLAAKSKSKGFITKEEIKEALESKKKTPEQIDQVLIFLSGMVKDTDD 68

Query: 62  KEKNKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKE 121
             ++    +K +   K        +K         KK E +    K  +    K+     
Sbjct: 69  ATESDIPKKKTKTAAKAAAAKAPAKKKLKDELDSSKKAEKKNALDKDDDLNYVKDIDVLN 128

Query: 122 EEEKKKEAEEKKKKRTKKKEKNKNKSRKEEEEEEKKKKKKKKKKKRTKKKEEEKRKNEK 180
           + +   + ++         + + +    +E+++E         +   KK+ +E  K   
Sbjct: 129 QADDDDDDDDD----DDLDDDDIDDDDDDEDDDEDDDDDDVDDEDEEKKEAKELEKLSD 183

Length = 509

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

 Score = 61.3 bits (148), Expect = 5e-10
 Identities = 58/192 (30%), Positives = 102/192 (53%), Gaps = 12/192 (6%)

Query: 2    KNKKEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKK 61
            K K EE KK  + + K +E  K +  K++ EE +  K ++ KK   +++K +E KK+ ++
Sbjct: 1437 KKKAEEAKKADEAKKKAEEAKKAEEAKKKAEEAK--KADEAKKKAEEAKKADEAKKKAEE 1494

Query: 62   KEKNKNKNRKEEKKKKKKRRTKKKEKNK--NKSRKEEKKKEAEEEKK--------KTKNK 111
             +K  ++ +K  + KKK    KK E+ K  ++++K E+ K+A+E KK        + K  
Sbjct: 1495 AKKKADEAKKAAEAKKKADEAKKAEEAKKADEAKKAEEAKKADEAKKAEEKKKADELKKA 1554

Query: 112  EKNKNKSRKEEEEKKKEAEEKKKKRTKKKEKNKNKSRKEEEEEEKKKKKKKKKKKRTKKK 171
            E+ K    K++ E+ K+AEE K    +K E+ K       EE  K  +++KK K    KK
Sbjct: 1555 EELKKAEEKKKAEEAKKAEEDKNMALRKAEEAKKAEEARIEEVMKLYEEEKKMKAEEAKK 1614

Query: 172  EEEKRKNEKAVR 183
             EE +   + ++
Sbjct: 1615 AEEAKIKAEELK 1626

Length = 2084

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

 Score = 61.3 bits (148), Expect = 6e-10
 Identities = 60/186 (32%), Positives = 95/186 (51%), Gaps = 6/186 (3%)

Query: 4    KKEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKKKE 63
            KK E+ KKK    KK  + K K+ + ++ E+  K  E  K  + K   E +K +  KK +
Sbjct: 1490 KKAEEAKKKADEAKKAAEAKKKADEAKKAEEAKKADEAKKAEEAKKADEAKKAEEKKKAD 1549

Query: 64   KNKNKN--RKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKE 121
            + K     +K E+KKK +   K +E      RK E+ K+AEE + +   K   + K  K 
Sbjct: 1550 ELKKAEELKKAEEKKKAEEAKKAEEDKNMALRKAEEAKKAEEARIEEVMKLYEEEKKMKA 1609

Query: 122  EEEKKKEAEEKKKKRTKKKEKNKNK----SRKEEEEEEKKKKKKKKKKKRTKKKEEEKRK 177
            EE KK E  + K +  KK E+ K K     +KE EE++K ++ KK +++   K  EE +K
Sbjct: 1610 EEAKKAEEAKIKAEELKKAEEEKKKVEQLKKKEAEEKKKAEELKKAEEENKIKAAEEAKK 1669

Query: 178  NEKAVR 183
             E+  +
Sbjct: 1670 AEEDKK 1675

Length = 2084

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

 Score = 60.5 bits (146), Expect = 9e-10
 Identities = 50/185 (27%), Positives = 97/185 (52%), Gaps = 5/185 (2%)

Query: 2    KNKKEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKK 61
            K K +E KK  + + K  E  K +  K+ +E K+ ++ +K  + K    K++  + +  +
Sbjct: 1496 KKKADEAKKAAEAKKKADEAKKAEEAKKADEAKKAEEAKKADEAKKAEEKKKADELKKAE 1555

Query: 62   KEKNKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKE 121
            + K   + +K E+ KK +       +   +++K E+ +  E  K   + K+    +++K 
Sbjct: 1556 ELKKAEEKKKAEEAKKAEEDKNMALRKAEEAKKAEEARIEEVMKLYEEEKKMKAEEAKKA 1615

Query: 122  EEEKKK-----EAEEKKKKRTKKKEKNKNKSRKEEEEEEKKKKKKKKKKKRTKKKEEEKR 176
            EE K K     +AEE+KKK  + K+K   + +K EE ++ +++ K K  +  KK EE+K+
Sbjct: 1616 EEAKIKAEELKKAEEEKKKVEQLKKKEAEEKKKAEELKKAEEENKIKAAEEAKKAEEDKK 1675

Query: 177  KNEKA 181
            K E+A
Sbjct: 1676 KAEEA 1680

Length = 2084

>gnl|CDD|225606 COG3064, TolA, Membrane protein involved in colicin uptake [Cell envelope biogenesis, outer membrane]

 Score = 59.6 bits (144), Expect = 9e-10
 Identities = 52/182 (28%), Positives = 90/182 (49%), Gaps = 10/182 (5%)

Query: 4   KKEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKKKE 63
           K E+++KKK+ +  ++ K K   +  E+E  +  +KE+ K  + + + EE +K+   +++
Sbjct: 76  KGEQQRKKKEEQVAEELKPK---QAAEQERLKQLEKERLKAQEQQKQAEEAEKQAQLEQK 132

Query: 64  KNKNKNRK---EEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRK 120
           + + + RK   E+KKK +  + K   +        E KK+AEE  K     E+ K K+  
Sbjct: 133 QQEEQARKAAAEQKKKAEAAKAKAAAEAAKLKAAAEAKKKAEEAAKA---AEEAKAKAEA 189

Query: 121 EEEEKKKEAEEKKKKRTKKKEKN-KNKSRKEEEEEEKKKKKKKKKKKRTKKKEEEKRKNE 179
              +KK EAE K      K E   K K+ K+ E   ++K   +KKK   K K ++     
Sbjct: 190 AAAKKKAEAEAKAAAEKAKAEAEAKAKAEKKAEAAAEEKAAAEKKKAAAKAKADKAAAAA 249

Query: 180 KA 181
           KA
Sbjct: 250 KA 251

Length = 387

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

 Score = 60.2 bits (145), Expect = 1e-09
 Identities = 56/188 (29%), Positives = 98/188 (52%), Gaps = 5/188 (2%)

Query: 4    KKEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKKKE 63
            KK+ ++ KK    KKK +   K   E ++    KKK    K   +++K +E KK  + K+
Sbjct: 1476 KKKAEEAKKADEAKKKAEEAKKKADEAKKAAEAKKKADEAKKAEEAKKADEAKKAEEAKK 1535

Query: 64   KNKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKEEE 123
             ++ K  +E+KK  + ++ ++ +K + K + EE KK  E++    +  E+ K       E
Sbjct: 1536 ADEAKKAEEKKKADELKKAEELKKAEEKKKAEEAKKAEEDKNMALRKAEEAKKAEEARIE 1595

Query: 124  EKKKEAEEKKKK-----RTKKKEKNKNKSRKEEEEEEKKKKKKKKKKKRTKKKEEEKRKN 178
            E  K  EE+KK      +  ++ K K +  K+ EEE+KK ++ KKK+   KKK EE +K 
Sbjct: 1596 EVMKLYEEEKKMKAEEAKKAEEAKIKAEELKKAEEEKKKVEQLKKKEAEEKKKAEELKKA 1655

Query: 179  EKAVRLTK 186
            E+  ++  
Sbjct: 1656 EEENKIKA 1663

Length = 2084

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

 Score = 60.2 bits (147), Expect = 1e-09
 Identities = 24/153 (15%), Positives = 56/153 (36%), Gaps = 1/153 (0%)

Query: 1   CKNKKEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTK 60
            K    E K       +++ + +   R+ EEE K  + +E       +  K E       
Sbjct: 24  LKELGIEVKSHSSTVEEEEARKEEAKREAEEEAKA-EAEEAAAAEAEEEAKAEAAAAAPA 82

Query: 61  KKEKNKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRK 120
           ++        +   +  +    +  E    + + ++  K+ +  K K K  ++   +  K
Sbjct: 83  EEAAEAAAAAEAAARPAEDEAARPAEAAARRPKAKKAAKKKKGPKPKKKKPKRKAARGGK 142

Query: 121 EEEEKKKEAEEKKKKRTKKKEKNKNKSRKEEEE 153
             +  K     + ++R +KK+K +  + K   E
Sbjct: 143 RGKGGKGRRRRRGRRRRRKKKKKQKPTEKIPRE 175

Length = 746

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

 Score = 59.9 bits (145), Expect = 1e-09
 Identities = 39/151 (25%), Positives = 75/151 (49%), Gaps = 1/151 (0%)

Query: 34  KRTKKKEKNKKNKNKSRKEEEKKKRTKKKEKNKNKNRKEEKKKKKKRRTKKKEKNKNKSR 93
           KR +K             +E K +  K++EK K +  KEEKKKKK++  ++ +  K K  
Sbjct: 78  KRVEKGGSKGPAAKTKPAKEPKNESGKEEEKEKEQV-KEEKKKKKEKPKEEPKDRKPKEE 136

Query: 94  KEEKKKEAEEEKKKTKNKEKNKNKSRKEEEEKKKEAEEKKKKRTKKKEKNKNKSRKEEEE 153
            +EK+   E+EK+K K  E+ +++  +++ E+ +     KK   KK    K +  +EE++
Sbjct: 137 AKEKRPPKEKEKEKEKKVEEPRDREEEKKRERVRAKSRPKKPPKKKPPNKKKEPPEEEKQ 196

Query: 154 EEKKKKKKKKKKKRTKKKEEEKRKNEKAVRL 184
            +  ++  K K +     EE +++ +     
Sbjct: 197 RQAAREAVKGKPEEPDVNEEREKEEDDGKDR 227

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 = 60.1 bits (146), Expect = 1e-09
 Identities = 43/196 (21%), Positives = 87/196 (44%), Gaps = 15/196 (7%)

Query: 2    KNKKEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKK 61
            K   +E++ K K + K  +  K K +K+E+++K++   +  K +   + K  +  ++ K 
Sbjct: 1150 KEIAKEQRLKSKTKGKASKLRKPKLKKKEKKKKKSSADKSKKASVVGNSKRVDSDEKRKL 1209

Query: 62   KEKNKNKNRK-------EEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEE--------KK 106
             +K  NK          +++++K K +    ++ K+K     K  E  +E        + 
Sbjct: 1210 DDKPDNKKSNSSGSDQEDDEEQKTKPKKSSVKRLKSKKNNSSKSSEDNDEFSSDDLSKEG 1269

Query: 107  KTKNKEKNKNKSRKEEEEKKKEAEEKKKKRTKKKEKNKNKSRKEEEEEEKKKKKKKKKKK 166
            K KN  K  +  +       K  + +    +K     K K +K  E      KKKKK +K
Sbjct: 1270 KPKNAPKRVSAVQYSPPPPSKRPDGESNGGSKPSSPTKKKVKKRLEGSLAALKKKKKSEK 1329

Query: 167  RTKKKEEEKRKNEKAV 182
            +T +K++ K + ++A 
Sbjct: 1330 KTARKKKSKTRVKQAS 1345

Length = 1388

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

 Score = 57.7 bits (140), Expect = 5e-09
 Identities = 30/187 (16%), Positives = 73/187 (39%), Gaps = 8/187 (4%)

Query: 2   KNKKEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEE-----KK 56
           K +   +++ KK+  K   K+K+K    +EE K   + +K    +               
Sbjct: 7   KAELAAEEEAKKKLKKLAAKSKSKGFITKEEIKEALESKKKTPEQIDQVLIFLSGMVKDT 66

Query: 57  KRTKKKEKNKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKK---TKNKEK 113
               + +  K K +   K    K   KKK K++  S K+ +KK A ++       K+ + 
Sbjct: 67  DDATESDIPKKKTKTAAKAAAAKAPAKKKLKDELDSSKKAEKKNALDKDDDLNYVKDIDV 126

Query: 114 NKNKSRKEEEEKKKEAEEKKKKRTKKKEKNKNKSRKEEEEEEKKKKKKKKKKKRTKKKEE 173
                  ++++   + ++         E +      ++ ++E ++KK+ K+ ++    ++
Sbjct: 127 LNQADDDDDDDDDDDLDDDDIDDDDDDEDDDEDDDDDDVDDEDEEKKEAKELEKLSDDDD 186

Query: 174 EKRKNEK 180
                + 
Sbjct: 187 FVWDEDD 193

Length = 509

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

 Score = 57.5 bits (140), Expect = 6e-09
 Identities = 44/169 (26%), Positives = 81/169 (47%), Gaps = 7/169 (4%)

Query: 1   CKNKKEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKN------KSRKEEE 54
            K   E K K+ +   K+  +   K  +  ++E   + KE+  K +N      + R+ E 
Sbjct: 25  RKKIAEAKIKEAEEEAKRILEEAKKEAEAIKKEALLEAKEEIHKLRNEFEKELRERRNEL 84

Query: 55  KKKRTKKKEKNKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKN 114
           +K   +  +K +N +RK E  +K++   +KKEK   + ++E +KKE E E+   +  ++ 
Sbjct: 85  QKLEKRLLQKEENLDRKLELLEKREEELEKKEKELEQKQQELEKKEEELEELIEEQLQEL 144

Query: 115 KNKSRKEEEEKKKEAEEKKKKRTKKKEKNKNKSRKEEEEEEKKKKKKKK 163
           +  S    EE K+   EK ++   + E        EEE +E+  KK K+
Sbjct: 145 ERISGLTAEEAKEILLEKVEEEA-RHEAAVLIKEIEEEAKEEADKKAKE 192

Length = 520

>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]

 Score = 57.4 bits (139), Expect = 8e-09
 Identities = 34/202 (16%), Positives = 85/202 (42%), Gaps = 16/202 (7%)

Query: 4   KKEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKKKE 63
           ++E ++ +++    +KE  + KS  EE  E+  + +E+  + K +  + E +    +++ 
Sbjct: 252 EEELEELQEELEEAEKEIEELKSELEELREELEELQEELLELKEEIEELEGEISLLRERL 311

Query: 64  KNKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKK---KTKNKEKNKNKSRK 120
           +      +E +++ ++ + K +   +    +E   +E E+      + K + + K  +  
Sbjct: 312 EELENELEELEERLEELKEKIEALKEELEERETLLEELEQLLAELEEAKEELEEKLSALL 371

Query: 121 EEEEKKKEAEEKK-------------KKRTKKKEKNKNKSRKEEEEEEKKKKKKKKKKKR 167
           EE E+  EA  ++             +    K+E    + R E   E  +  K++ K+  
Sbjct: 372 EELEELFEALREELAELEAELAEIRNELEELKREIESLEERLERLSERLEDLKEELKELE 431

Query: 168 TKKKEEEKRKNEKAVRLTKLSA 189
            + +E +    E    L +L  
Sbjct: 432 AELEELQTELEELNEELEELEE 453

Length = 1163

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

 Score = 56.8 bits (137), Expect = 1e-08
 Identities = 35/141 (24%), Positives = 75/141 (53%), Gaps = 1/141 (0%)

Query: 41  KNKKNKNKSRKEEEKKKRTKKKEKNKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKE 100
           K  ++K  S +  ++ ++   K         +E K +  +  ++KEK + K  K++KK++
Sbjct: 65  KCAESKLSSDEAVKRVEKGGSKGPAAKTKPAKEPKNESGK-EEEKEKEQVKEEKKKKKEK 123

Query: 101 AEEEKKKTKNKEKNKNKSRKEEEEKKKEAEEKKKKRTKKKEKNKNKSRKEEEEEEKKKKK 160
            +EE K  K KE+ K K   +E+EK+KE + ++ +  ++++K +    K   ++  KKK 
Sbjct: 124 PKEEPKDRKPKEEAKEKRPPKEKEKEKEKKVEEPRDREEEKKRERVRAKSRPKKPPKKKP 183

Query: 161 KKKKKKRTKKKEEEKRKNEKA 181
             KKK+  +++++ +   E  
Sbjct: 184 PNKKKEPPEEEKQRQAAREAV 204

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 = 56.4 bits (136), Expect = 1e-08
 Identities = 45/169 (26%), Positives = 92/169 (54%), Gaps = 4/169 (2%)

Query: 2   KNKKEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKK--EKNKKNKNKSRKEEEKKKRT 59
           K K++ K++KKK++ K KE+ K++  KEE +EKR  K+  ++ +K   + R  EE+KKR 
Sbjct: 108 KEKEQVKEEKKKKKEKPKEEPKDRKPKEEAKEKRPPKEKEKEKEKKVEEPRDREEEKKRE 167

Query: 60  KKKEKNKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSR 119
           + + K++ K   ++K   KK+   ++EK +  +R+  K K  E +  + + KE++  K R
Sbjct: 168 RVRAKSRPKKPPKKKPPNKKKEPPEEEKQRQAAREAVKGKPEEPDVNEEREKEEDDGKDR 227

Query: 120 KEEEEKKKEAEEKKKKRTKKKEKNKNKSRKEEEEEEKKKKKKKKKKKRT 168
             E       E++ ++ ++   ++ +  +K +        + ++  KRT
Sbjct: 228 --ETTTSPMEEDESRQSSEISRRSSSSLKKPDPSPSMASPETRESSKRT 274

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|225606 COG3064, TolA, Membrane protein involved in colicin uptake [Cell envelope biogenesis, outer membrane]

 Score = 56.1 bits (135), Expect = 1e-08
 Identities = 41/184 (22%), Positives = 87/184 (47%), Gaps = 8/184 (4%)

Query: 6   EEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKKKEKN 65
           ++  + + +++  K+  + + +KEE+  +  K K+  ++ + K  ++E  K + ++K+  
Sbjct: 62  QQYGRIQSQQSSAKKGEQQRKKKEEQVAEELKPKQAAEQERLKQLEKERLKAQEQQKQAE 121

Query: 66  KNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKN----KSRKE 121
           + + + + ++K+++ + +K    + K  +  K K A E  K     E  K         E
Sbjct: 122 EAEKQAQLEQKQQEEQARKAAAEQKKKAEAAKAKAAAEAAKLKAAAEAKKKAEEAAKAAE 181

Query: 122 EEEKKKEAEEKKKKRTKKKEKNKNKSRKEEEE----EEKKKKKKKKKKKRTKKKEEEKRK 177
           E + K EA   KKK   + +    K++ E E     E+K +   ++K    KKK   K K
Sbjct: 182 EAKAKAEAAAAKKKAEAEAKAAAEKAKAEAEAKAKAEKKAEAAAEEKAAAEKKKAAAKAK 241

Query: 178 NEKA 181
            +KA
Sbjct: 242 ADKA 245

Length = 387

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

 Score = 56.9 bits (137), Expect = 1e-08
 Identities = 42/183 (22%), Positives = 94/183 (51%), Gaps = 4/183 (2%)

Query: 2   KNKKEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKK 61
              KE+ + +++          N+ R +  +E    ++E+ + +K +  KEEE   +  K
Sbjct: 214 YQLKEKLELEEENLLYLDYLKLNEERIDLLQELLRDEQEEIESSKQELEKEEEILAQVLK 273

Query: 62  KEKNKNKNRKEEKKKK----KKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNK 117
           + K + K +K ++++     K+    K E  K + RK + +++ +E +K+ K  EK   K
Sbjct: 274 ENKEEEKEKKLQEEELKLLAKEEEELKSELLKLERRKVDDEEKLKESEKELKKLEKELKK 333

Query: 118 SRKEEEEKKKEAEEKKKKRTKKKEKNKNKSRKEEEEEEKKKKKKKKKKKRTKKKEEEKRK 177
            ++E EE +KE +E + KR  ++E+ +   + +E+ E+ +++   KKK  +++     + 
Sbjct: 334 EKEEIEELEKELKELEIKREAEEEEEEQLEKLQEKLEQLEEELLAKKKLESERLSSAAKL 393

Query: 178 NEK 180
            E+
Sbjct: 394 KEE 396

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 = 56.2 bits (136), Expect = 2e-08
 Identities = 36/190 (18%), Positives = 82/190 (43%), Gaps = 9/190 (4%)

Query: 3    NKKEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKKK 62
             + EEK+  K++R K K K K    ++ + +K+ KKK+K+  +K+K        KR    
Sbjct: 1145 EEVEEKEIAKEQRLKSKTKGKASKLRKPKLKKKEKKKKKSSADKSKKASVVGNSKRVDSD 1204

Query: 63   EKNKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKEE 122
            EK K  ++ + KK       ++ ++ +    K+   K  + +K  +    ++ ++   ++
Sbjct: 1205 EKRKLDDKPDNKKSNSSGSDQEDDEEQKTKPKKSSVKRLKSKKNNSSKSSEDNDEFSSDD 1264

Query: 123  EEKKKEAEEKK---------KKRTKKKEKNKNKSRKEEEEEEKKKKKKKKKKKRTKKKEE 173
              K+ + +                 K+   ++    +     KKK KK+ +      K++
Sbjct: 1265 LSKEGKPKNAPKRVSAVQYSPPPPSKRPDGESNGGSKPSSPTKKKVKKRLEGSLAALKKK 1324

Query: 174  EKRKNEKAVR 183
            +K + + A +
Sbjct: 1325 KKSEKKTARK 1334

Length = 1388

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

 Score = 55.9 bits (135), Expect = 2e-08
 Identities = 33/105 (31%), Positives = 43/105 (40%), Gaps = 3/105 (2%)

Query: 75  KKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKEEEEKKKEAEEKKK 134
           +K K +       N     KE     +EEE K      K   K  K  E KKK  ++KKK
Sbjct: 17  QKSKLQPISYIYSNVLVLSKEILSTFSEEENKVATTSTKKDKKEDKNNESKKKSEKKKKK 76

Query: 135 KRTKKKEKNKNKSRKEEEEEEKKKKKKKKKKKRTKKKEEEKRKNE 179
              KK++K      + +   +  KK KK KKK  K K  E   N 
Sbjct: 77  ---KKEKKEPKSEGETKLGFKTPKKSKKTKKKPPKPKPNEDVDNA 118

Length = 413

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

 Score = 55.8 bits (134), Expect = 2e-08
 Identities = 42/164 (25%), Positives = 81/164 (49%), Gaps = 18/164 (10%)

Query: 9   KKKKKRRTKKKEKNKNKSR-----KEEEEEKRTKKKEKNKKNKNKSRKEEEK-KKRTKKK 62
           KK  +   +  EK  N  R     KE E ++  K+ ++ K+  +K + + +K +++    
Sbjct: 180 KKVVEALREDNEKGVNFRRDMTDLKERESQEDAKRAQQLKEELDKKQIDADKAQQKADFA 239

Query: 63  EKNKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKEE 122
           + N +K R E ++K+++   K   K  + S  +E K+ AE +K++ +          K +
Sbjct: 240 QDNADKQRDEVRQKQQE--AKNLPKPADTSSPKEDKQVAENQKREIE----------KAQ 287

Query: 123 EEKKKEAEEKKKKRTKKKEKNKNKSRKEEEEEEKKKKKKKKKKK 166
            E KK  EE  K +  K    K +S+  E+E E K+ + +KK++
Sbjct: 288 IEIKKNDEEALKAKDHKAFDLKQESKASEKEAEDKELEAQKKRE 331

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

>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]

 Score = 55.1 bits (133), Expect = 4e-08
 Identities = 36/182 (19%), Positives = 94/182 (51%), Gaps = 1/182 (0%)

Query: 4   KKEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKKKE 63
           +   ++ +++    ++E  + + R EE EE+    +E   K K +  + EEK++  +++ 
Sbjct: 736 QSRLEELEEELEELEEELEELQERLEELEEELESLEEALAKLKEEIEELEEKRQALQEEL 795

Query: 64  KNKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKEEE 123
           +   +  +E +++      + +   + + R E++ +E EEE ++ + K     +  +E E
Sbjct: 796 EELEEELEEAERRLDALERELESLEQRRERLEQEIEELEEEIEELEEKLDELEEELEELE 855

Query: 124 EKKKEAEEK-KKKRTKKKEKNKNKSRKEEEEEEKKKKKKKKKKKRTKKKEEEKRKNEKAV 182
           ++ +E +E+ ++   +K+E        EEE+EE +++ ++ + +  + KEE ++  E+  
Sbjct: 856 KELEELKEELEELEAEKEELEDELKELEEEKEELEEELRELESELAELKEEIEKLRERLE 915

Query: 183 RL 184
            L
Sbjct: 916 EL 917

Length = 1163

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

 Score = 55.1 bits (133), Expect = 5e-08
 Identities = 45/200 (22%), Positives = 81/200 (40%), Gaps = 11/200 (5%)

Query: 1    CKNKKEEKKKKKKRRTKKKEKNKNKSRKE-EEEEKRTKKKEKNKKNKNKSRKEEEKKKRT 59
             +  K + K K  +  K K K K K +K+   ++ +      N K  +   K +   K  
Sbjct: 1155 EQRLKSKTKGKASKLRKPKLKKKEKKKKKSSADKSKKASVVGNSKRVDSDEKRKLDDKPD 1214

Query: 60   KKKEKNKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEE--------KKKTKNK 111
             KK  +   ++++++++K K +    ++ K+K     K  E  +E        + K KN 
Sbjct: 1215 NKKSNSSGSDQEDDEEQKTKPKKSSVKRLKSKKNNSSKSSEDNDEFSSDDLSKEGKPKNA 1274

Query: 112  EKNKNKSRKEEEEKKKEAEEKKK--KRTKKKEKNKNKSRKEEEEEEKKKKKKKKKKKRTK 169
             K  +  +       K  + +     +     K K K R E      KKKKK +KK   K
Sbjct: 1275 PKRVSAVQYSPPPPSKRPDGESNGGSKPSSPTKKKVKKRLEGSLAALKKKKKSEKKTARK 1334

Query: 170  KKEEEKRKNEKAVRLTKLSA 189
            KK + + K   A + ++L  
Sbjct: 1335 KKSKTRVKQASASQSSRLLR 1354

Length = 1388

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

 Score = 54.2 bits (131), Expect = 6e-08
 Identities = 36/86 (41%), Positives = 53/86 (61%), Gaps = 3/86 (3%)

Query: 52  EEEKKKRTKKKEKNKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNK 111
           EEE +  T  K+    K +K  +K +KKR  +KKEK K       KKKE EEE++K K +
Sbjct: 396 EEEIEFLTGSKKA-TKKIKKIVEKAEKKREEEKKEKKKKA--FAGKKKEEEEEEEKEKKE 452

Query: 112 EKNKNKSRKEEEEKKKEAEEKKKKRT 137
           E+ + +  + EEEK++E E+KKK+ T
Sbjct: 453 EEKEEEEEEAEEEKEEEEEKKKKQAT 478

Length = 482

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

 Score = 54.2 bits (131), Expect = 7e-08
 Identities = 31/81 (38%), Positives = 52/81 (64%)

Query: 82  TKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKEEEEKKKEAEEKKKKRTKKKE 141
           T+++ +    S+K  KK +   EK + K +E+ K K +K    KKKE EE+++K  K++E
Sbjct: 395 TEEEIEFLTGSKKATKKIKKIVEKAEKKREEEKKEKKKKAFAGKKKEEEEEEEKEKKEEE 454

Query: 142 KNKNKSRKEEEEEEKKKKKKK 162
           K + +   EEE+EE+++KKKK
Sbjct: 455 KEEEEEEAEEEKEEEEEKKKK 475

Length = 482

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

 Score = 53.8 bits (130), Expect = 7e-08
 Identities = 24/74 (32%), Positives = 48/74 (64%)

Query: 69  NRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKEEEEKKKE 128
             K+  KK KK   K ++K + + ++++KK  A ++K++ + +EK K +  KEEEE++ E
Sbjct: 404 GSKKATKKIKKIVEKAEKKREEEKKEKKKKAFAGKKKEEEEEEEKEKKEEEKEEEEEEAE 463

Query: 129 AEEKKKKRTKKKEK 142
            E+++++  KKK+ 
Sbjct: 464 EEKEEEEEKKKKQA 477

Length = 482

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

 Score = 53.8 bits (130), Expect = 9e-08
 Identities = 28/158 (17%), Positives = 59/158 (37%), Gaps = 2/158 (1%)

Query: 18  KKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKKKEKNKNKNRKEEKKKK 77
                K +   EEE +K+ KK     K+K    KEE K+    KK+  +     +     
Sbjct: 2   TTASTKAELAAEEEAKKKLKKLAAKSKSKGFITKEEIKEALESKKKTPEQI--DQVLIFL 59

Query: 78  KKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKEEEEKKKEAEEKKKKRT 137
                   +  ++   K++ K  A+    K   K+K K++    ++ +KK A +K     
Sbjct: 60  SGMVKDTDDATESDIPKKKTKTAAKAAAAKAPAKKKLKDELDSSKKAEKKNALDKDDDLN 119

Query: 138 KKKEKNKNKSRKEEEEEEKKKKKKKKKKKRTKKKEEEK 175
             K+ +      ++++++                E++ 
Sbjct: 120 YVKDIDVLNQADDDDDDDDDDDLDDDDIDDDDDDEDDD 157

Length = 509

>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]

 Score = 53.9 bits (130), Expect = 9e-08
 Identities = 31/190 (16%), Positives = 86/190 (45%), Gaps = 6/190 (3%)

Query: 1   CKNKKEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTK 60
            +  + E ++ ++R  + KEK +    + EE E   ++ E+      ++++E E+K    
Sbjct: 311 LEELENELEELEERLEELKEKIEALKEELEERETLLEELEQLLAELEEAKEELEEKLSAL 370

Query: 61  KKEKNKNKNRKEEKKKKKKRRTKKKEKNKNK-SRKEEKKKEAEEEKKKTKNKEKNKNKSR 119
            +E    +   E  +++      +  + +N+    + + +  EE  ++   + ++  +  
Sbjct: 371 LEEL---EELFEALREELAELEAELAEIRNELEELKREIESLEERLERLSERLEDLKEEL 427

Query: 120 KEEEEKKKEAEEKKKKRTKKKEKNKNKSRKEEEEEEKKKKKKKKKKKRTKKKEEEKRKNE 179
           KE E + +E + + +     +E  + + + EE  +  K+ +++  + + + +  EK  + 
Sbjct: 428 KELEAELEELQTELE--ELNEELEELEEQLEELRDRLKELERELAELQEELQRLEKELSS 485

Query: 180 KAVRLTKLSA 189
              RL +L A
Sbjct: 486 LEARLDRLEA 495

Length = 1163

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

 Score = 53.6 bits (128), Expect = 1e-07
 Identities = 44/187 (23%), Positives = 87/187 (46%), Gaps = 4/187 (2%)

Query: 2    KNKKEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKK 61
            +  +E +K +  R+ +   K + + + EE  +    KK +  K   +++K+ E+ K+ ++
Sbjct: 1188 RKAEELRKAEDARKAEAARKAEEERKAEEARKAEDAKKAEAVKKAEEAKKDAEEAKKAEE 1247

Query: 62   KEKNKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKE 121
            +  N+   + EE +     R +   K +   + +E KK  E++K     K + K   +K 
Sbjct: 1248 ERNNEEIRKFEEARMAHFARRQAAIKAEEARKADELKKAEEKKKADEAKKAEEK---KKA 1304

Query: 122  EEEKKKEAEEKKKKRTKKK-EKNKNKSRKEEEEEEKKKKKKKKKKKRTKKKEEEKRKNEK 180
            +E KKK  E KK    KKK E+ K K+   +++ E+ KK  +  K   +   +E    E+
Sbjct: 1305 DEAKKKAEEAKKADEAKKKAEEAKKKADAAKKKAEEAKKAAEAAKAEAEAAADEAEAAEE 1364

Query: 181  AVRLTKL 187
                 + 
Sbjct: 1365 KAEAAEK 1371

Length = 2084

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

 Score = 52.6 bits (126), Expect = 2e-07
 Identities = 42/159 (26%), Positives = 76/159 (47%), Gaps = 5/159 (3%)

Query: 2   KNKKEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNK-----KNKNKSRKEEEKK 56
           K KK+EK K++ +  K KE+ K K   +E+E+++ KK E+ +     K + + R +   K
Sbjct: 117 KKKKKEKPKEEPKDRKPKEEAKEKRPPKEKEKEKEKKVEEPRDREEEKKRERVRAKSRPK 176

Query: 57  KRTKKKEKNKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKN 116
           K  KKK  NK K   EE+K+++  R   K K +     EE++KE ++ K +       + 
Sbjct: 177 KPPKKKPPNKKKEPPEEEKQRQAAREAVKGKPEEPDVNEEREKEEDDGKDRETTTSPMEE 236

Query: 117 KSRKEEEEKKKEAEEKKKKRTKKKEKNKNKSRKEEEEEE 155
              ++  E  + +    KK          ++R+  +  E
Sbjct: 237 DESRQSSEISRRSSSSLKKPDPSPSMASPETRESSKRTE 275

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|225606 COG3064, TolA, Membrane protein involved in colicin uptake [Cell envelope biogenesis, outer membrane]

 Score = 52.3 bits (125), Expect = 2e-07
 Identities = 45/181 (24%), Positives = 80/181 (44%), Gaps = 12/181 (6%)

Query: 2   KNKKEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKK 61
           K K+  ++++ K+  K++ K + + ++ EE EK  + + + K+ + ++RK   ++K  KK
Sbjct: 93  KPKQAAEQERLKQLEKERLKAQEQQKQAEEAEK--QAQLEQKQQEEQARKAAAEQK--KK 148

Query: 62  KEKNKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKE 121
            E  K K   E  K K     KKK +   K+ +E K K      KK    E      + +
Sbjct: 149 AEAAKAKAAAEAAKLKAAAEAKKKAEEAAKAAEEAKAKAEAAAAKKKAEAEAKAAAEKAK 208

Query: 122 EEEKKKEAEEKKKKRTKKKEKNKNKSRKEEEEEEKKKKKKKKKKKRTKKKEEEKRKNEKA 181
            E + K   EKK +   ++        K   E++K   K K  K     K  E++    A
Sbjct: 209 AEAEAKAKAEKKAEAAAEE--------KAAAEKKKAAAKAKADKAAAAAKAAERKAAAAA 260

Query: 182 V 182
           +
Sbjct: 261 L 261

Length = 387

>gnl|CDD|220271 pfam09507, CDC27, DNA polymerase subunit Cdc27

 Score = 52.5 bits (126), Expect = 2e-07
 Identities = 43/193 (22%), Positives = 81/193 (41%), Gaps = 20/193 (10%)

Query: 1   CKNKKEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTK 60
               K  KK +   +    EK + K+  +    KR   K+ N  +    +K +EKK++ +
Sbjct: 175 EVKVKSAKKTQDTSKETTTEKTEGKTSVKAASLKRNPPKKSNIMSSFFKKKTKEKKEKKE 234

Query: 61  KKEKNKNKNRKEEKKKKKK-----------RRTKKKEKNKNKSRKEEKKKEAEEEKKKTK 109
             E    +  +EE  K+                 + E     S +    +E  EEK+K K
Sbjct: 235 ASESTVKEESEEESGKRDVILEDESAEPTGLDEDEDEDEPKPSGERSDSEEETEEKEKEK 294

Query: 110 NKEKNKNKSRKEEEEKKKEAEEKKKKRTK-KKEKNKNKSRKEEEEEE--------KKKKK 160
            K   K    ++E+E+ +   E   +  + ++ +     +KEEE+EE        +++ +
Sbjct: 295 RKRLKKMMEDEDEDEEMEIVPESPVEEEESEEPEPPPLPKKEEEKEEVTVSPDGGRRRGR 354

Query: 161 KKKKKKRTKKKEE 173
           ++  KK+T K EE
Sbjct: 355 RRVMKKKTFKDEE 367

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|236545 PRK09510, tolA, cell envelope integrity inner membrane protein TolA; Provisional

 Score = 51.7 bits (124), Expect = 3e-07
 Identities = 34/157 (21%), Positives = 64/157 (40%), Gaps = 5/157 (3%)

Query: 4   KKEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKK---RTK 60
           + ++ +K++    ++K++ +  +++   ++K+ ++         K++ E E K+     K
Sbjct: 102 RLKQLEKERLAAQEQKKQAEEAAKQAALKQKQAEEAAAKAAAAAKAKAEAEAKRAAAAAK 161

Query: 61  KKEKNKNKNRKEEKKKKKKRRTKKK--EKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKS 118
           K      K  + E  KK     KKK   +   K+  E KKK   E KKK   + K K  +
Sbjct: 162 KAAAEAKKKAEAEAAKKAAAEAKKKAEAEAAAKAAAEAKKKAEAEAKKKAAAEAKKKAAA 221

Query: 119 RKEEEEKKKEAEEKKKKRTKKKEKNKNKSRKEEEEEE 155
             +    K  AE K         K   K+   +   E
Sbjct: 222 EAKAAAAKAAAEAKAAAEKAAAAKAAEKAAAAKAAAE 258

Length = 387

>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]

 Score = 52.8 bits (127), Expect = 3e-07
 Identities = 36/173 (20%), Positives = 88/173 (50%)

Query: 2   KNKKEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKK 61
           + +  E+   K +   ++ + K ++ +EE EE   + +E  ++     R+ E  ++R ++
Sbjct: 766 ELESLEEALAKLKEEIEELEEKRQALQEELEELEEELEEAERRLDALERELESLEQRRER 825

Query: 62  KEKNKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKE 121
            E+   +  +E ++ ++K    ++E  + +   EE K+E EE + + +  E    +  +E
Sbjct: 826 LEQEIEELEEEIEELEEKLDELEEELEELEKELEELKEELEELEAEKEELEDELKELEEE 885

Query: 122 EEEKKKEAEEKKKKRTKKKEKNKNKSRKEEEEEEKKKKKKKKKKKRTKKKEEE 174
           +EE ++E  E + +  + KE+ +    + EE E K ++ + +  +  ++ EEE
Sbjct: 886 KEELEEELRELESELAELKEEIEKLRERLEELEAKLERLEVELPELEEELEEE 938

Length = 1163

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

 Score = 52.3 bits (125), Expect = 3e-07
 Identities = 40/179 (22%), Positives = 93/179 (51%)

Query: 3   NKKEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKKK 62
             ++E+ +  K+  +K+E+   +  KE +EE++ KK ++ +       +EE K +  K +
Sbjct: 248 RDEQEEIESSKQELEKEEEILAQVLKENKEEEKEKKLQEEELKLLAKEEEELKSELLKLE 307

Query: 63  EKNKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKEE 122
            +  +   K ++ +K+ ++ +K+ K + +  +E +K+  E E K+   +E+ +   + +E
Sbjct: 308 RRKVDDEEKLKESEKELKKLEKELKKEKEEIEELEKELKELEIKREAEEEEEEQLEKLQE 367

Query: 123 EEKKKEAEEKKKKRTKKKEKNKNKSRKEEEEEEKKKKKKKKKKKRTKKKEEEKRKNEKA 181
           + ++ E E   KK+ + +  +     KEEE E K +++K+ K      ++EE    E+ 
Sbjct: 368 KLEQLEEELLAKKKLESERLSSAAKLKEEELELKNEEEKEAKLLLELSEQEEDLLKEEK 426

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|224212 COG1293, COG1293, Predicted RNA-binding protein homologous to eukaryotic snRNP [Transcription]

 Score = 52.0 bits (125), Expect = 3e-07
 Identities = 34/171 (19%), Positives = 69/171 (40%), Gaps = 6/171 (3%)

Query: 4   KKEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEE--EKKKRTKK 61
           ++++ K+      KK EK   K   + E+++   ++ +    + + + E      +  ++
Sbjct: 276 ERDKIKQLASELEKKLEKELKKLENKLEKQEDELEELEKAAEELRQKGELLYANLQLIEE 335

Query: 62  KEKNKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKE 121
             K+         ++ K    K K  ++N  R  +K K+ +  K     +        KE
Sbjct: 336 GLKSVRLADFYGNEEIKIELDKSKTPSENAQRYFKKYKKLKGAKVNLDRQLSEL----KE 391

Query: 122 EEEKKKEAEEKKKKRTKKKEKNKNKSRKEEEEEEKKKKKKKKKKKRTKKKE 172
                + A+   +K   KK   + +    EE   K KKKK+KKK+  +K  
Sbjct: 392 AIAYYESAKTALEKAEGKKAIEEIREELIEEGLLKSKKKKRKKKEWFEKFR 442

Length = 564

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

 Score = 51.5 bits (124), Expect = 4e-07
 Identities = 19/141 (13%), Positives = 43/141 (30%), Gaps = 3/141 (2%)

Query: 42  NKKNKNKSRKEEEKKKRTKKKEKNKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEA 101
                 K+    E++ + K K+       K    K++ +   + +K   +   +     +
Sbjct: 1   MTTASTKAELAAEEEAKKKLKKLAAKSKSKGFITKEEIKEALESKKKTPEQIDQVLIFLS 60

Query: 102 EEEKKKTKNKEKNKNKSRKEEEEKKKEAEEKKKKRTKKKEKNKNKSRKEEEEEEKKKKKK 161
              K      E +  K + +   K       K    KK +   + S+K E++    K   
Sbjct: 61  GMVKDTDDATESDIPKKKTKTAAKAAA---AKAPAKKKLKDELDSSKKAEKKNALDKDDD 117

Query: 162 KKKKKRTKKKEEEKRKNEKAV 182
               K      +    ++   
Sbjct: 118 LNYVKDIDVLNQADDDDDDDD 138

Length = 509

>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]

 Score = 52.0 bits (125), Expect = 4e-07
 Identities = 31/167 (18%), Positives = 75/167 (44%)

Query: 15  RTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKKKEKNKNKNRKEEK 74
           + +K+E  +   R EE  E+     E+ +K   K  ++ EK +R ++ +    +      
Sbjct: 171 KERKEEAERKLERTEENLERLEDLLEELEKQLEKLERQAEKAERYQELKAELRELELALL 230

Query: 75  KKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKEEEEKKKEAEEKKK 134
             K K   K+ E+ + +  + E++ E  +E+ +   KE  + KS  EE  ++ E  +++ 
Sbjct: 231 LAKLKELRKELEELEEELSRLEEELEELQEELEEAEKEIEELKSELEELREELEELQEEL 290

Query: 135 KRTKKKEKNKNKSRKEEEEEEKKKKKKKKKKKRTKKKEEEKRKNEKA 181
              K++ +          E  ++ + + ++ +   ++ +EK +  K 
Sbjct: 291 LELKEEIEELEGEISLLRERLEELENELEELEERLEELKEKIEALKE 337

Length = 1163

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

 Score = 51.5 bits (123), Expect = 4e-07
 Identities = 34/149 (22%), Positives = 74/149 (49%), Gaps = 8/149 (5%)

Query: 37  KKKEKNKKNKNKSR-----KEEEKKKRTKKKEKNKNK-NRKEEKKKKKKRRTKKKEKNKN 90
             +E N+K  N  R     KE E ++  K+ ++ K + ++K+    K +++    + N +
Sbjct: 185 ALREDNEKGVNFRRDMTDLKERESQEDAKRAQQLKEELDKKQIDADKAQQKADFAQDNAD 244

Query: 91  KSRKEEKKKEAEEEKKKTKNKEKNKNKSRKEEEEKKKEAEEKKKKRTKKKEKNKNKSRKE 150
           K R E ++K+ E +         +  + ++  E +K+E E K +   KK ++   K+ K+
Sbjct: 245 KQRDEVRQKQQEAKNLPKPADTSSPKEDKQVAENQKREIE-KAQIEIKKNDEEALKA-KD 302

Query: 151 EEEEEKKKKKKKKKKKRTKKKEEEKRKNE 179
            +  + K++ K  +K+   K+ E ++K E
Sbjct: 303 HKAFDLKQESKASEKEAEDKELEAQKKRE 331

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

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

 Score = 51.5 bits (124), Expect = 5e-07
 Identities = 26/127 (20%), Positives = 47/127 (37%), Gaps = 1/127 (0%)

Query: 61  KKEKNKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRK 120
                K +   EE+ KKK ++   K K+K    KEE K+  E +KK  +  ++       
Sbjct: 2   TTASTKAELAAEEEAKKKLKKLAAKSKSKGFITKEEIKEALESKKKTPEQIDQVLIFLSG 61

Query: 121 EEEEKKKEAEEKKKKRTKKKEKNKNKSRKEEEEEEKKKKKKKKKKKRTKKKEEEKRKNEK 180
             ++     E    K+  K    K  + K   +++ K +    KK   K   ++      
Sbjct: 62  MVKDTDDATESDIPKKKTKTAA-KAAAAKAPAKKKLKDELDSSKKAEKKNALDKDDDLNY 120

Query: 181 AVRLTKL 187
              +  L
Sbjct: 121 VKDIDVL 127

Length = 509

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

 Score = 51.5 bits (124), Expect = 5e-07
 Identities = 24/174 (13%), Positives = 67/174 (38%), Gaps = 9/174 (5%)

Query: 5   KEEKKKKKKRRTKKKEKNKN---------KSRKEEEEEKRTKKKEKNKKNKNKSRKEEEK 55
           KEE K+  + + K  E+            K   +  E    KKK K       ++   +K
Sbjct: 35  KEEIKEALESKKKTPEQIDQVLIFLSGMVKDTDDATESDIPKKKTKTAAKAAAAKAPAKK 94

Query: 56  KKRTKKKEKNKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNK 115
           K + +     K + +    K       K  +        ++   + + +     + + ++
Sbjct: 95  KLKDELDSSKKAEKKNALDKDDDLNYVKDIDVLNQADDDDDDDDDDDLDDDDIDDDDDDE 154

Query: 116 NKSRKEEEEKKKEAEEKKKKRTKKKEKNKNKSRKEEEEEEKKKKKKKKKKKRTK 169
           +    ++++   + +E+KK+  + ++ + +     +E++ +  ++ +K  K T 
Sbjct: 155 DDDEDDDDDDVDDEDEEKKEAKELEKLSDDDDFVWDEDDSEALRQARKDAKLTA 208

Length = 509

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

 Score = 51.3 bits (124), Expect = 5e-07
 Identities = 29/124 (23%), Positives = 67/124 (54%), Gaps = 8/124 (6%)

Query: 55  KKKRTKKKEKNKNKNRKEEKKKKKKRRTKKKE-----KNKNKSRKEEKKKEAEEEKKKTK 109
           KK    K ++ + + ++  ++ KK+    KKE     K +    + E +KE  E + + +
Sbjct: 26  KKIAEAKIKEAEEEAKRILEEAKKEAEAIKKEALLEAKEEIHKLRNEFEKELRERRNELQ 85

Query: 110 NKEKNKNKSRKEEEEKKKEAEEKKKKRTKKKEKNKNKSRKEEEEEEKKKKKKKKKKKRTK 169
             EK +   ++E  ++K E  EK+++  +KKEK   +  K++E E+K+++ ++  +++ +
Sbjct: 86  KLEK-RLLQKEENLDRKLELLEKREEELEKKEKELEQ--KQQELEKKEEELEELIEEQLQ 142

Query: 170 KKEE 173
           + E 
Sbjct: 143 ELER 146

Length = 520

>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]

 Score = 51.3 bits (123), Expect = 6e-07
 Identities = 27/183 (14%), Positives = 78/183 (42%), Gaps = 1/183 (0%)

Query: 7   EKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKE-KNKKNKNKSRKEEEKKKRTKKKEKN 65
           ++ +K+    +++     +  +E +EE    +KE +  K++ +  +EE ++ + +  E  
Sbjct: 235 KELRKELEELEEELSRLEEELEELQEELEEAEKEIEELKSELEELREELEELQEELLELK 294

Query: 66  KNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKEEEEK 125
           +     E +    + R ++ E    +  +  ++ + + E  K + +E+       E+   
Sbjct: 295 EEIEELEGEISLLRERLEELENELEELEERLEELKEKIEALKEELEERETLLEELEQLLA 354

Query: 126 KKEAEEKKKKRTKKKEKNKNKSRKEEEEEEKKKKKKKKKKKRTKKKEEEKRKNEKAVRLT 185
           + E  +++ +        + +   E   EE  + + +  + R + +E ++       RL 
Sbjct: 355 ELEEAKEELEEKLSALLEELEELFEALREELAELEAELAEIRNELEELKREIESLEERLE 414

Query: 186 KLS 188
           +LS
Sbjct: 415 RLS 417

Length = 1163

>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]

 Score = 51.3 bits (123), Expect = 7e-07
 Identities = 29/193 (15%), Positives = 79/193 (40%), Gaps = 5/193 (2%)

Query: 2   KNKKEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKK 61
           K +  E +        K+ + + +  +EE      + +E  ++ +   ++ EE K   ++
Sbjct: 219 KAELRELELALLLAKLKELRKELEELEEELSRLEEELEELQEELEEAEKEIEELKSELEE 278

Query: 62  KEKNKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEK-----NKN 116
             +   + ++E  + K++    + E +  + R EE + E EE +++ +  ++      + 
Sbjct: 279 LREELEELQEELLELKEEIEELEGEISLLRERLEELENELEELEERLEELKEKIEALKEE 338

Query: 117 KSRKEEEEKKKEAEEKKKKRTKKKEKNKNKSRKEEEEEEKKKKKKKKKKKRTKKKEEEKR 176
              +E   ++ E    + +  K++ + K  +  EE EE  +  +++  +   +  E    
Sbjct: 339 LEERETLLEELEQLLAELEEAKEELEEKLSALLEELEELFEALREELAELEAELAEIRNE 398

Query: 177 KNEKAVRLTKLSA 189
             E    +  L  
Sbjct: 399 LEELKREIESLEE 411

Length = 1163

>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]

 Score = 51.3 bits (123), Expect = 7e-07
 Identities = 32/201 (15%), Positives = 88/201 (43%), Gaps = 5/201 (2%)

Query: 6   EEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKKKEKN 65
           EE K+K +   ++ E+ +    + E+     ++ ++  + K  +  EE ++     +E+ 
Sbjct: 326 EELKEKIEALKEELEERETLLEELEQLLAELEEAKEELEEKLSALLEELEELFEALREEL 385

Query: 66  KNKNRKEEKKKKKKRRTKK-----KEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRK 120
                +  + + +    K+     +E+ +  S + E  KE  +E +    + + + +   
Sbjct: 386 AELEAELAEIRNELEELKREIESLEERLERLSERLEDLKEELKELEAELEELQTELEELN 445

Query: 121 EEEEKKKEAEEKKKKRTKKKEKNKNKSRKEEEEEEKKKKKKKKKKKRTKKKEEEKRKNEK 180
           EE E+ +E  E+ + R K+ E+   + ++E +  EK+    + +  R + ++   +    
Sbjct: 446 EELEELEEQLEELRDRLKELERELAELQEELQRLEKELSSLEARLDRLEAEQRASQGVRA 505

Query: 181 AVRLTKLSAFGISGYLLQWIR 201
            +   +    G+ G + + I+
Sbjct: 506 VLEALESGLPGVYGPVAELIK 526

Length = 1163

>gnl|CDD|218177 pfam04615, Utp14, Utp14 protein

 Score = 51.2 bits (123), Expect = 7e-07
 Identities = 40/169 (23%), Positives = 81/169 (47%), Gaps = 8/169 (4%)

Query: 18  KKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKKKEKNKNKNRKEEKKKK 77
           ++ + + K   + E E+  ++ E  +++  +  +E  KK   ++K   +N  ++ E KK 
Sbjct: 380 QRAEARKKEENDAEIEELRRELEGEEESDEEENEEPSKKNVGRRKFGPENGEKEAESKKL 439

Query: 78  KKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKEEEEKKKEAEE------ 131
           KK    + ++ K    +EE + E E + +K  NK   +++  ++EEE+++  EE      
Sbjct: 440 KKENKNEFKEKKESDEEEELEDEEEAKVEKVANKLLKRSEKAQKEEEEEELDEENPWLKT 499

Query: 132 --KKKKRTKKKEKNKNKSRKEEEEEEKKKKKKKKKKKRTKKKEEEKRKN 178
                K  KK++  K  S K ++   K  K   K KK+ KK++     +
Sbjct: 500 TSSVGKSAKKQDSKKKSSSKLDKAANKISKAAVKVKKKKKKEKSIDLDD 548

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

 Score = 51.1 bits (122), Expect = 8e-07
 Identities = 38/184 (20%), Positives = 97/184 (52%)

Query: 6   EEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKKKEKN 65
            EK+KKK+R  K  E+ +N +    + E+   ++ K K+   K+ +  + K++ + +E+N
Sbjct: 167 REKRKKKERLKKLIEETENLAELIIDLEELKLQELKLKEQAKKALEYYQLKEKLELEEEN 226

Query: 66  KNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKEEEEK 125
                  +  +++    ++  +++ +  +  K++  +EE+   +  ++NK + ++++ ++
Sbjct: 227 LLYLDYLKLNEERIDLLQELLRDEQEEIESSKQELEKEEEILAQVLKENKEEEKEKKLQE 286

Query: 126 KKEAEEKKKKRTKKKEKNKNKSRKEEEEEEKKKKKKKKKKKRTKKKEEEKRKNEKAVRLT 185
           ++     K++   K E  K + RK ++EE+ K+ +K+ KK   + K+E++   E    L 
Sbjct: 287 EELKLLAKEEEELKSELLKLERRKVDDEEKLKESEKELKKLEKELKKEKEEIEELEKELK 346

Query: 186 KLSA 189
           +L  
Sbjct: 347 ELEI 350

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 = 50.5 bits (121), Expect = 8e-07
 Identities = 22/91 (24%), Positives = 46/91 (50%), Gaps = 1/91 (1%)

Query: 2   KNKKEEKKKKKKRRTKKKEKNKNK-SRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTK 60
              +EE K       K K+++KN  S+K+ E++K+ KK++K  K++ +++   +  K++K
Sbjct: 41  TFSEEENKVATTSTKKDKKEDKNNESKKKSEKKKKKKKEKKEPKSEGETKLGFKTPKKSK 100

Query: 61  KKEKNKNKNRKEEKKKKKKRRTKKKEKNKNK 91
           K +K   K +  E       +  +  +  N 
Sbjct: 101 KTKKKPPKPKPNEDVDNAFNKIAELAEKSNV 131

Length = 413

>gnl|CDD|218177 pfam04615, Utp14, Utp14 protein

 Score = 50.8 bits (122), Expect = 8e-07
 Identities = 38/184 (20%), Positives = 86/184 (46%)

Query: 3   NKKEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKKK 62
           +  E     +K+  K KE   ++        K  ++ E  KK +N +  EE +++   ++
Sbjct: 346 DDGENPWMLRKKLGKLKEGEDDEENSGLLSMKFMQRAEARKKEENDAEIEELRRELEGEE 405

Query: 63  EKNKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKEE 122
           E ++ +N +  KK   +R+   +   K    K+ KK+   E K+K ++ E+ + +  +E 
Sbjct: 406 ESDEEENEEPSKKNVGRRKFGPENGEKEAESKKLKKENKNEFKEKKESDEEEELEDEEEA 465

Query: 123 EEKKKEAEEKKKKRTKKKEKNKNKSRKEEEEEEKKKKKKKKKKKRTKKKEEEKRKNEKAV 182
           + +K   +  K+    +KE+ + +  +E    +      K  KK+  KK+   + ++ A 
Sbjct: 466 KVEKVANKLLKRSEKAQKEEEEEELDEENPWLKTTSSVGKSAKKQDSKKKSSSKLDKAAN 525

Query: 183 RLTK 186
           +++K
Sbjct: 526 KISK 529

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|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]

 Score = 50.9 bits (122), Expect = 9e-07
 Identities = 31/188 (16%), Positives = 87/188 (46%), Gaps = 2/188 (1%)

Query: 4   KKEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKKKE 63
           +K E++ +K  R ++ +    +        K  + +++ ++ + +  + EE+ +  +++ 
Sbjct: 203 EKLERQAEKAERYQELKAELRELELALLLAKLKELRKELEELEEELSRLEEELEELQEEL 262

Query: 64  KNKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKEEE 123
           +   K  +E K + ++ R + +E  +     +E+ +E E E    + + +      +E E
Sbjct: 263 EEAEKEIEELKSELEELREELEELQEELLELKEEIEELEGEISLLRERLEELENELEELE 322

Query: 124 EKKKEAEEKKKKRTKKKEKNKNKSRKEEEEEE--KKKKKKKKKKKRTKKKEEEKRKNEKA 181
           E+ +E +EK +   ++ E+ +    + E+     ++ K++ ++K     +E E+      
Sbjct: 323 ERLEELKEKIEALKEELEERETLLEELEQLLAELEEAKEELEEKLSALLEELEELFEALR 382

Query: 182 VRLTKLSA 189
             L +L A
Sbjct: 383 EELAELEA 390

Length = 1163

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

 Score = 50.3 bits (121), Expect = 9e-07
 Identities = 27/79 (34%), Positives = 53/79 (67%)

Query: 102 EEEKKKTKNKEKNKNKSRKEEEEKKKEAEEKKKKRTKKKEKNKNKSRKEEEEEEKKKKKK 161
           EEE +     +K   K +K  E+ +K+ EE+KK++ KK    K K  +EEEE+EKK+++K
Sbjct: 396 EEEIEFLTGSKKATKKIKKIVEKAEKKREEEKKEKKKKAFAGKKKEEEEEEEKEKKEEEK 455

Query: 162 KKKKKRTKKKEEEKRKNEK 180
           +++++  ++++EE+ + +K
Sbjct: 456 EEEEEEAEEEKEEEEEKKK 474

Length = 482

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

 Score = 50.4 bits (121), Expect = 1e-06
 Identities = 45/185 (24%), Positives = 83/185 (44%), Gaps = 6/185 (3%)

Query: 2    KNKKEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKK 61
            K K E+   + +++ K+ EK KN + K+   E   K +E  ++ +    KE  K++R K 
Sbjct: 1101 KEKVEKLNAELEKKEKELEKLKNTTPKDMWLEDLDKFEEALEEQEEVEEKEIAKEQRLKS 1160

Query: 62   KEKNKNKNRKEEKKKKKKRRTKKKEK------NKNKSRKEEKKKEAEEEKKKTKNKEKNK 115
            K K K    ++ K KKK+++ KK         +   + K     E  +   K  NK+ N 
Sbjct: 1161 KTKGKASKLRKPKLKKKEKKKKKSSADKSKKASVVGNSKRVDSDEKRKLDDKPDNKKSNS 1220

Query: 116  NKSRKEEEEKKKEAEEKKKKRTKKKEKNKNKSRKEEEEEEKKKKKKKKKKKRTKKKEEEK 175
            + S +E++E++K   +K   +  K +KN +    E+ +E       K+ K +   K    
Sbjct: 1221 SGSDQEDDEEQKTKPKKSSVKRLKSKKNNSSKSSEDNDEFSSDDLSKEGKPKNAPKRVSA 1280

Query: 176  RKNEK 180
             +   
Sbjct: 1281 VQYSP 1285

Length = 1388

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

 Score = 50.2 bits (121), Expect = 1e-06
 Identities = 26/118 (22%), Positives = 67/118 (56%), Gaps = 8/118 (6%)

Query: 66  KNKNRKEEKKKKKKRRTKKKEKNKN-KSRKEEKKKEAEEEKKKTKNKEKNKNKSRKEE-- 122
           K     + K+ +++ +   +E  K  ++ K+E   EA+EE  K +N+ + + + R+ E  
Sbjct: 26  KKIAEAKIKEAEEEAKRILEEAKKEAEAIKKEALLEAKEEIHKLRNEFEKELRERRNELQ 85

Query: 123 --EEK---KKEAEEKKKKRTKKKEKNKNKSRKEEEEEEKKKKKKKKKKKRTKKKEEEK 175
             E++   K+E  ++K +  +K+E+   K  KE E+++++ +KK+++ +   +++ ++
Sbjct: 86  KLEKRLLQKEENLDRKLELLEKREEELEKKEKELEQKQQELEKKEEELEELIEEQLQE 143

Length = 520

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

 Score = 50.2 bits (121), Expect = 1e-06
 Identities = 43/124 (34%), Positives = 68/124 (54%), Gaps = 11/124 (8%)

Query: 77  KKKRRTKKKE-KNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKEEEEK---KKEAE-E 131
           KK    K KE + + K   EE KKEAE  KK+   + K +    + E EK   ++  E +
Sbjct: 26  KKIAEAKIKEAEEEAKRILEEAKKEAEAIKKEALLEAKEEIHKLRNEFEKELRERRNELQ 85

Query: 132 KKKKRTKKKEKNKNKS----RKEEEEEEKKKKKKKKKKKRTKKKEEE--KRKNEKAVRLT 185
           K +KR  +KE+N ++      K EEE EKK+K+ ++K++  +KKEEE  +   E+   L 
Sbjct: 86  KLEKRLLQKEENLDRKLELLEKREEELEKKEKELEQKQQELEKKEEELEELIEEQLQELE 145

Query: 186 KLSA 189
           ++S 
Sbjct: 146 RISG 149

Length = 520

>gnl|CDD|220271 pfam09507, CDC27, DNA polymerase subunit Cdc27

 Score = 49.8 bits (119), Expect = 1e-06
 Identities = 33/169 (19%), Positives = 69/169 (40%), Gaps = 5/169 (2%)

Query: 15  RTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKKKEKNKNKNRKEEK 74
            +   +   N  R   +  K     E     K KS K+ +   +    EK + K   +  
Sbjct: 150 ASPALKPTANGKRPSSKPPKSIMSPEV----KVKSAKKTQDTSKETTTEKTEGKTSVKAA 205

Query: 75  KKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNK-NKSRKEEEEKKKEAEEKK 133
             K+    K    +    +K ++KKE +E  + T  +E  + +  R    E +       
Sbjct: 206 SLKRNPPKKSNIMSSFFKKKTKEKKEKKEASESTVKEESEEESGKRDVILEDESAEPTGL 265

Query: 134 KKRTKKKEKNKNKSRKEEEEEEKKKKKKKKKKKRTKKKEEEKRKNEKAV 182
            +   + E   +  R + EEE ++K+K+K+K+ +   ++E++ +  + V
Sbjct: 266 DEDEDEDEPKPSGERSDSEEETEEKEKEKRKRLKKMMEDEDEDEEMEIV 314

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

 Score = 50.6 bits (122), Expect = 1e-06
 Identities = 34/135 (25%), Positives = 66/135 (48%), Gaps = 11/135 (8%)

Query: 32  EEKRTKKKEKNKKNKNKSRKEEEKKKRTKKKEKNKNKNRKEEKKKKKKRRTKKKEKNKNK 91
           EE   + ++K ++ +    KE EK K   +++K K +  +++  ++ ++  ++  K    
Sbjct: 526 EELERELEQKAEEAEAL-LKEAEKLKEELEEKKEKLQEEEDKLLEEAEKEAQQAIK---- 580

Query: 92  SRKEEKKKEAEEEKKKTKNKEKNKNKSRKEEE--EKKKEAEEKKKKRTKKKEKNKNKSRK 149
               E KKEA+E  K+ +  +K    S K  E  E +K   +  +K+ KKK+K K K  +
Sbjct: 581 ----EAKKEADEIIKELRQLQKGGYASVKAHELIEARKRLNKANEKKEKKKKKQKEKQEE 636

Query: 150 EEEEEEKKKKKKKKK 164
            +  +E K     +K
Sbjct: 637 LKVGDEVKYLSLGQK 651

Length = 782

>gnl|CDD|235334 PRK05035, PRK05035, electron transport complex protein RnfC; Provisional

 Score = 50.3 bits (121), Expect = 1e-06
 Identities = 34/197 (17%), Positives = 69/197 (35%), Gaps = 23/197 (11%)

Query: 2   KNKKEEKKKKKKRRTKKKEKN-------KNKSRKEEEEEKRTKKKEKNKKNKN-KSRKEE 53
           K  +E + KK       K+K+       + K++K    +    K      N    + +E 
Sbjct: 466 KAAREARHKKAAEARAAKDKDAVAAALARVKAKKAAATQPIVIKAGARPDNSAVIAAREA 525

Query: 54  EKKKRTKKKEKNKNKNRKEEKKKK--------KKRRTKKKEKNKNKSRKEEKKK---EAE 102
            K +   ++ + +     + KK          K ++  ++  N     + + KK    A 
Sbjct: 526 RKAQARARQAEKQAAAAADPKKAAVAAAIARAKAKKAAQQAANAEAEEEVDPKKAAVAAA 585

Query: 103 EEKKKTKNKEKNKNKSRKEEEE----KKKEAEEKKKKRTKKKEKNKNKSRKEEEEEEKKK 158
             + K K   +    +  EE+      KK A      R K K+  +  + + EE  + +K
Sbjct: 586 IARAKAKKAAQQAASAEPEEQVAEVDPKKAAVAAAIARAKAKKAEQQANAEPEEPVDPRK 645

Query: 159 KKKKKKKKRTKKKEEEK 175
                   R K ++  +
Sbjct: 646 AAVAAAIARAKARKAAQ 662

Length = 695

>gnl|CDD|223496 COG0419, SbcC, ATPase involved in DNA repair [DNA replication, recombination, and repair]

 Score = 50.5 bits (121), Expect = 1e-06
 Identities = 38/189 (20%), Positives = 94/189 (49%), Gaps = 2/189 (1%)

Query: 2   KNKKEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSR--KEEEKKKRT 59
           K +K E   ++    K+K + +    +  + E R ++ ++  +     R  KEE ++ R 
Sbjct: 534 KLEKLENLLEELEELKEKLQLQQLKEELRQLEDRLQELKELLEELRLLRTRKEELEELRE 593

Query: 60  KKKEKNKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSR 119
           + KE  K     EE+  + +   +  E ++ ++  EE ++E E E +K   + + +   +
Sbjct: 594 RLKELKKKLKELEERLSQLEELLQSLELSEAENELEEAEEELESELEKLNLQAELEELLQ 653

Query: 120 KEEEEKKKEAEEKKKKRTKKKEKNKNKSRKEEEEEEKKKKKKKKKKKRTKKKEEEKRKNE 179
              EE +++ EE + +  ++ ++ +N+ + EE+ EE ++ +++ ++ R + +E  K+  E
Sbjct: 654 AALEELEEKVEELEAEIRRELQRIENEEQLEEKLEELEQLEEELEQLREELEELLKKLGE 713

Query: 180 KAVRLTKLS 188
               + +L 
Sbjct: 714 IEQLIEELE 722

Length = 908

>gnl|CDD|225606 COG3064, TolA, Membrane protein involved in colicin uptake [Cell envelope biogenesis, outer membrane]

 Score = 48.8 bits (116), Expect = 2e-06
 Identities = 30/139 (21%), Positives = 67/139 (48%), Gaps = 6/139 (4%)

Query: 50  RKEEEKKKRTKKKEKNKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTK 109
           + E+++KK+ ++  +     +  E+++ K+   ++ +  + + + EE +K+A+ E+K+ +
Sbjct: 76  KGEQQRKKKEEQVAEELKPKQAAEQERLKQLEKERLKAQEQQKQAEEAEKQAQLEQKQQE 135

Query: 110 NKEKNK--NKSRKEEEEKKKEAEEKKKKRTKKKEKNKNKSRKEEEEEEKKK----KKKKK 163
            + +     + +K E  K K A E  K +   + K K +   +  EE K K      KKK
Sbjct: 136 EQARKAAAEQKKKAEAAKAKAAAEAAKLKAAAEAKKKAEEAAKAAEEAKAKAEAAAAKKK 195

Query: 164 KKKRTKKKEEEKRKNEKAV 182
            +   K   E+ +   +A 
Sbjct: 196 AEAEAKAAAEKAKAEAEAK 214

Length = 387

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

 Score = 50.0 bits (120), Expect = 2e-06
 Identities = 27/151 (17%), Positives = 60/151 (39%)

Query: 6    EEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKKKEKN 65
            +E  +++K + KK    + KS+K    +      E +  + +K  K +   KR    + +
Sbjct: 1225 QEDDEEQKTKPKKSSVKRLKSKKNNSSKSSEDNDEFSSDDLSKEGKPKNAPKRVSAVQYS 1284

Query: 66   KNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKEEEEK 125
                 K    +            K   ++ E    A ++KKK++ K   K KS+   ++ 
Sbjct: 1285 PPPPSKRPDGESNGGSKPSSPTKKKVKKRLEGSLAALKKKKKSEKKTARKKKSKTRVKQA 1344

Query: 126  KKEAEEKKKKRTKKKEKNKNKSRKEEEEEEK 156
                  +  +R +KK+ + +    ++ E + 
Sbjct: 1345 SASQSSRLLRRPRKKKSDSSSEDDDDSEVDD 1375

Length = 1388

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

 Score = 50.0 bits (120), Expect = 2e-06
 Identities = 39/173 (22%), Positives = 80/173 (46%), Gaps = 5/173 (2%)

Query: 13   KRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKKKEKNKNKNRKE 72
            K + +K      K  KE E+ K T  K+   ++ +K  +  E+++  ++KE  K +  K 
Sbjct: 1101 KEKVEKLNAELEKKEKELEKLKNTTPKDMWLEDLDKFEEALEEQEEVEEKEIAKEQRLKS 1160

Query: 73   EKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKEEEEKKKEAEEK 132
            + K K  +  K K K     +KE+KKK++  +K K  +   N  +   +E+ K  +  + 
Sbjct: 1161 KTKGKASKLRKPKLK-----KKEKKKKKSSADKSKKASVVGNSKRVDSDEKRKLDDKPDN 1215

Query: 133  KKKRTKKKEKNKNKSRKEEEEEEKKKKKKKKKKKRTKKKEEEKRKNEKAVRLT 185
            KK  +   ++  ++ +K + ++   K+ K KK   +K  E+    +   +   
Sbjct: 1216 KKSNSSGSDQEDDEEQKTKPKKSSVKRLKSKKNNSSKSSEDNDEFSSDDLSKE 1268

Length = 1388

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

 Score = 49.7 bits (119), Expect = 2e-06
 Identities = 38/188 (20%), Positives = 71/188 (37%), Gaps = 17/188 (9%)

Query: 4    KKEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSR----KEEEKKKRT 59
            KKE+KKKK      KK      S++ + +EKR    + + K  N S      +EE+K + 
Sbjct: 1176 KKEKKKKKSSADKSKKASVVGNSKRVDSDEKRKLDDKPDNKKSNSSGSDQEDDEEQKTKP 1235

Query: 60   KKKEKNKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKE------AEEEKKKTKNKEK 113
            KK    + K++K    K  +   +    + +K  K +   +              +   +
Sbjct: 1236 KKSSVKRLKSKKNNSSKSSEDNDEFSSDDLSKEGKPKNAPKRVSAVQYSPPPPSKRPDGE 1295

Query: 114  NKNKSRKEEEEKKKEAEEKKKKRTKKKEKNK-------NKSRKEEEEEEKKKKKKKKKKK 166
            +   S+     KKK  +  +      K+K K        K  K   ++    +  +  ++
Sbjct: 1296 SNGGSKPSSPTKKKVKKRLEGSLAALKKKKKSEKKTARKKKSKTRVKQASASQSSRLLRR 1355

Query: 167  RTKKKEEE 174
              KKK + 
Sbjct: 1356 PRKKKSDS 1363

Length = 1388

>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]

 Score = 49.7 bits (119), Expect = 2e-06
 Identities = 28/187 (14%), Positives = 81/187 (43%), Gaps = 9/187 (4%)

Query: 2   KNKKEEKKKKKKRRTK---------KKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKE 52
           +  +  ++ K + R           K+ + + +  +EE      + +E  ++ +   ++ 
Sbjct: 210 EKAERYQELKAELRELELALLLAKLKELRKELEELEEELSRLEEELEELQEELEEAEKEI 269

Query: 53  EEKKKRTKKKEKNKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKE 112
           EE K   ++  +   + ++E  + K++    + E +  + R EE + E EE +++ +  +
Sbjct: 270 EELKSELEELREELEELQEELLELKEEIEELEGEISLLRERLEELENELEELEERLEELK 329

Query: 113 KNKNKSRKEEEEKKKEAEEKKKKRTKKKEKNKNKSRKEEEEEEKKKKKKKKKKKRTKKKE 172
           +     ++E EE++   EE ++   + +E  +    K     E+ ++  +  ++   + E
Sbjct: 330 EKIEALKEELEERETLLEELEQLLAELEEAKEELEEKLSALLEELEELFEALREELAELE 389

Query: 173 EEKRKNE 179
            E  +  
Sbjct: 390 AELAEIR 396

Length = 1163

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

 Score = 49.3 bits (118), Expect = 2e-06
 Identities = 21/128 (16%), Positives = 41/128 (32%), Gaps = 5/128 (3%)

Query: 37  KKKEKNKKNKNKSRKEEEKKKRTKKKEKNKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEE 96
                  +                  ++  +   +EE K       K K+++KN   K++
Sbjct: 10  SFFSGTTQKSKLQPISYIYSNVLVLSKEILSTFSEEENKVATTSTKKDKKEDKNNESKKK 69

Query: 97  KKKEAEEEKKKTKNKEKNKNKSRKEEEEKKKEAEEKKKKRTKKKEKNKNKSRKEEEEEEK 156
                 E+KKK K ++K      + +   K   + KK K+   K K          +  +
Sbjct: 70  -----SEKKKKKKKEKKEPKSEGETKLGFKTPKKSKKTKKKPPKPKPNEDVDNAFNKIAE 124

Query: 157 KKKKKKKK 164
             +K    
Sbjct: 125 LAEKSNVY 132

Length = 413

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

 Score = 49.5 bits (119), Expect = 2e-06
 Identities = 25/78 (32%), Positives = 51/78 (65%)

Query: 95  EEKKKEAEEEKKKTKNKEKNKNKSRKEEEEKKKEAEEKKKKRTKKKEKNKNKSRKEEEEE 154
           EE+ +     KK TK  +K   K+ K+ EE+KKE ++K     KK+E+ + +  K+EEE+
Sbjct: 396 EEEIEFLTGSKKATKKIKKIVEKAEKKREEEKKEKKKKAFAGKKKEEEEEEEKEKKEEEK 455

Query: 155 EKKKKKKKKKKKRTKKKE 172
           E+++++ +++K+  ++K+
Sbjct: 456 EEEEEEAEEEKEEEEEKK 473

Length = 482

>gnl|CDD|188306 TIGR03319, RNase_Y, ribonuclease Y

 Score = 49.5 bits (119), Expect = 2e-06
 Identities = 42/165 (25%), Positives = 78/165 (47%), Gaps = 14/165 (8%)

Query: 27  RKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTK---KKEKNKNKNRKEEKKKKKKRRTK 83
           RK   E+K    +E  K+   +++KE E  K+      KE+      + E++ K++R   
Sbjct: 19  RKRIAEKKLGSAEELAKRIIEEAKKEAETLKKEALLEAKEEVHKLRAELERELKERRNEL 78

Query: 84  KKEKNKNKSRKEEKKKEAEEEKKKTKN---KEKNKNKSRKEEEEKKKEAEEKKKKRTKKK 140
           ++ + +   R+E   ++ E   KK +N   KEK  +   K  +EK++E EE   ++ ++ 
Sbjct: 79  QRLERRLLQREETLDRKMESLDKKEENLEKKEKELSNKEKNLDEKEEELEELIAEQREEL 138

Query: 141 EK--------NKNKSRKEEEEEEKKKKKKKKKKKRTKKKEEEKRK 177
           E+         K    +E EEE + +  K  K+   + KEE  +K
Sbjct: 139 ERISGLTQEEAKEILLEEVEEEARHEAAKLIKEIEEEAKEEADKK 183

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

 Score = 49.2 bits (118), Expect = 2e-06
 Identities = 21/70 (30%), Positives = 34/70 (48%)

Query: 111 KEKNKNKSRKEEEEKKKEAEEKKKKRTKKKEKNKNKSRKEEEEEEKKKKKKKKKKKRTKK 170
           +E  K +   E   K K   EKK  +  KK   K   +KE+E+E+ K KK+ +  K   K
Sbjct: 365 EEPLKARVIDELRPKTKAPSEKKTGKPSKKVLAKRAEKKEKEKEKPKVKKRHRDTKNIGK 424

Query: 171 KEEEKRKNEK 180
           + +    +E+
Sbjct: 425 RRKPSGTSEE 434

Length = 434

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

 Score = 49.2 bits (118), Expect = 2e-06
 Identities = 20/66 (30%), Positives = 30/66 (45%), Gaps = 1/66 (1%)

Query: 25  KSRKEEEEEKRTKK-KEKNKKNKNKSRKEEEKKKRTKKKEKNKNKNRKEEKKKKKKRRTK 83
           K+R  +E   +TK   EK     +K    +  +K+ K+KEK K K R  + K   KRR  
Sbjct: 369 KARVIDELRPKTKAPSEKKTGKPSKKVLAKRAEKKEKEKEKPKVKKRHRDTKNIGKRRKP 428

Query: 84  KKEKNK 89
                +
Sbjct: 429 SGTSEE 434

Length = 434

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

 Score = 49.1 bits (118), Expect = 3e-06
 Identities = 25/80 (31%), Positives = 50/80 (62%)

Query: 28  KEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKKKEKNKNKNRKEEKKKKKKRRTKKKEK 87
           +EE E     KK   K  K   + E+++++  K+K+K     +K+E+++++++  K++EK
Sbjct: 396 EEEIEFLTGSKKATKKIKKIVEKAEKKREEEKKEKKKKAFAGKKKEEEEEEEKEKKEEEK 455

Query: 88  NKNKSRKEEKKKEAEEEKKK 107
            + +   EE+K+E EE+KKK
Sbjct: 456 EEEEEEAEEEKEEEEEKKKK 475

Length = 482

>gnl|CDD|172341 PRK13808, PRK13808, adenylate kinase; Provisional

 Score = 48.7 bits (116), Expect = 3e-06
 Identities = 31/137 (22%), Positives = 49/137 (35%)

Query: 4   KKEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKKKE 63
               KK  K    K   K  +   K   ++   KK  K   +  K+ K   K  +  KK 
Sbjct: 196 AANAKKAAKTPAAKSGAKKASAKAKSAAKKVSKKKAAKTAVSAKKAAKTAAKAAKKAKKT 255

Query: 64  KNKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKEEE 123
             K   +  +  KK  ++  K      K   +  K +A+ +KK  K            + 
Sbjct: 256 AKKALKKAAKAVKKAAKKAAKAAAKAAKGAAKATKGKAKAKKKAGKKAAAGSKAKATAKA 315

Query: 124 EKKKEAEEKKKKRTKKK 140
            K+    +K KK TKK+
Sbjct: 316 PKRGAKGKKAKKVTKKR 332

Length = 333

>gnl|CDD|202096 pfam02029, Caldesmon, Caldesmon

 Score = 48.5 bits (115), Expect = 3e-06
 Identities = 45/178 (25%), Positives = 92/178 (51%), Gaps = 9/178 (5%)

Query: 16  TKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKKKEKNKNKNRKEEKK 75
            +++EK +++  +EE EE     K + K +   + + ++++K  + +E+ K K    E+ 
Sbjct: 111 VEEEEKEESREEREEVEETEGVTKSEQKNDWRDAEECQKEEKEPEPEEEEKPKRGSLEEN 170

Query: 76  KKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKEEEEKKKEAEEKKKK 135
             +    K K      SR   +  + E  K+  K K+K +  + + EE KKK  EE++K 
Sbjct: 171 NGEFMTHKLKHTENTFSRGGAEGAQVEAGKEFEKLKQKQQEAALELEELKKKR-EERRKV 229

Query: 136 RTKKKEKNKNKSRKEEEEEEKKKKKKKKKKKRTKKKEEEKRKNEKAVRLTKLSAFGIS 193
             +++++ K        +EE  +K +++++KR  K+E E+R+ E A +  K+   G+S
Sbjct: 230 LEEEEQRRK--------QEEADRKSREEEEKRRLKEEIERRRAEAAEKRQKVPEDGLS 279

Length = 431

>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]

 Score = 48.9 bits (117), Expect = 4e-06
 Identities = 28/185 (15%), Positives = 83/185 (44%), Gaps = 3/185 (1%)

Query: 2   KNKKEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKK 61
           + ++E  + K++    + E +  + R EE E +  + +E+ ++ K K    +E+ +  + 
Sbjct: 285 ELQEELLELKEEIEELEGEISLLRERLEELENELEELEERLEELKEKIEALKEELEERET 344

Query: 62  KEKNKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKE 121
             +   +   E ++ K++   K           EE  +   EE  + + +        +E
Sbjct: 345 LLEELEQLLAELEEAKEELEEKLSA---LLEELEELFEALREELAELEAELAEIRNELEE 401

Query: 122 EEEKKKEAEEKKKKRTKKKEKNKNKSRKEEEEEEKKKKKKKKKKKRTKKKEEEKRKNEKA 181
            + + +  EE+ ++ +++ E  K + ++ E E E+ + + ++  +  ++ EE+  +    
Sbjct: 402 LKREIESLEERLERLSERLEDLKEELKELEAELEELQTELEELNEELEELEEQLEELRDR 461

Query: 182 VRLTK 186
           ++  +
Sbjct: 462 LKELE 466

Length = 1163

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

 Score = 48.8 bits (116), Expect = 4e-06
 Identities = 44/186 (23%), Positives = 94/186 (50%)

Query: 2   KNKKEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKK 61
           K +++EKK +++      ++ +    +  + E+R    E+  K   K  K+ EK+ + +K
Sbjct: 276 KEEEKEKKLQEEELKLLAKEEEELKSELLKLERRKVDDEEKLKESEKELKKLEKELKKEK 335

Query: 62  KEKNKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKE 121
           +E  + +   +E + K++   +++E+ +    K E+ +E    KKK +++  +     KE
Sbjct: 336 EEIEELEKELKELEIKREAEEEEEEQLEKLQEKLEQLEEELLAKKKLESERLSSAAKLKE 395

Query: 122 EEEKKKEAEEKKKKRTKKKEKNKNKSRKEEEEEEKKKKKKKKKKKRTKKKEEEKRKNEKA 181
           EE + K  EEK+ K   +  + +    KEE++EE K  ++ ++   TK+ +  + K E  
Sbjct: 396 EELELKNEEEKEAKLLLELSEQEEDLLKEEKKEELKIVEELEESLETKQGKLTEEKEELE 455

Query: 182 VRLTKL 187
            +  KL
Sbjct: 456 KQALKL 461

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|233757 TIGR02168, SMC_prok_B, chromosome segregation protein SMC, common bacterial type

 Score = 48.9 bits (117), Expect = 4e-06
 Identities = 35/186 (18%), Positives = 81/186 (43%), Gaps = 2/186 (1%)

Query: 4   KKEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKKKE 63
           +K E+ K+ K   ++ E      R EE  E+  + +E+ K+   +  +E   + +  +++
Sbjct: 210 EKAERYKELKAELRELELALLVLRLEELREELEELQEELKEA-EEELEELTAELQELEEK 268

Query: 64  KNKNKNRKEEKKKKKKRRTKK-KEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKEE 122
             + +    E +++ +   K+        SR E++K+   E     + + +      +E 
Sbjct: 269 LEELRLEVSELEEEIEELQKELYALANEISRLEQQKQILRERLANLERQLEELEAQLEEL 328

Query: 123 EEKKKEAEEKKKKRTKKKEKNKNKSRKEEEEEEKKKKKKKKKKKRTKKKEEEKRKNEKAV 182
           E K  E  E+  +  +K E+ K +    E E E+ + + ++ + R ++ EE+       V
Sbjct: 329 ESKLDELAEELAELEEKLEELKEELESLEAELEELEAELEELESRLEELEEQLETLRSKV 388

Query: 183 RLTKLS 188
              +L 
Sbjct: 389 AQLELQ 394

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|240246 PTZ00053, PTZ00053, methionine aminopeptidase 2; Provisional

 Score = 48.6 bits (116), Expect = 4e-06
 Identities = 23/115 (20%), Positives = 55/115 (47%), Gaps = 6/115 (5%)

Query: 17  KKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKKKEKNKNKNRKEEKKK 76
              E  +N+ ++++++ K+   K+KNKK+K     ++          +  ++N++ E K+
Sbjct: 1   AMNENGENEVKQQKQQNKQKGTKKKNKKSKKDVDDDDA------FLAELISENQEAENKQ 54

Query: 77  KKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKEEEEKKKEAEE 131
             K++ KKK+K K K+  E      +     +    ++ +  RK     ++E ++
Sbjct: 55  NNKKKKKKKKKKKKKNLGEAYDLAYDLPVVWSSAAFQDNSHIRKLGNWPEQEWKQ 109

Length = 470

>gnl|CDD|222447 pfam13904, DUF4207, Domain of unknown function (DUF4207)

 Score = 47.4 bits (113), Expect = 4e-06
 Identities = 39/161 (24%), Positives = 91/161 (56%), Gaps = 12/161 (7%)

Query: 15  RTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKKKEKNKNKNRKEEK 74
           R+ K+ K + ++++  E     K+ ++ KK +   +  EEK+K+ ++KE+ + + R+   
Sbjct: 74  RSLKEVKLERQAQEAYENWLSAKQAQRQKKLQ---KLLEEKQKQEREKEREEAELRQRLA 130

Query: 75  KKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKEEEEKKKEAEEKKK 134
           K+K +   ++K +   K R  + KKEA E    + +            + ++  ++E+ K
Sbjct: 131 KEKYEEWCRQKAQQAAKQRTPKHKKEAAESASSSLSGSA---------KPERNVSQEEAK 181

Query: 135 KRTKKKEKNKNKSRKEEEEEEKKKKKKKKKKKRTKKKEEEK 175
           KR ++ E  K K ++++ EEE++K++KK++++  +K++ E+
Sbjct: 182 KRLQEWELKKLKQQQQKREEERRKQRKKQQEEEERKQKAEE 222

This family is found in eukaryotes; it has several conserved tryptophan residues. The function is not known. Length = 261

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

 Score = 48.5 bits (116), Expect = 5e-06
 Identities = 36/174 (20%), Positives = 73/174 (41%), Gaps = 1/174 (0%)

Query: 3    NKKEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKKK 62
            +K+ +  +K+K   K   K  N S  ++E+++  K K K    K    K+    K ++  
Sbjct: 1198 SKRVDSDEKRKLDDKPDNKKSNSSGSDQEDDEEQKTKPKKSSVKRLKSKKNNSSKSSEDN 1257

Query: 63   EK-NKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKE 121
            ++ + +   KE K K   +R    + +     K    +     K  +  K+K K +    
Sbjct: 1258 DEFSSDDLSKEGKPKNAPKRVSAVQYSPPPPSKRPDGESNGGSKPSSPTKKKVKKRLEGS 1317

Query: 122  EEEKKKEAEEKKKKRTKKKEKNKNKSRKEEEEEEKKKKKKKKKKKRTKKKEEEK 175
                KK+ + +KK   KKK K + K     +     ++ +KKK   + + +++ 
Sbjct: 1318 LAALKKKKKSEKKTARKKKSKTRVKQASASQSSRLLRRPRKKKSDSSSEDDDDS 1371

Length = 1388

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

 Score = 48.8 bits (116), Expect = 5e-06
 Identities = 39/176 (22%), Positives = 92/176 (52%)

Query: 3   NKKEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKKK 62
           N++     ++  R +++E   +K   E+EEE   +  ++NK+ + + + +EE+ K   K+
Sbjct: 236 NEERIDLLQELLRDEQEEIESSKQELEKEEEILAQVLKENKEEEKEKKLQEEELKLLAKE 295

Query: 63  EKNKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKEE 122
           E+       + +++K     K KE  K   + E++ K+ +EE ++ + + K     R+ E
Sbjct: 296 EEELKSELLKLERRKVDDEEKLKESEKELKKLEKELKKEKEEIEELEKELKELEIKREAE 355

Query: 123 EEKKKEAEEKKKKRTKKKEKNKNKSRKEEEEEEKKKKKKKKKKKRTKKKEEEKRKN 178
           EE++++ E+ ++K  + +E+   K + E E      K K+++ +   ++E+E +  
Sbjct: 356 EEEEEQLEKLQEKLEQLEEELLAKKKLESERLSSAAKLKEEELELKNEEEKEAKLL 411

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 = 48.2 bits (115), Expect = 5e-06
 Identities = 28/117 (23%), Positives = 50/117 (42%), Gaps = 3/117 (2%)

Query: 2   KNKKEEKKKKKKRRTK-KKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTK 60
           +  K +             ++  +   +EE +   T  K+  K++KN   K++ +KK+ K
Sbjct: 17  QKSKLQPISYIYSNVLVLSKEILSTFSEEENKVATTSTKKDKKEDKNNESKKKSEKKKKK 76

Query: 61  KKEKNKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNK 117
           KKEK + K+  E K   K    KK +K K K  K +  ++ +    K     +  N 
Sbjct: 77  KKEKKEPKSEGETKLGFKT--PKKSKKTKKKPPKPKPNEDVDNAFNKIAELAEKSNV 131

Length = 413

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

 Score = 48.1 bits (114), Expect = 5e-06
 Identities = 37/157 (23%), Positives = 75/157 (47%), Gaps = 11/157 (7%)

Query: 4   KKEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKKKE 63
           K+ E ++  KR  + KE+     +K+ + +K  +K +  + N +K R E  +K   +++ 
Sbjct: 204 KERESQEDAKRAQQLKEELD---KKQIDADKAQQKADFAQDNADKQRDEVRQK---QQEA 257

Query: 64  KNKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKEEE 123
           KN  K       K+ K+  + +++   K++ E KK + E  K K       K +S+  E+
Sbjct: 258 KNLPKPADTSSPKEDKQVAENQKREIEKAQIEIKKNDEEALKAKDHKAFDLKQESKASEK 317

Query: 124 EKKKEAEEKKKKRTK-----KKEKNKNKSRKEEEEEE 155
           E + +  E +KKR       +K K + +++     E+
Sbjct: 318 EAEDKELEAQKKREPVAEDLQKTKPQVEAQPTSLNED 354

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

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

 Score = 48.4 bits (116), Expect = 5e-06
 Identities = 32/86 (37%), Positives = 51/86 (59%), Gaps = 6/86 (6%)

Query: 29  EEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKKKEKNKNKNRKEEKKKKKKRRTKKKEKN 88
           EEE E  T  K+     K K   E+ +KKR ++K++ K    K+    KKK   +++EK 
Sbjct: 396 EEEIEFLTGSKKA--TKKIKKIVEKAEKKREEEKKEKK----KKAFAGKKKEEEEEEEKE 449

Query: 89  KNKSRKEEKKKEAEEEKKKTKNKEKN 114
           K +  KEE+++EAEEEK++ + K+K 
Sbjct: 450 KKEEEKEEEEEEAEEEKEEEEEKKKK 475

Length = 482

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

 Score = 48.0 bits (115), Expect = 5e-06
 Identities = 31/88 (35%), Positives = 51/88 (57%), Gaps = 14/88 (15%)

Query: 81  RTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKEEEEKKKEAEEKKKKRTKKK 140
             K  +K K    K EKK+E E+++KK K     K +  +EEE++KKE E++++      
Sbjct: 405 SKKATKKIKKIVEKAEKKREEEKKEKKKKAFAGKKKEEEEEEEKEKKEEEKEEE------ 458

Query: 141 EKNKNKSRKEEEEEEKKKKKKKKKKKRT 168
                   +EE EEEK+++++KKKK+ T
Sbjct: 459 --------EEEAEEEKEEEEEKKKKQAT 478

Length = 482

>gnl|CDD|224212 COG1293, COG1293, Predicted RNA-binding protein homologous to eukaryotic snRNP [Transcription]

 Score = 48.2 bits (115), Expect = 5e-06
 Identities = 38/171 (22%), Positives = 72/171 (42%), Gaps = 6/171 (3%)

Query: 10  KKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKKKEKNKNKN 69
           +K +R   K+  ++ + + E+E +K   K EK +    +  K  E+ ++   K +    N
Sbjct: 273 EKFERDKIKQLASELEKKLEKELKKLENKLEKQEDELEELEKAAEELRQ---KGELLYAN 329

Query: 70  RKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKEEEEKKKEA 129
            +  ++  K  R      N+    + +K K   E  ++   K K    ++   + +  E 
Sbjct: 330 LQLIEEGLKSVRLADFYGNEEIKIELDKSKTPSENAQRYFKKYKKLKGAKVNLDRQLSEL 389

Query: 130 EEKKKKRTKKK---EKNKNKSRKEEEEEEKKKKKKKKKKKRTKKKEEEKRK 177
           +E        K   EK + K   EE  EE  ++   K KK+ +KK+E   K
Sbjct: 390 KEAIAYYESAKTALEKAEGKKAIEEIREELIEEGLLKSKKKKRKKKEWFEK 440

Length = 564

>gnl|CDD|224212 COG1293, COG1293, Predicted RNA-binding protein homologous to eukaryotic snRNP [Transcription]

 Score = 48.2 bits (115), Expect = 5e-06
 Identities = 36/163 (22%), Positives = 64/163 (39%), Gaps = 15/163 (9%)

Query: 2   KNKKEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKN---------------KKNK 46
              K+   + +K+  K+ +K +NK  K+E+E +  +K  +                ++  
Sbjct: 278 DKIKQLASELEKKLEKELKKLENKLEKQEDELEELEKAAEELRQKGELLYANLQLIEEGL 337

Query: 47  NKSRKEEEKKKRTKKKEKNKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKK 106
              R  +       K E +K+K   E  ++  K+  K K    N  R+  + KEA    +
Sbjct: 338 KSVRLADFYGNEEIKIELDKSKTPSENAQRYFKKYKKLKGAKVNLDRQLSELKEAIAYYE 397

Query: 107 KTKNKEKNKNKSRKEEEEKKKEAEEKKKKRTKKKEKNKNKSRK 149
             K   +     +  EE +++  EE   K  KKK K K    K
Sbjct: 398 SAKTALEKAEGKKAIEEIREELIEEGLLKSKKKKRKKKEWFEK 440

Length = 564

>gnl|CDD|215521 PLN02967, PLN02967, kinase

 Score = 48.5 bits (115), Expect = 5e-06
 Identities = 30/124 (24%), Positives = 56/124 (45%), Gaps = 20/124 (16%)

Query: 71  KEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEE----------KKKTKNKEKNKNKSRK 120
              K + ++ R + K      SRK+ +   A +E          KK T++ ++   K+  
Sbjct: 27  GFNKFRGERWRLQNKFLLAAGSRKKIESALAVDEEPDENGAVSKKKPTRSVKRATKKTVV 86

Query: 121 EEEEKKKE----------AEEKKKKRTKKKEKNKNKSRKEEEEEEKKKKKKKKKKKRTKK 170
           E  E  +E          A +K+ K+T ++ + K  +   + EEEK +KK +K++K  K 
Sbjct: 87  EISEPLEEGSELVVNEDAALDKESKKTPRRTRRKAAAASSDVEEEKTEKKVRKRRKVKKM 146

Query: 171 KEEE 174
            E+ 
Sbjct: 147 DEDV 150

Length = 581

>gnl|CDD|235175 PRK03918, PRK03918, chromosome segregation protein; Provisional

 Score = 48.5 bits (116), Expect = 5e-06
 Identities = 47/183 (25%), Positives = 92/183 (50%), Gaps = 8/183 (4%)

Query: 2   KNKKEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKK 61
           K  KE ++ K++    +KE    +  K + EEK  + +E+ ++ K +  + EEK K  K+
Sbjct: 228 KEVKELEELKEEIEELEKELESLEGSKRKLEEKIRELEERIEELKKEIEELEEKVKELKE 287

Query: 62  KEKNKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKE 121
            ++   +  K   +  ++   + +E  K  SR EE+    EE  K+ + KE+   + +K+
Sbjct: 288 LKEKAEEYIKL-SEFYEEYLDELREIEKRLSRLEEEINGIEERIKELEEKEERLEELKKK 346

Query: 122 EEEKKKEAEEKKKK-------RTKKKEKNKNKSRKEEEEEEKKKKKKKKKKKRTKKKEEE 174
            +E +K  EE +++       + KK+E  + K R      EK +K+ ++ +K  ++ EEE
Sbjct: 347 LKELEKRLEELEERHELYEEAKAKKEELERLKKRLTGLTPEKLEKELEELEKAKEEIEEE 406

Query: 175 KRK 177
             K
Sbjct: 407 ISK 409

Length = 880

>gnl|CDD|233467 TIGR01554, major_cap_HK97, phage major capsid protein, HK97 family

 Score = 47.7 bits (114), Expect = 5e-06
 Identities = 32/160 (20%), Positives = 63/160 (39%), Gaps = 18/160 (11%)

Query: 73  EKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKEEEEKKKEAEEK 132
            K+ ++      KE  K     +EK  EAEEEK +    ++       ++ + + +  E+
Sbjct: 1   LKELREALAELAKELRKLTE--DEKLAEAEEEKAEYDALKE-----EIDKLDAEIDRLEE 53

Query: 133 KKKRTKKKEKNKNKSRKEEEEEEKKKKKKKKKKKRTKKKEEEKRKNEKAVRLTKLSAFGI 192
                + K     +    EEEEE+ K +  + +   +  ++   +  KA+     S    
Sbjct: 54  LLDELEAKPAASGEGGGGEEEEEEAKAEAAEFRAYLRGGDDALAEERKALSTGTDSD--- 110

Query: 193 SGYLL--QWIRNFL------SGWIQIVRVGTSTSEPIHIP 224
            GYL+  ++    +      S   Q+  V   +S  + IP
Sbjct: 111 GGYLVPEEFSTEIIELLREYSPLRQLATVIPVSSGSLTIP 150

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|235250 PRK04195, PRK04195, replication factor C large subunit; Provisional

 Score = 48.0 bits (115), Expect = 6e-06
 Identities = 27/81 (33%), Positives = 52/81 (64%)

Query: 100 EAEEEKKKTKNKEKNKNKSRKEEEEKKKEAEEKKKKRTKKKEKNKNKSRKEEEEEEKKKK 159
             EE +  T +K+  K   +  E+ +KK  EEKK+K+ K     K +  +EEE+E+K+++
Sbjct: 395 TEEEIEFLTGSKKATKKIKKIVEKAEKKREEEKKEKKKKAFAGKKKEEEEEEEKEKKEEE 454

Query: 160 KKKKKKKRTKKKEEEKRKNEK 180
           K++++++  ++KEEE+ K +K
Sbjct: 455 KEEEEEEAEEEKEEEEEKKKK 475

Length = 482

>gnl|CDD|202096 pfam02029, Caldesmon, Caldesmon

 Score = 47.7 bits (113), Expect = 6e-06
 Identities = 44/172 (25%), Positives = 82/172 (47%), Gaps = 2/172 (1%)

Query: 1   CKNKKEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTK 60
               K E+K   +   + +++ K    +EEE+ KR   +E N +      K  E      
Sbjct: 130 EGVTKSEQKNDWRDAEECQKEEKEPEPEEEEKPKRGSLEENNGEFMTHKLKHTENTFSRG 189

Query: 61  KKEKNKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRK 120
             E  + +  KE +K K+K++    E  + K ++EE++K  EEE++  + K++  ++  +
Sbjct: 190 GAEGAQVEAGKEFEKLKQKQQEAALELEELKKKREERRKVLEEEEQ--RRKQEEADRKSR 247

Query: 121 EEEEKKKEAEEKKKKRTKKKEKNKNKSRKEEEEEEKKKKKKKKKKKRTKKKE 172
           EEEEK++  EE +++R +  EK +        E++K  K    K    K  E
Sbjct: 248 EEEEKRRLKEEIERRRAEAAEKRQKVPEDGLSEDKKPFKCFTPKGSSLKITE 299

Length = 431

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

 Score = 48.0 bits (114), Expect = 7e-06
 Identities = 37/189 (19%), Positives = 95/189 (50%), Gaps = 4/189 (2%)

Query: 1   CKNKKEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTK 60
            + K +E K K++     K+  +    KE+ E +       +    N+ R +  ++    
Sbjct: 194 EELKLQELKLKEQA----KKALEYYQLKEKLELEEENLLYLDYLKLNEERIDLLQELLRD 249

Query: 61  KKEKNKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRK 120
           ++E+ ++  ++ EK+++   +  K+ K + K +K ++++     K++ + K +     R+
Sbjct: 250 EQEEIESSKQELEKEEEILAQVLKENKEEEKEKKLQEEELKLLAKEEEELKSELLKLERR 309

Query: 121 EEEEKKKEAEEKKKKRTKKKEKNKNKSRKEEEEEEKKKKKKKKKKKRTKKKEEEKRKNEK 180
           + ++++K  E +K+ +  +KE  K K   EE E+E K+ + K++ +  ++++ EK + + 
Sbjct: 310 KVDDEEKLKESEKELKKLEKELKKEKEEIEELEKELKELEIKREAEEEEEEQLEKLQEKL 369

Query: 181 AVRLTKLSA 189
                +L A
Sbjct: 370 EQLEEELLA 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|217051 pfam02463, SMC_N, RecF/RecN/SMC N terminal domain

 Score = 48.0 bits (114), Expect = 7e-06
 Identities = 46/179 (25%), Positives = 100/179 (55%)

Query: 2   KNKKEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKK 61
           + KK+E++ K++ +  K EK +  + K +E + +  ++ K  + K K ++EEE+K R KK
Sbjct: 701 EIKKKEQRIKEELKKLKLEKEELLADKVQEAQDKINEELKLLEQKIKEKEEEEEKSRLKK 760

Query: 62  KEKNKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKE 121
           +E+ + K+    K+K+     +K EK K +  KEEK K  EEE +  + + K + +  +E
Sbjct: 761 EEEEEEKSELSLKEKELAEEEEKTEKLKVEEEKEEKLKAQEEELRALEEELKEEAELLEE 820

Query: 122 EEEKKKEAEEKKKKRTKKKEKNKNKSRKEEEEEEKKKKKKKKKKKRTKKKEEEKRKNEK 180
           E+   ++ E+ K++  ++      + +K E+  E++ ++ +++  + +  +E   K E+
Sbjct: 821 EQLLIEQEEKIKEEELEELALELKEEQKLEKLAEEELERLEEEITKEELLQELLLKEEE 879

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|172341 PRK13808, PRK13808, adenylate kinase; Provisional

 Score = 47.2 bits (112), Expect = 7e-06
 Identities = 36/137 (26%), Positives = 57/137 (41%), Gaps = 1/137 (0%)

Query: 50  RKEEEKKKRTKKKEKNKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTK 109
                KK       K+  K    + K   K+ +KKK      S K+  K  A+  KK  K
Sbjct: 195 GAANAKKAAKTPAAKSGAKKASAKAKSAAKKVSKKKAAKTAVSAKKAAKTAAKAAKKAKK 254

Query: 110 NKEKNKNKSRKEEEEKKKEAEEKKKKRTKKKEKNKNKSRKEEEEEEKKKKKKKKKKKRTK 169
             +K   K+ K  ++  K+A +   K  K   K   K + + +++  KK     K K T 
Sbjct: 255 TAKKALKKAAKAVKKAAKKAAKAAAKAAKGAAK-ATKGKAKAKKKAGKKAAAGSKAKATA 313

Query: 170 KKEEEKRKNEKAVRLTK 186
           K  +   K +KA ++TK
Sbjct: 314 KAPKRGAKGKKAKKVTK 330

Length = 333

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

 Score = 48.0 bits (114), Expect = 8e-06
 Identities = 40/188 (21%), Positives = 95/188 (50%)

Query: 2   KNKKEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKK 61
            +K+E +K+++      KE  + +  K+ +EE+     ++ ++ K++  K E +K   ++
Sbjct: 256 SSKQELEKEEEILAQVLKENKEEEKEKKLQEEELKLLAKEEEELKSELLKLERRKVDDEE 315

Query: 62  KEKNKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKE 121
           K K   K  K+ +K+ KK + + +E  K     E K++  EEE+++ +  ++   +  +E
Sbjct: 316 KLKESEKELKKLEKELKKEKEEIEELEKELKELEIKREAEEEEEEQLEKLQEKLEQLEEE 375

Query: 122 EEEKKKEAEEKKKKRTKKKEKNKNKSRKEEEEEEKKKKKKKKKKKRTKKKEEEKRKNEKA 181
              KKK   E+     K KE+      +EE+E +   +  ++++   K++++E+ K  + 
Sbjct: 376 LLAKKKLESERLSSAAKLKEEELELKNEEEKEAKLLLELSEQEEDLLKEEKKEELKIVEE 435

Query: 182 VRLTKLSA 189
           +  +  + 
Sbjct: 436 LEESLETK 443

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|237258 PRK12903, secA, preprotein translocase subunit SecA; Reviewed

 Score = 47.7 bits (114), Expect = 8e-06
 Identities = 25/122 (20%), Positives = 50/122 (40%), Gaps = 4/122 (3%)

Query: 5   KEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKKKEK 64
            ++  + ++ R K     + +     EE +   +++KN K + K    E ++   + +  
Sbjct: 808 IDQIIESEEERLKALRIQREEMLMRPEELELINEEQKNLKQEIKLELSEIQEAEEEIQNI 867

Query: 65  NKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKEEEE 124
           N+NKN   E K       KK  K         K   + +E K+ +   K K K  ++ +E
Sbjct: 868 NENKNEFVEFKND----PKKLNKLIIAKDVLIKLVISSDEIKQDEKTTKKKKKDLEKTDE 923

Query: 125 KK 126
           + 
Sbjct: 924 EA 925

Length = 925

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

 Score = 47.0 bits (112), Expect = 9e-06
 Identities = 30/117 (25%), Positives = 50/117 (42%), Gaps = 3/117 (2%)

Query: 25  KSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTK--KKEKNKNKNRKEEKKKKKKRRT 82
           +  K +             K    +  EEE K  T   KK+K ++KN + +KK +KK++ 
Sbjct: 17  QKSKLQPISYIYSNVLVLSKEILSTFSEEENKVATTSTKKDKKEDKNNESKKKSEKKKKK 76

Query: 83  KKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKEEEEKKKEAEEKKKKRTKK 139
           KK++K   KS  E K      +K K   K+  K K  ++ +    +  E  +K    
Sbjct: 77  KKEKKEP-KSEGETKLGFKTPKKSKKTKKKPPKPKPNEDVDNAFNKIAELAEKSNVY 132

Length = 413

>gnl|CDD|172341 PRK13808, PRK13808, adenylate kinase; Provisional

 Score = 46.8 bits (111), Expect = 9e-06
 Identities = 38/139 (27%), Positives = 56/139 (40%), Gaps = 2/139 (1%)

Query: 38  KKEKNKKNKNKSRKEEEKKKRTKKKEKNKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEK 97
                K  K  + K   KK   K K   K  ++K  K  K     KK  K   K+ K+ K
Sbjct: 196 AANAKKAAKTPAAKSGAKKASAKAKSAAKKVSKK--KAAKTAVSAKKAAKTAAKAAKKAK 253

Query: 98  KKEAEEEKKKTKNKEKNKNKSRKEEEEKKKEAEEKKKKRTKKKEKNKNKSRKEEEEEEKK 157
           K   +  KK  K  +K   K+ K   +  K A +  K + K K+K   K+    + +   
Sbjct: 254 KTAKKALKKAAKAVKKAAKKAAKAAAKAAKGAAKATKGKAKAKKKAGKKAAAGSKAKATA 313

Query: 158 KKKKKKKKKRTKKKEEEKR 176
           K  K+  K +  KK  +KR
Sbjct: 314 KAPKRGAKGKKAKKVTKKR 332

Length = 333

>gnl|CDD|235175 PRK03918, PRK03918, chromosome segregation protein; Provisional

 Score = 47.8 bits (114), Expect = 9e-06
 Identities = 48/187 (25%), Positives = 96/187 (51%), Gaps = 5/187 (2%)

Query: 2   KNKKEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKK 61
           K K++E ++  +   +   +      + E+ EK  K+ E+ K+   +  KE E  + +K+
Sbjct: 196 KEKEKELEEVLREINEISSELPELREELEKLEKEVKELEELKEEIEELEKELESLEGSKR 255

Query: 62  KEKNKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKE 121
           K + K +  +E  ++ KK   + +EK K     +E K++AEE  K ++  E+  ++ R+ 
Sbjct: 256 KLEEKIRELEERIEELKKEIEELEEKVK---ELKELKEKAEEYIKLSEFYEEYLDELREI 312

Query: 122 EEEKKKEAEEKKKKRTKKKEKNKNKSRKEEEEEEKKKKKKKKK--KKRTKKKEEEKRKNE 179
           E+   +  EE      + KE  + + R EE +++ K+ +K+ +  ++R +  EE K K E
Sbjct: 313 EKRLSRLEEEINGIEERIKELEEKEERLEELKKKLKELEKRLEELEERHELYEEAKAKKE 372

Query: 180 KAVRLTK 186
           +  RL K
Sbjct: 373 ELERLKK 379

Length = 880

>gnl|CDD|235175 PRK03918, PRK03918, chromosome segregation protein; Provisional

 Score = 47.8 bits (114), Expect = 9e-06
 Identities = 38/182 (20%), Positives = 85/182 (46%), Gaps = 1/182 (0%)

Query: 2   KNKKEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKK 61
           K + E  +K  KR    +E  K K ++ EE  +   +         +  ++ EK+ +  +
Sbjct: 175 KRRIERLEKFIKRTENIEELIKEKEKELEEVLREINEISSELPELREELEKLEKEVKELE 234

Query: 62  KEKNKNKNRKEEKKKKKKRRTKKKEKNKN-KSRKEEKKKEAEEEKKKTKNKEKNKNKSRK 120
           + K + +  ++E +  +  + K +EK +  + R EE KKE EE ++K K  ++ K K+ +
Sbjct: 235 ELKEEIEELEKELESLEGSKRKLEEKIRELEERIEELKKEIEELEEKVKELKELKEKAEE 294

Query: 121 EEEEKKKEAEEKKKKRTKKKEKNKNKSRKEEEEEEKKKKKKKKKKKRTKKKEEEKRKNEK 180
             +  +   E   + R  +K  ++ +      EE  K+ ++K+++    KK+ ++ +   
Sbjct: 295 YIKLSEFYEEYLDELREIEKRLSRLEEEINGIEERIKELEEKEERLEELKKKLKELEKRL 354

Query: 181 AV 182
             
Sbjct: 355 EE 356

Length = 880

>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]

 Score = 47.0 bits (112), Expect = 1e-05
 Identities = 35/194 (18%), Positives = 94/194 (48%), Gaps = 12/194 (6%)

Query: 2   KNKKEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNK--------NKSRKEE 53
           ++  EE +++ +   ++ E+ K +    EEE ++ + + +  + +         + ++  
Sbjct: 701 EDLLEELRRQLEELERQLEELKRELAALEEELEQLQSRLEELEEELEELEEELEELQERL 760

Query: 54  EKKKRTKKKEKNKNKNRKEE----KKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTK 109
           E+ +   +  +      KEE    ++K++  + + +E  +     E +    E E +  +
Sbjct: 761 EELEEELESLEEALAKLKEEIEELEEKRQALQEELEELEEELEEAERRLDALERELESLE 820

Query: 110 NKEKNKNKSRKEEEEKKKEAEEKKKKRTKKKEKNKNKSRKEEEEEEKKKKKKKKKKKRTK 169
            + +   +  +E EE+ +E EEK  +  ++ E+ + +  + +EE E+ + +K++ +   K
Sbjct: 821 QRRERLEQEIEELEEEIEELEEKLDELEEELEELEKELEELKEELEELEAEKEELEDELK 880

Query: 170 KKEEEKRKNEKAVR 183
           + EEEK + E+ +R
Sbjct: 881 ELEEEKEELEEELR 894

Length = 1163

>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]

 Score = 47.0 bits (112), Expect = 1e-05
 Identities = 37/193 (19%), Positives = 89/193 (46%), Gaps = 13/193 (6%)

Query: 5   KEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKKKEK 64
           KEE ++ +   +  +E+ +    + EE E+R ++ ++  +   +  +E E      ++  
Sbjct: 294 KEEIEELEGEISLLRERLEELENELEELEERLEELKEKIEALKEELEERETLLEELEQLL 353

Query: 65  NKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKK-------------TKNK 111
            + +  KEE ++K     ++ E+     R+E  + EAE  + +              +  
Sbjct: 354 AELEEAKEELEEKLSALLEELEELFEALREELAELEAELAEIRNELEELKREIESLEERL 413

Query: 112 EKNKNKSRKEEEEKKKEAEEKKKKRTKKKEKNKNKSRKEEEEEEKKKKKKKKKKKRTKKK 171
           E+   +    +EE K+   E ++ +T+ +E N+     EE+ EE + + K+ +++  + +
Sbjct: 414 ERLSERLEDLKEELKELEAELEELQTELEELNEELEELEEQLEELRDRLKELERELAELQ 473

Query: 172 EEEKRKNEKAVRL 184
           EE +R  ++   L
Sbjct: 474 EELQRLEKELSSL 486

Length = 1163

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

 Score = 47.7 bits (113), Expect = 1e-05
 Identities = 44/181 (24%), Positives = 90/181 (49%)

Query: 4   KKEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKKKE 63
             +E+K K+  +  KK + + K  KEE EE   + KE   K + +  +EE+ +K  +K E
Sbjct: 311 VDDEEKLKESEKELKKLEKELKKEKEEIEELEKELKELEIKREAEEEEEEQLEKLQEKLE 370

Query: 64  KNKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKEEE 123
           + + +   ++K + ++  +  K K +    K E++KEA+   + ++ +E    + +KEE 
Sbjct: 371 QLEEELLAKKKLESERLSSAAKLKEEELELKNEEEKEAKLLLELSEQEEDLLKEEKKEEL 430

Query: 124 EKKKEAEEKKKKRTKKKEKNKNKSRKEEEEEEKKKKKKKKKKKRTKKKEEEKRKNEKAVR 183
           +  +E EE  + +  K  + K +  K+  +  K K + KK +   K+ +  K   +  + 
Sbjct: 431 KIVEELEESLETKQGKLTEEKEELEKQALKLLKDKLELKKSEDLLKETKLVKLLEQLELL 490

Query: 184 L 184
           L
Sbjct: 491 L 491

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|235250 PRK04195, PRK04195, replication factor C large subunit; Provisional

 Score = 46.8 bits (112), Expect = 1e-05
 Identities = 23/82 (28%), Positives = 53/82 (64%)

Query: 94  KEEKKKEAEEEKKKTKNKEKNKNKSRKEEEEKKKEAEEKKKKRTKKKEKNKNKSRKEEEE 153
           +EE +     +K   K K+  +   +K EEEKK++ ++    + K++E+ + K +KEEE+
Sbjct: 396 EEEIEFLTGSKKATKKIKKIVEKAEKKREEEKKEKKKKAFAGKKKEEEEEEEKEKKEEEK 455

Query: 154 EEKKKKKKKKKKKRTKKKEEEK 175
           EE++++ +++K++  +KK+++ 
Sbjct: 456 EEEEEEAEEEKEEEEEKKKKQA 477

Length = 482

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

 Score = 46.8 bits (112), Expect = 1e-05
 Identities = 23/74 (31%), Positives = 46/74 (62%)

Query: 74  KKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKEEEEKKKEAEEKK 133
            KK  K+  K  EK + K  +E+K+K+ +    K K +E+ + K +KEEE++++E E ++
Sbjct: 405 SKKATKKIKKIVEKAEKKREEEKKEKKKKAFAGKKKEEEEEEEKEKKEEEKEEEEEEAEE 464

Query: 134 KKRTKKKEKNKNKS 147
           +K  ++++K K  +
Sbjct: 465 EKEEEEEKKKKQAT 478

Length = 482

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

 Score = 46.8 bits (112), Expect = 1e-05
 Identities = 23/75 (30%), Positives = 47/75 (62%)

Query: 8   KKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKKKEKNKN 67
             KK  ++ KK  +   K R+EE++EK+ K     KK + +  ++E+K++  +++E+   
Sbjct: 404 GSKKATKKIKKIVEKAEKKREEEKKEKKKKAFAGKKKEEEEEEEKEKKEEEKEEEEEEAE 463

Query: 68  KNRKEEKKKKKKRRT 82
           + ++EE++KKKK+ T
Sbjct: 464 EEKEEEEEKKKKQAT 478

Length = 482

>gnl|CDD|218177 pfam04615, Utp14, Utp14 protein

 Score = 47.0 bits (112), Expect = 1e-05
 Identities = 33/139 (23%), Positives = 66/139 (47%)

Query: 17  KKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKKKEKNKNKNRKEEKKK 76
           KK    +    +  E+E  +KK +K  KN+ K +KE ++++  + +E+ K +    +  K
Sbjct: 417 KKNVGRRKFGPENGEKEAESKKLKKENKNEFKEKKESDEEEELEDEEEAKVEKVANKLLK 476

Query: 77  KKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKEEEEKKKEAEEKKKKR 136
           + ++  K++E+ +        K  +   K   K   K K+ S+ ++   K      K K+
Sbjct: 477 RSEKAQKEEEEEELDEENPWLKTTSSVGKSAKKQDSKKKSSSKLDKAANKISKAAVKVKK 536

Query: 137 TKKKEKNKNKSRKEEEEEE 155
            KKKEK+ +      +EE+
Sbjct: 537 KKKKEKSIDLDDDLIDEED 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|233757 TIGR02168, SMC_prok_B, chromosome segregation protein SMC, common bacterial type

 Score = 47.0 bits (112), Expect = 1e-05
 Identities = 30/199 (15%), Positives = 88/199 (44%), Gaps = 9/199 (4%)

Query: 2   KNKKEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKK 61
           ++K +E  ++     +K E+ K +    E E +  + + +  +++ +  +E+ +  R+K 
Sbjct: 329 ESKLDELAEELAELEEKLEELKEELESLEAELEELEAELEELESRLEELEEQLETLRSKV 388

Query: 62  KEKNKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSR-- 119
            +        +      +    +    + + R+E  ++E EE  KK +  E  + ++   
Sbjct: 389 AQL-----ELQIASLNNEIERLEARLERLEDRRERLQQEIEELLKKLEEAELKELQAELE 443

Query: 120 --KEEEEKKKEAEEKKKKRTKKKEKNKNKSRKEEEEEEKKKKKKKKKKKRTKKKEEEKRK 177
             +EE E+ +E  E+ ++  ++  +   ++ +  +  E++  + + +    ++ +E    
Sbjct: 444 ELEEELEELQEELERLEEALEELREELEEAEQALDAAERELAQLQARLDSLERLQENLEG 503

Query: 178 NEKAVRLTKLSAFGISGYL 196
             + V+    +  G+SG L
Sbjct: 504 FSEGVKALLKNQSGLSGIL 522

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|240246 PTZ00053, PTZ00053, methionine aminopeptidase 2; Provisional

 Score = 47.0 bits (112), Expect = 1e-05
 Identities = 19/87 (21%), Positives = 47/87 (54%)

Query: 2  KNKKEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKK 61
          +N+ +++K++ K++  KK+  K+K   ++++    +   +N++ +NK   +++KKK+ KK
Sbjct: 7  ENEVKQQKQQNKQKGTKKKNKKSKKDVDDDDAFLAELISENQEAENKQNNKKKKKKKKKK 66

Query: 62 KEKNKNKNRKEEKKKKKKRRTKKKEKN 88
          K+KN  +             +   + N
Sbjct: 67 KKKNLGEAYDLAYDLPVVWSSAAFQDN 93

Length = 470

>gnl|CDD|215698 pfam00078, RVT_1, Reverse transcriptase (RNA-dependent DNA polymerase)

 Score = 45.4 bits (108), Expect = 1e-05
 Identities = 26/124 (20%), Positives = 50/124 (40%), Gaps = 17/124 (13%)

Query: 186 KLSAFGISGYLLQWIRNFLSGWIQIVRVGTSTSEPIHIPSGCIQGGHMSGLLFSLFIN-- 243
            L+AFG+    ++W             +        +   G  QG  +S LLF+LF+N  
Sbjct: 75  PLTAFGLPQRFIRWRTF--------SVLVNGNPGGRYEWRGLPQGSVLSPLLFNLFMNEL 126

Query: 244 --DIAEIFPGFNFWLFADDLKVALRVGGQREVDSMQSMLSRLYHWCSINKMELNIGKCMV 301
              + + FPG  +  +ADD+ +       +  + +Q +L  +  +     ++LN  K  +
Sbjct: 127 LRPLRKRFPGLTYLRYADDILIFS-----KSPEELQEILEEVLEFLKELGLKLNPEKTKI 181

Query: 302 MTYH 305
               
Sbjct: 182 THSD 185

A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. Length = 194

>gnl|CDD|236766 PRK10811, rne, ribonuclease E; Reviewed

 Score = 47.3 bits (113), Expect = 1e-05
 Identities = 21/141 (14%), Positives = 78/141 (55%), Gaps = 4/141 (2%)

Query: 30  EEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKKKEKNKNKNRKEEKKKKKKRRTKKKEKNK 89
            EE K  ++     + K + +++  K ++  ++++N+ ++ ++ + +++ R   ++E  +
Sbjct: 583 GEETKPQEQPAPKAEAKPERQQDRRKPRQNNRRDRNERRDTRDNRTRREGREN-REENRR 641

Query: 90  NKSRKEEKKKEAEEEKKKTKN-KEKNKNKSRKEE--EEKKKEAEEKKKKRTKKKEKNKNK 146
           N+ + +++  E  E ++     K + +++ ++    E +++  +EK++ + + K  N  +
Sbjct: 642 NRRQAQQQTAETRESQQAEVTEKARTQDEQQQAPRRERQRRRNDEKRQAQQEAKALNVEE 701

Query: 147 SRKEEEEEEKKKKKKKKKKKR 167
              +E E+E++ ++ + ++K+
Sbjct: 702 QSVQETEQEERVQQVQPRRKQ 722

Length = 1068

>gnl|CDD|178945 PRK00247, PRK00247, putative inner membrane protein translocase component YidC; Validated

 Score = 46.8 bits (111), Expect = 1e-05
 Identities = 29/141 (20%), Positives = 56/141 (39%), Gaps = 16/141 (11%)

Query: 2   KNKKEEKKKKKKRRTKKKEKNKNKS----------RKEEEEEKRTKKKEKNKKNKNKSRK 51
           + +  EK+K+KK       +N+ +             E  E K+T+  EKN+    K  K
Sbjct: 291 RAQYREKQKEKKAFLWTLRRNRLRMIITPWRAPELHAENAEIKKTRTAEKNEAKARK--K 348

Query: 52  EEEKKKRTKKKEKNKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNK 111
           E  +K+R  ++E N+   ++      + R  +   K K K   +     +  E   ++N+
Sbjct: 349 EIAQKRRAAEREINREARQERAAAMARARARRAAVKAKKKGLID----ASPNEDTPSENE 404

Query: 112 EKNKNKSRKEEEEKKKEAEEK 132
           E   +  + E     +   E 
Sbjct: 405 ESKGSPPQVEATTTAEPNREP 425

Length = 429

>gnl|CDD|115057 pfam06375, BLVR, Bovine leukaemia virus receptor (BLVR)

 Score = 47.0 bits (111), Expect = 1e-05
 Identities = 49/213 (23%), Positives = 88/213 (41%), Gaps = 41/213 (19%)

Query: 2   KNKKEEKKKKKKRRTKKKEKNKNKSRKE------------EEEEKRTKKKEKNKKNKNK- 48
           K+K+E+KK++K++R +++  +      E            EE  +     +++ K+ N  
Sbjct: 96  KDKREKKKREKEKRGRRRHHSLGTESDEDIAPAQMVDIVTEEMPENALPSDEDDKDPNDP 155

Query: 49  --------------SRKEEEKKKRTKKKEKNKNKNRKEEKKKKKKRRTKKKEKNKNKSRK 94
                         S K   +K R  +  K+  K      +KK K+  KK++K K K R 
Sbjct: 156 YRALDIDLDKPLADSEKLPVQKHRNAETSKSPEKGDVPAVEKKSKKPKKKEKKEKEKERD 215

Query: 95  EEKKKEAEEEKK--------------KTKNKEKNKNKSRKEEEEKKKEAEEKKKKRTKKK 140
           ++KKKE E  K                 +  E +   +        +  E K  +  + K
Sbjct: 216 KDKKKEVEGFKSLLLALDDSPASAASVAEADEASLANTVSGTAPDSEPDEPKDAEAEETK 275

Query: 141 EKNKNKSRKEEEEEEKKKKKKKKKKKRTKKKEE 173
           +  K+K +K+ +E+E+KKKKKK    R    + 
Sbjct: 276 KSPKHKKKKQRKEKEEKKKKKKHHHHRCHHSDG 308

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|215641 PLN03237, PLN03237, DNA topoisomerase 2; Provisional

 Score = 47.2 bits (112), Expect = 1e-05
 Identities = 37/185 (20%), Positives = 73/185 (39%), Gaps = 4/185 (2%)

Query: 5    KEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKKKEK 64
            KE+ K ++ R   ++   + +S   ++  ++  KK   KK   K+ + E  ++       
Sbjct: 1170 KEDAKAEEAREKLQRAAARGESGAAKKVSRQAPKKPAPKKTTKKASESETTEETYGSSAM 1229

Query: 65   NKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKEEEE 124
                N  E  K K +   KKK     K ++EE +    +++    N +    +S K EE 
Sbjct: 1230 ETE-NVAEVVKPKGRAGAKKKAPAAAKEKEEEDEILDLKDRLAAYNLDSAPAQSAKMEET 1288

Query: 125  KKKEAEEKKKKRTKKKEKNKNKSRKEEEEEE---KKKKKKKKKKKRTKKKEEEKRKNEKA 181
             K     +   R K        S  ++++++   +    ++ KKK  +K     +K  K 
Sbjct: 1289 VKAVPARRAAARKKPLASVSVISDSDDDDDDFAVEVSLAERLKKKGGRKPAAANKKAAKP 1348

Query: 182  VRLTK 186
                K
Sbjct: 1349 PAAAK 1353

Length = 1465

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

 Score = 47.1 bits (111), Expect = 2e-05
 Identities = 55/195 (28%), Positives = 95/195 (48%), Gaps = 18/195 (9%)

Query: 5    KEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKKKEK 64
            +E +K +  +R +   K ++  + EE  +    KK +  +   + RK EE +K    ++ 
Sbjct: 1143 EEARKAEDAKRVEIARKAEDARKAEEARKAEDAKKAEAARKAEEVRKAEELRKAEDARKA 1202

Query: 65   NKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKEE-- 122
               +  +EE+K ++ R+ +  +K +   + EE KK+AEE KK    +E+N  + RK E  
Sbjct: 1203 EAARKAEEERKAEEARKAEDAKKAEAVKKAEEAKKDAEEAKKA--EEERNNEEIRKFEEA 1260

Query: 123  --------------EEKKKEAEEKKKKRTKKKEKNKNKSRKEEEEEEKKKKKKKKKKKRT 168
                          EE +K  E KK +  KK ++ K    K++ +E KKK ++ KK    
Sbjct: 1261 RMAHFARRQAAIKAEEARKADELKKAEEKKKADEAKKAEEKKKADEAKKKAEEAKKADEA 1320

Query: 169  KKKEEEKRKNEKAVR 183
            KKK EE +K   A +
Sbjct: 1321 KKKAEEAKKKADAAK 1335

Length = 2084

>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]

 Score = 47.0 bits (112), Expect = 2e-05
 Identities = 27/176 (15%), Positives = 87/176 (49%)

Query: 4   KKEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKKKE 63
           +++ +  +++    ++E  + + R +  E +    +++ ++ + +  + EE+ +  ++K 
Sbjct: 785 EEKRQALQEELEELEEELEEAERRLDALERELESLEQRRERLEQEIEELEEEIEELEEKL 844

Query: 64  KNKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKEEE 123
               +  +E +K+ ++ + + +E    K   E++ KE EEEK++ + + +       E +
Sbjct: 845 DELEEELEELEKELEELKEELEELEAEKEELEDELKELEEEKEELEEELRELESELAELK 904

Query: 124 EKKKEAEEKKKKRTKKKEKNKNKSRKEEEEEEKKKKKKKKKKKRTKKKEEEKRKNE 179
           E+ ++  E+ ++   K E+ + +  + EEE E++ +   + +   + +  E+    
Sbjct: 905 EEIEKLRERLEELEAKLERLEVELPELEEELEEEYEDTLETELEREIERLEEEIEA 960

Length = 1163

>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]

 Score = 46.6 bits (111), Expect = 2e-05
 Identities = 33/185 (17%), Positives = 90/185 (48%), Gaps = 10/185 (5%)

Query: 6   EEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRT------ 59
           +E+K++ +R+ ++ E+N  +     EE ++  +K + +  K +  +E + + R       
Sbjct: 171 KERKEEAERKLERTEENLERLEDLLEELEKQLEKLERQAEKAERYQELKAELRELELALL 230

Query: 60  ----KKKEKNKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNK 115
               K+  K   +  +E  + +++    ++E  + +   EE K E EE +++ +  ++  
Sbjct: 231 LAKLKELRKELEELEEELSRLEEELEELQEELEEAEKEIEELKSELEELREELEELQEEL 290

Query: 116 NKSRKEEEEKKKEAEEKKKKRTKKKEKNKNKSRKEEEEEEKKKKKKKKKKKRTKKKEEEK 175
            + ++E EE + E    +++  + + + +    + EE +EK +  K++ ++R    EE +
Sbjct: 291 LELKEEIEELEGEISLLRERLEELENELEELEERLEELKEKIEALKEELEERETLLEELE 350

Query: 176 RKNEK 180
           +   +
Sbjct: 351 QLLAE 355

Length = 1163

>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]

 Score = 46.6 bits (111), Expect = 2e-05
 Identities = 30/186 (16%), Positives = 83/186 (44%), Gaps = 4/186 (2%)

Query: 3   NKKEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKKK 62
            + EE  ++ +   ++ EK   K  ++ E+ +R ++ +   +    +    + K+  K+ 
Sbjct: 182 ERTEENLERLEDLLEELEKQLEKLERQAEKAERYQELKAELRELELALLLAKLKELRKEL 241

Query: 63  EKNKNK-NRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKE 121
           E+ + + +R EE+ ++ +   ++ EK   + + E ++   E E+ + +  E  +     E
Sbjct: 242 EELEEELSRLEEELEELQEELEEAEKEIEELKSELEELREELEELQEELLELKEEIEELE 301

Query: 122 EEEKKKEAEEKKKKRTKKKEKNKNKSRKEEEEEEKKK---KKKKKKKKRTKKKEEEKRKN 178
            E        ++ +   ++ + + +  KE+ E  K++   ++   ++      E E+ K 
Sbjct: 302 GEISLLRERLEELENELEELEERLEELKEKIEALKEELEERETLLEELEQLLAELEEAKE 361

Query: 179 EKAVRL 184
           E   +L
Sbjct: 362 ELEEKL 367

Length = 1163

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

 Score = 46.5 bits (110), Expect = 2e-05
 Identities = 39/187 (20%), Positives = 91/187 (48%)

Query: 1   CKNKKEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTK 60
            + K    +  K+   +++ + K +S   + E  R +++ K K+ + K   ++ K ++ +
Sbjct: 663 SELKASLSELTKELLAEQELQEKAESELAKNEILRRQEEIKKKEQRIKEELKKLKLEKEE 722

Query: 61  KKEKNKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRK 120
                  + + +  ++ K    K KEK + + +   KK+E EEEK +   KEK   +  +
Sbjct: 723 LLADKVQEAQDKINEELKLLEQKIKEKEEEEEKSRLKKEEEEEEKSELSLKEKELAEEEE 782

Query: 121 EEEEKKKEAEEKKKKRTKKKEKNKNKSRKEEEEEEKKKKKKKKKKKRTKKKEEEKRKNEK 180
           + E+ K E E+++K + +++E    +   +EE E  ++++   +++   K+EE +    +
Sbjct: 783 KTEKLKVEEEKEEKLKAQEEELRALEEELKEEAELLEEEQLLIEQEEKIKEEELEELALE 842

Query: 181 AVRLTKL 187
                KL
Sbjct: 843 LKEEQKL 849

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 = 46.5 bits (110), Expect = 2e-05
 Identities = 43/186 (23%), Positives = 103/186 (55%), Gaps = 2/186 (1%)

Query: 2   KNKKEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKK 61
           +  KE++++++K R KK+E+ + KS    +E++  +++EK +K K    +E+E+K + ++
Sbjct: 744 QKIKEKEEEEEKSRLKKEEEEEEKSELSLKEKELAEEEEKTEKLKV--EEEKEEKLKAQE 801

Query: 62  KEKNKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKE 121
           +E    +   +E+ +  +      E+ +    +E ++   E ++++   K   +   R E
Sbjct: 802 EELRALEEELKEEAELLEEEQLLIEQEEKIKEEELEELALELKEEQKLEKLAEEELERLE 861

Query: 122 EEEKKKEAEEKKKKRTKKKEKNKNKSRKEEEEEEKKKKKKKKKKKRTKKKEEEKRKNEKA 181
           EE  K+E  ++   + ++ E+ K K   E +EE++K++KK+ +++  K    E+++NE  
Sbjct: 862 EEITKEELLQELLLKEEELEEQKLKDELESKEEKEKEEKKELEEESQKDNLLEEKENEIE 921

Query: 182 VRLTKL 187
            R+ + 
Sbjct: 922 ERIAEE 927

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|218177 pfam04615, Utp14, Utp14 protein

 Score = 46.6 bits (111), Expect = 2e-05
 Identities = 40/181 (22%), Positives = 77/181 (42%), Gaps = 17/181 (9%)

Query: 6   EEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKKKEKN 65
           E +KK++     ++ + + +  +E +EE+  +  +KN   +    +  EK+  +KK +K 
Sbjct: 383 EARKKEENDAEIEELRRELEGEEESDEEENEEPSKKNVGRRKFGPENGEKEAESKKLKKE 442

Query: 66  KNKNRKEEKKK-------KKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKS 118
                KE+K+         ++    +K  NK   R E+ +KE EEE+   +N       S
Sbjct: 443 NKNEFKEKKESDEEEELEDEEEAKVEKVANKLLKRSEKAQKEEEEEELDEENPWLKTTSS 502

Query: 119 RKEEEEKKKEAEEKKKKRTKKKEKNKNKSRKEEEEEEKKKKKKKKKKKRTKKKEEEKRKN 178
                       +  KK+  KK+ +    +   +  +   K KKKKKK      ++   +
Sbjct: 503 VG----------KSAKKQDSKKKSSSKLDKAANKISKAAVKVKKKKKKEKSIDLDDDLID 552

Query: 179 E 179
           E
Sbjct: 553 E 553

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|115057 pfam06375, BLVR, Bovine leukaemia virus receptor (BLVR)

 Score = 46.6 bits (110), Expect = 2e-05
 Identities = 45/212 (21%), Positives = 90/212 (42%), Gaps = 34/212 (16%)

Query: 2   KNKKEEKKKKKKRRTKKKEKNKNKSRKEEEEEKR----------TKKKEKNKKNKNKSRK 51
           + + E+ K++KK+R K+K   +       E ++           T++  +N    ++  K
Sbjct: 91  RQRLEKDKREKKKREKEKRGRRRHHSLGTESDEDIAPAQMVDIVTEEMPENALPSDEDDK 150

Query: 52  EEEKKKR------------TKKKEKNKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKK 99
           +     R            ++K    K++N +  K  +K      ++K+K   +KE+K+K
Sbjct: 151 DPNDPYRALDIDLDKPLADSEKLPVQKHRNAETSKSPEKGDVPAVEKKSKKPKKKEKKEK 210

Query: 100 EAEEEKKKTKNKEKNKN------------KSRKEEEEKKKEAEEKKKKRTKKKEKNKNKS 147
           E E +K K K  E  K+             S  E +E              + ++ K+  
Sbjct: 211 EKERDKDKKKEVEGFKSLLLALDDSPASAASVAEADEASLANTVSGTAPDSEPDEPKDAE 270

Query: 148 RKEEEEEEKKKKKKKKKKKRTKKKEEEKRKNE 179
            +E ++  K KKKK++K+K  KKK+++   + 
Sbjct: 271 AEETKKSPKHKKKKQRKEKEEKKKKKKHHHHR 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|233758 TIGR02169, SMC_prok_A, chromosome segregation protein SMC, primarily archaeal type

 Score = 46.6 bits (111), Expect = 2e-05
 Identities = 36/195 (18%), Positives = 87/195 (44%), Gaps = 4/195 (2%)

Query: 7   EKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKKKEKNK 66
           E++ +++R+ + K   +    KEE E+ R + +E +K+        +E K   +K EK K
Sbjct: 342 EREIEEERKRRDKLTEEYAELKEELEDLRAELEEVDKEFA---ETRDELKDYREKLEKLK 398

Query: 67  NKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKEEEEKK 126
            +   E K++  + + + +  ++  +         E +  + + ++++K    K++E K 
Sbjct: 399 RE-INELKRELDRLQEELQRLSEELADLNAAIAGIEAKINELEEEKEDKALEIKKQEWKL 457

Query: 127 KEAEEKKKKRTKKKEKNKNKSRKEEEEEEKKKKKKKKKKKRTKKKEEEKRKNEKAVRLTK 186
           ++      K  ++    K +  + E+E  K +++  + + + +  EE  R       + K
Sbjct: 458 EQLAADLSKYEQELYDLKEEYDRVEKELSKLQRELAEAEAQARASEERVRGGRAVEEVLK 517

Query: 187 LSAFGISGYLLQWIR 201
            S  G+ G + Q   
Sbjct: 518 ASIQGVHGTVAQLGS 532

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|214395 CHL00204, ycf1, Ycf1; Provisional

 Score = 46.6 bits (111), Expect = 2e-05
 Identities = 24/89 (26%), Positives = 48/89 (53%)

Query: 64   KNKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKEEE 123
             N+N N+K  +KKK    + +K+  + ++R +E+K+ A + + ++  ++K   +S    +
Sbjct: 1494 GNENVNKKINQKKKGFIPSNEKKSIEIENRNQEEKEPAGQGELESDKEKKGNLESVLSNQ 1553

Query: 124  EKKKEAEEKKKKRTKKKEKNKNKSRKEEE 152
            EK  E +  +    K+K K + KS  E E
Sbjct: 1554 EKNIEEDYAESDIKKRKNKKQYKSNTEAE 1582

Length = 1832

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

 Score = 45.9 bits (108), Expect = 3e-05
 Identities = 46/180 (25%), Positives = 92/180 (51%), Gaps = 2/180 (1%)

Query: 4    KKEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKKKE 63
            K E+ +K ++ R  +  K    +RK E+  K  + ++     K ++ ++ E+ ++ ++  
Sbjct: 1135 KAEDARKAEEARKAEDAKRVEIARKAEDARKAEEARKAEDAKKAEAARKAEEVRKAEELR 1194

Query: 64   KNKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKEEE 123
            K ++  + E  +K ++ R  ++ +    ++K E  K+AEE KK  +  +K + +   EE 
Sbjct: 1195 KAEDARKAEAARKAEEERKAEEARKAEDAKKAEAVKKAEEAKKDAEEAKKAEEERNNEEI 1254

Query: 124  EKKKEAEEKKKKRTKKKEKNKNKSRKEE--EEEEKKKKKKKKKKKRTKKKEEEKRKNEKA 181
             K +EA      R +   K +   + +E  + EEKKK  + KK +  KK +E K+K E+A
Sbjct: 1255 RKFEEARMAHFARRQAAIKAEEARKADELKKAEEKKKADEAKKAEEKKKADEAKKKAEEA 1314

Length = 2084

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

 Score = 45.7 bits (109), Expect = 3e-05
 Identities = 27/77 (35%), Positives = 47/77 (61%), Gaps = 3/77 (3%)

Query: 11  KKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKKKEKNKNKNR 70
             K+ TKK +K   K+ K+ EEEK+ KKK+     K +  +EEEK+K   K+E+ + +  
Sbjct: 404 GSKKATKKIKKIVEKAEKKREEEKKEKKKKAFAGKKKEEEEEEEKEK---KEEEKEEEEE 460

Query: 71  KEEKKKKKKRRTKKKEK 87
           + E++K+++   KKK+ 
Sbjct: 461 EAEEEKEEEEEKKKKQA 477

Length = 482

>gnl|CDD|237258 PRK12903, secA, preprotein translocase subunit SecA; Reviewed

 Score = 45.8 bits (109), Expect = 3e-05
 Identities = 26/152 (17%), Positives = 58/152 (38%), Gaps = 8/152 (5%)

Query: 23  KNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKKKEKNKNKNRKEEKKKKKKRRT 82
            N + ++            N  + N   +E   +    ++E+ K    + E+   +    
Sbjct: 777 NNPNAEKILIITEILSDGINNSDINDRPQELIDQIIESEEERLKALRIQREEMLMRPEEL 836

Query: 83  KKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKEEEEKKKEAEEKKKKRTKKKEK 142
           +   + +   ++E K + +E ++ + + +  N+NK    E  + K   +K  K    K+ 
Sbjct: 837 ELINEEQKNLKQEIKLELSEIQEAEEEIQNINENK---NEFVEFKNDPKKLNKLIIAKDV 893

Query: 143 NKNK-----SRKEEEEEEKKKKKKKKKKKRTK 169
                      K++E+  KKKKK  +K     
Sbjct: 894 LIKLVISSDEIKQDEKTTKKKKKDLEKTDEEA 925

Length = 925

>gnl|CDD|236766 PRK10811, rne, ribonuclease E; Reviewed

 Score = 46.2 bits (110), Expect = 3e-05
 Identities = 27/151 (17%), Positives = 79/151 (52%), Gaps = 12/151 (7%)

Query: 17  KKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKKKEKNKNKNRKEEKKK 76
           + K + +   + E + E++  ++ K ++N  + R  E +  R  +  +   +NR+E ++ 
Sbjct: 585 ETKPQEQPAPKAEAKPERQQDRR-KPRQNNRRDR-NERRDTRDNRTRREGRENREENRRN 642

Query: 77  KKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKEEEEKKKEAEEKKKKR 136
           +++ + +  E  +++  +  +K   ++E+++   +E+     R+  +EK++  +E K   
Sbjct: 643 RRQAQQQTAETRESQQAEVTEKARTQDEQQQAPRRERQ----RRRNDEKRQAQQEAKALN 698

Query: 137 TKKKEKNKNKSRKEEEEEEKKKKKKKKKKKR 167
            +       +S +E E+EE+ ++ + ++K+R
Sbjct: 699 VE------EQSVQETEQEERVQQVQPRRKQR 723

Length = 1068

>gnl|CDD|178945 PRK00247, PRK00247, putative inner membrane protein translocase component YidC; Validated

 Score = 45.6 bits (108), Expect = 3e-05
 Identities = 24/138 (17%), Positives = 54/138 (39%), Gaps = 6/138 (4%)

Query: 27  RKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKKKEKNKNKNRKEEKKKKKKRRTKKKE 86
            +E+++EK+       ++N+ +      +      +     K R  EK + K R  KK+ 
Sbjct: 294 YREKQKEKKAFLWTL-RRNRLRMIITPWRAPELHAENAEIKKTRTAEKNEAKAR--KKEI 350

Query: 87  KNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKEEEEKKKEAEEKKKKRTKKKEKNKNK 146
             K ++ + E  +EA +E+     + + +   R   + KKK   +         E  ++K
Sbjct: 351 AQKRRAAEREINREARQERAAAMARARAR---RAAVKAKKKGLIDASPNEDTPSENEESK 407

Query: 147 SRKEEEEEEKKKKKKKKK 164
               + E     +  ++ 
Sbjct: 408 GSPPQVEATTTAEPNREP 425

Length = 429

>gnl|CDD|178945 PRK00247, PRK00247, putative inner membrane protein translocase component YidC; Validated

 Score = 45.6 bits (108), Expect = 3e-05
 Identities = 33/117 (28%), Positives = 54/117 (46%), Gaps = 8/117 (6%)

Query: 68  KNRKEEKKKKKKRRTKKKEKNKNKS-----RKEEKKKEAEEEKKKTKNKEKNKNKSRKEE 122
           + +  EK+K+KK       +N+ +      R  E   E  E KK T+  EKN+ K+RK+E
Sbjct: 291 RAQYREKQKEKKAFLWTLRRNRLRMIITPWRAPELHAENAEIKK-TRTAEKNEAKARKKE 349

Query: 123 EEKKKEAEEKKKKRTKKKEKNKNKSRKEEEEEEKKKKKKKKKKKRTKKKEEEKRKNE 179
             +K+ A E++  R  ++E+    +R          K KKK        E+   +NE
Sbjct: 350 IAQKRRAAEREINREARQERAAAMARA--RARRAAVKAKKKGLIDASPNEDTPSENE 404

Length = 429

>gnl|CDD|219563 pfam07767, Nop53, Nop53 (60S ribosomal biogenesis)

 Score = 45.9 bits (109), Expect = 3e-05
 Identities = 33/148 (22%), Positives = 73/148 (49%), Gaps = 1/148 (0%)

Query: 2   KNKKEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKK 61
             ++ EK+ K +++ ++ E+ + K  ++   E     +      +      EE+      
Sbjct: 199 LQEEYEKEVKAEKKRQELERVEEKKLEKMAPEASRLDEMSEGLLEESDDDGEEESDDESA 258

Query: 62  KEKNKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKE 121
            E  +++     K  + KR+TK + +NK K RKE +++  EE++ K K  +  + K   +
Sbjct: 259 WEGFESEYEPINKPVRPKRKTKAQ-RNKEKRRKELEREAKEEKQLKKKLAQLARLKEIAK 317

Query: 122 EEEKKKEAEEKKKKRTKKKEKNKNKSRK 149
           E  +K++A  +KK++ K++ + K   R+
Sbjct: 318 EVAQKEKARARKKEQRKERGEKKKLKRR 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|217884 pfam04086, SRP-alpha_N, Signal recognition particle, alpha subunit, N-terminal

 Score = 45.1 bits (107), Expect = 3e-05
 Identities = 31/132 (23%), Positives = 62/132 (46%)

Query: 51  KEEEKKKRTKKKEKNKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKN 110
           +E EK+ + + K     +  +E KK KK   +  + K K    K +++K+A+E     ++
Sbjct: 95  RELEKESKKQAKSPKAMRTFEESKKSKKTVDSMIERKPKEPGLKRKQRKKAQESATSPES 154

Query: 111 KEKNKNKSRKEEEEKKKEAEEKKKKRTKKKEKNKNKSRKEEEEEEKKKKKKKKKKKRTKK 170
              +   S +       +A+E   +R KK  K  + +   +E+  K K   KK  K+ +K
Sbjct: 155 SPSSTPNSSRPSTPHLLKAKEGPSRRAKKAAKLSSTASSGDEKSPKSKAAPKKAGKKMRK 214

Query: 171 KEEEKRKNEKAV 182
            + +  +++ AV
Sbjct: 215 WDLDGDEDDDAV 226

SRP is a complex of six distinct polypeptides and a 7S RNA that is essential for transferring nascent polypeptide chains that are destined for export from the cell to the translocation apparatus of the endoplasmic reticulum (ER) membrane. SRP binds hydrophobic signal sequences as they emerge from the ribosome, and arrests translation. Length = 272

>gnl|CDD|218752 pfam05793, TFIIF_alpha, Transcription initiation factor IIF, alpha subunit (TFIIF-alpha)

 Score = 45.7 bits (108), Expect = 3e-05
 Identities = 36/175 (20%), Positives = 68/175 (38%), Gaps = 15/175 (8%)

Query: 13  KRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSR------------KEEEKKKRTK 60
            +  K          +E E EK    + K+ K K+                E+  ++++K
Sbjct: 183 MKAAKNGPAAFGDEDEETEGEKGGGGRGKDLKIKDLEGDDEDDGDESDKGGEDGDEEKSK 242

Query: 61  KKEKNKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRK 120
           KK+K   KN+K+    KK +R    + ++  S   +   +   E+    +   + N   +
Sbjct: 243 KKKKKLAKNKKKLDDDKKGKRGGDDDADEYDS---DDGDDEGREEDYISDSSASGNDPEE 299

Query: 121 EEEEKKKEAEEKKKKRTKKKEKNKNKSRKEEEEEEKKKKKKKKKKKRTKKKEEEK 175
            E++   E   K +    +  +   + + EEE    KK KK KK K  K   ++ 
Sbjct: 300 REDKLSPEIPAKPEIEQDEDSEESEEEKNEEEGGLSKKGKKLKKLKGKKNGLDKD 354

Transcription initiation factor IIF, alpha subunit (TFIIF-alpha) or RNA polymerase II-associating protein 74 (RAP74) is the large subunit of transcription factor IIF (TFIIF), which is essential for accurate initiation and stimulates elongation by RNA polymerase II. Length = 528

>gnl|CDD|218737 pfam05764, YL1, YL1 nuclear protein

 Score = 44.7 bits (106), Expect = 3e-05
 Identities = 46/156 (29%), Positives = 76/156 (48%), Gaps = 12/156 (7%)

Query: 29  EEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKKKEKNKNKNRKEEKKKKKKRRTKKKEKN 88
            E+E +R ++ +K K+ K K+ KE  KKK+ K     K+      + KKK  R       
Sbjct: 74  GEKELQREERLKKKKRVKTKAYKEPTKKKKKKDPTAAKSPKAAAPRPKKKSERISWAPTL 133

Query: 89  KNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKEEEEKKKEAEEKKKKRT----------K 138
            +  R++  +    + K+ T  + K +   RK+ + K ++ +EKKK++           K
Sbjct: 134 LDSPRRKSSRSSTVQNKEATHERLKEREIRRKKIQAKARKRKEKKKEKELTQEERLAEAK 193

Query: 139 KKEKNKNKS--RKEEEEEEKKKKKKKKKKKRTKKKE 172
           + E+   KS  R EE+EEEKKK K +  KKR   + 
Sbjct: 194 ETERINLKSLERYEEQEEEKKKAKIQALKKRRLYEG 229

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|226894 COG4499, COG4499, Predicted membrane protein [Function unknown]

 Score = 45.6 bits (108), Expect = 3e-05
 Identities = 24/90 (26%), Positives = 46/90 (51%), Gaps = 6/90 (6%)

Query: 77  KKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKEEEEKKKEAEEKKKKR 136
           K     K         R+E  K+  ++ +  TK   + K+++   EE + K  EEK K+ 
Sbjct: 351 KLYEEVKSNTDLSGDKRQELLKEYNKKLQDYTKKLGEVKDETDASEEAEAKAKEEKLKQE 410

Query: 137 TKKKEKNKNKSRKEEEEEEKKKKKKKKKKK 166
             +K++      KE+ +E+K+K++K ++KK
Sbjct: 411 ENEKKQ------KEQADEDKEKRQKDERKK 434

Length = 434

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

 Score = 43.9 bits (104), Expect = 3e-05
 Identities = 30/113 (26%), Positives = 65/113 (57%), Gaps = 1/113 (0%)

Query: 51  KEEEKKKRTKKKEKNK-NKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTK 109
            E +KKK+   +E  K  K  +E++K K K++  KK+K+K+K +K++KK +  E+K + +
Sbjct: 58  TEAKKKKKELAEEIEKVKKEYEEKQKWKWKKKKSKKKKDKDKDKKDDKKDDKSEKKDEKE 117

Query: 110 NKEKNKNKSRKEEEEKKKEAEEKKKKRTKKKEKNKNKSRKEEEEEEKKKKKKK 162
            ++K ++ ++   E     +E K +K    K+  +++  ++   E  KK+ ++
Sbjct: 118 AEDKLEDLTKSYSETLSTLSELKPRKYALHKDIYQSRLDRKRRAEVAKKEAEE 170

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

>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]

 Score = 45.5 bits (108), Expect = 4e-05
 Identities = 36/181 (19%), Positives = 86/181 (47%), Gaps = 6/181 (3%)

Query: 7   EKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKKKEKNK 66
           +++ ++     +  +      KEE EE   K++   ++ +    + EE ++R    E+  
Sbjct: 757 QERLEELEEELESLEEALAKLKEEIEELEEKRQALQEELEELEEELEEAERRLDALEREL 816

Query: 67  NKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKEEEEKK 126
               +  ++ +++    ++E  + + + +E ++E EE +K+    E+ K +  + E EK+
Sbjct: 817 ESLEQRRERLEQEIEELEEEIEELEEKLDELEEELEELEKE---LEELKEELEELEAEKE 873

Query: 127 KEAEEKKKKRTKKKEKNKNKSRKEEEEEEKKKKKKKKKKKRTKKKEEEKRKNEKAVRLTK 186
           +  +E K+   +K+E  +      E E E  + K++ +K R + +E E +     V L +
Sbjct: 874 ELEDELKELEEEKEELEE---ELRELESELAELKEEIEKLRERLEELEAKLERLEVELPE 930

Query: 187 L 187
           L
Sbjct: 931 L 931

Length = 1163

>gnl|CDD|172341 PRK13808, PRK13808, adenylate kinase; Provisional

 Score = 44.9 bits (106), Expect = 4e-05
 Identities = 35/139 (25%), Positives = 57/139 (41%), Gaps = 4/139 (2%)

Query: 24  NKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKKKEKNKNKNRKEEKKKKKKRRTK 83
           N  +  +    ++  K+ + K K+ ++K  +KK         K      +  KK K+  K
Sbjct: 198 NAKKAAKTPAAKSGAKKASAKAKSAAKKVSKKKAAKTAVSAKKAAKTAAKAAKKAKKTAK 257

Query: 84  KKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKEEEEKKKEAEEKKKKRTKKKEKN 143
           K  K   K+ K+  KK A+   K  K   K      K     KK+A +K    +K K   
Sbjct: 258 KALKKAAKAVKKAAKKAAKAAAKAAKGAAKATKGKAK----AKKKAGKKAAAGSKAKATA 313

Query: 144 KNKSRKEEEEEEKKKKKKK 162
           K   R  + ++ KK  KK+
Sbjct: 314 KAPKRGAKGKKAKKVTKKR 332

Length = 333

>gnl|CDD|234767 PRK00448, polC, DNA polymerase III PolC; Validated

 Score = 45.6 bits (109), Expect = 4e-05
 Identities = 38/174 (21%), Positives = 69/174 (39%), Gaps = 1/174 (0%)

Query: 5   KEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKK-KEKNKKNKNKSRKEEEKKKRTKKKE 63
           K+        +     + +N +  EE       +  EK KKN    +   +K+K   +  
Sbjct: 65  KQSFSHIADIKVTFSIEVENITFTEELLLDYWNEIIEKAKKNSPLFKSLLKKQKVEVEGN 124

Query: 64  KNKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKEEE 123
           K   K   E ++   K++   K   + +       K   E     +  EK + +  +E+E
Sbjct: 125 KLIIKVNNEIERDHLKKKHLPKLIKQYEKFGFGILKIDFEIDDSKEELEKFEAQKEEEDE 184

Query: 124 EKKKEAEEKKKKRTKKKEKNKNKSRKEEEEEEKKKKKKKKKKKRTKKKEEEKRK 177
           +  KEA E  KK   +K+K       +E   +  KK  K++    K+  EE+R+
Sbjct: 185 KLAKEALEAMKKLEAEKKKQSKNFDPKEGPVQIGKKIDKEEITPMKEINEEERR 238

Length = 1437

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

 Score = 45.7 bits (108), Expect = 4e-05
 Identities = 32/125 (25%), Positives = 63/125 (50%), Gaps = 4/125 (3%)

Query: 14  RRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEE--EKKKRTKKKEKNKNKNRK 71
           R  ++   N N   +E+++EK+ +K     K K   +KEE       +  KE++  +N K
Sbjct: 4   RNRREANINNNDRMQEKDDEKQDQKNRMELKEKVLDKKEEVVTDNVDSPVKEQSSQENLK 63

Query: 72  EEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEE--KKKTKNKEKNKNKSRKEEEEKKKEA 129
              + KK  + + K+  +    KEE +KE + E  +K   + E  ++  +K E+ K ++A
Sbjct: 64  IADEVKKSTKEESKQLLEVLKTKEEHQKEIQYEILQKTIPSFEPKESILKKLEDIKPEQA 123

Query: 130 EEKKK 134
           +++ K
Sbjct: 124 KKQTK 128

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 = 45.3 bits (107), Expect = 5e-05
 Identities = 38/180 (21%), Positives = 91/180 (50%)

Query: 1   CKNKKEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTK 60
            + +K   KK+++   K +   K K   EEEE+    K E+ K+ K K+++EE +    +
Sbjct: 751 EEEEKSRLKKEEEEEEKSELSLKEKELAEEEEKTEKLKVEEEKEEKLKAQEEELRALEEE 810

Query: 61  KKEKNKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRK 120
            KE+ +    ++   +++++  +++ +      KEE+K E   E++  + +E+   +   
Sbjct: 811 LKEEAELLEEEQLLIEQEEKIKEEELEELALELKEEQKLEKLAEEELERLEEEITKEELL 870

Query: 121 EEEEKKKEAEEKKKKRTKKKEKNKNKSRKEEEEEEKKKKKKKKKKKRTKKKEEEKRKNEK 180
           +E   K+E  E++K + + + K + +  +++E EE+ +K    ++K  + +E    +   
Sbjct: 871 QELLLKEEELEEQKLKDELESKEEKEKEEKKELEEESQKDNLLEEKENEIEERIAEEAII 930

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 = 5e-05
 Identities = 39/186 (20%), Positives = 95/186 (51%)

Query: 2   KNKKEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKK 61
             +K E +  K    +++E+ K K ++ +EE K+ K +++          +++  +  K 
Sbjct: 682 LQEKAESELAKNEILRRQEEIKKKEQRIKEELKKLKLEKEELLADKVQEAQDKINEELKL 741

Query: 62  KEKNKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKE 121
            E+   +  +EE+K + K+  +++EK++   +++E  +E E+ +K    +EK +    +E
Sbjct: 742 LEQKIKEKEEEEEKSRLKKEEEEEEKSELSLKEKELAEEEEKTEKLKVEEEKEEKLKAQE 801

Query: 122 EEEKKKEAEEKKKKRTKKKEKNKNKSRKEEEEEEKKKKKKKKKKKRTKKKEEEKRKNEKA 181
           EE +  E E K++    ++E+   +  ++ +EEE ++   + K+++  +K  E+      
Sbjct: 802 EELRALEEELKEEAELLEEEQLLIEQEEKIKEEELEELALELKEEQKLEKLAEEELERLE 861

Query: 182 VRLTKL 187
             +TK 
Sbjct: 862 EEITKE 867

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|235250 PRK04195, PRK04195, replication factor C large subunit; Provisional

 Score = 44.9 bits (107), Expect = 5e-05
 Identities = 21/62 (33%), Positives = 43/62 (69%)

Query: 2   KNKKEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKK 61
           K  ++ +KK+++ + +KK+K     +KEEEEE+  +KKE+ K+ + +  +EE++++  KK
Sbjct: 414 KIVEKAEKKREEEKKEKKKKAFAGKKKEEEEEEEKEKKEEEKEEEEEEAEEEKEEEEEKK 473

Query: 62  KE 63
           K+
Sbjct: 474 KK 475

Length = 482

>gnl|CDD|220271 pfam09507, CDC27, DNA polymerase subunit Cdc27

 Score = 44.8 bits (106), Expect = 5e-05
 Identities = 41/201 (20%), Positives = 87/201 (43%), Gaps = 22/201 (10%)

Query: 6   EEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKKKEKN 65
            +KK K+K+  K+  ++  K   EEE  KR    E          ++E++ +     E++
Sbjct: 222 FKKKTKEKKEKKEASESTVKEESEEESGKRDVILEDESAEPTGLDEDEDEDEPKPSGERS 281

Query: 66  KNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKEEEEK 125
            ++   EEK+K+K++R KK  +++++  + E   E+  E+++++ + +     +KEEE++
Sbjct: 282 DSEEETEEKEKEKRKRLKKMMEDEDEDEEMEIVPESPVEEEESE-EPEPPPLPKKEEEKE 340

Query: 126 KKEAEEKKKKRTKKKEKNKNKSRKEEE---------------------EEEKKKKKKKKK 164
           +        +R  ++   K K+ K+EE                        K K K    
Sbjct: 341 EVTVSPDGGRRRGRRRVMKKKTFKDEEGYLVTKKVYEWESFSEDEAEPPPTKPKPKVSTP 400

Query: 165 KKRTKKKEEEKRKNEKAVRLT 185
                 K+ +  K +K   + 
Sbjct: 401 AVPAAAKKPKAPKKKKQSSIM 421

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|215521 PLN02967, PLN02967, kinase

 Score = 45.0 bits (106), Expect = 5e-05
 Identities = 28/132 (21%), Positives = 55/132 (41%), Gaps = 13/132 (9%)

Query: 5   KEEKKKKKKRRTKKKEKNKNKSRKEEEE-----EKRTKKKEKNKKNKNKSRKEEEKKKRT 59
              K + ++ R + K      SRK+ E      E+  +    +KK   +S K   KK   
Sbjct: 27  GFNKFRGERWRLQNKFLLAAGSRKKIESALAVDEEPDENGAVSKKKPTRSVKRATKKTVV 86

Query: 60  KKKEKNKNKNR--------KEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNK 111
           +  E  +  +          +++ KK  RRT++K    +   +EEK ++   +++K K  
Sbjct: 87  EISEPLEEGSELVVNEDAALDKESKKTPRRTRRKAAAASSDVEEEKTEKKVRKRRKVKKM 146

Query: 112 EKNKNKSRKEEE 123
           +++      E E
Sbjct: 147 DEDVEDQGSESE 158

Length = 581

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

 Score = 43.1 bits (102), Expect = 5e-05
 Identities = 23/83 (27%), Positives = 47/83 (56%)

Query: 84  KKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKEEEEKKKEAEEKKKKRTKKKEKN 143
           KK+K +     E+ KKE EE++K    K+K+K K  K++++K  + ++K +K+ +K+ ++
Sbjct: 61  KKKKKELAEEIEKVKKEYEEKQKWKWKKKKSKKKKDKDKDKKDDKKDDKSEKKDEKEAED 120

Query: 144 KNKSRKEEEEEEKKKKKKKKKKK 166
           K +   +   E      + K +K
Sbjct: 121 KLEDLTKSYSETLSTLSELKPRK 143

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

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

 Score = 44.6 bits (105), Expect = 6e-05
 Identities = 31/144 (21%), Positives = 63/144 (43%), Gaps = 4/144 (2%)

Query: 5   KEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKKKEK 64
           KEE  KK+    K ++K        +++    ++K++  KN  K       K+  +  E 
Sbjct: 219 KEELDKKQIDADKAQQKADFAQDNADKQRDEVRQKQQEAKNLPKPADTSSPKEDKQVAEN 278

Query: 65  NKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKE-EE 123
            K +  K + + KK      K K+    +  + K+E++  +K+ ++KE    K R+   E
Sbjct: 279 QKREIEKAQIEIKKNDEEALKAKD---HKAFDLKQESKASEKEAEDKELEAQKKREPVAE 335

Query: 124 EKKKEAEEKKKKRTKKKEKNKNKS 147
           + +K   + + + T   E   + S
Sbjct: 336 DLQKTKPQVEAQPTSLNEDAIDSS 359

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

>gnl|CDD|233757 TIGR02168, SMC_prok_B, chromosome segregation protein SMC, common bacterial type

 Score = 45.0 bits (107), Expect = 6e-05
 Identities = 29/183 (15%), Positives = 85/183 (46%), Gaps = 4/183 (2%)

Query: 3   NKKEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKKK 62
             +  + +++K+  +++  N  +  +E E +    + + ++  +  +  EE+ +    K+
Sbjct: 294 ANEISRLEQQKQILRERLANLERQLEELEAQLEELESKLDELAEELAELEEKLE--ELKE 351

Query: 63  EKNKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKE- 121
           E    +   EE + + +    + E+ + +      K    E +  + N E  + ++R E 
Sbjct: 352 ELESLEAELEELEAELEELESRLEELEEQLETLRSKVAQLELQIASLNNEIERLEARLER 411

Query: 122 -EEEKKKEAEEKKKKRTKKKEKNKNKSRKEEEEEEKKKKKKKKKKKRTKKKEEEKRKNEK 180
            E+ +++  +E ++   K +E    + + E EE E++ ++ +++ +R ++  EE R+  +
Sbjct: 412 LEDRRERLQQEIEELLKKLEEAELKELQAELEELEEELEELQEELERLEEALEELREELE 471

Query: 181 AVR 183
              
Sbjct: 472 EAE 474

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|236766 PRK10811, rne, ribonuclease E; Reviewed

 Score = 45.0 bits (107), Expect = 6e-05
 Identities = 22/137 (16%), Positives = 68/137 (49%), Gaps = 8/137 (5%)

Query: 4   KKEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKKKE 63
           +   K + K  R + + K +  +R++  E + T+     ++   ++R+E  + +R  +++
Sbjct: 591 QPAPKAEAKPERQQDRRKPRQNNRRDRNERRDTRDNRTRREG-RENREENRRNRRQAQQQ 649

Query: 64  KNKNKNRK--EEKKKKKKRRTKKKE--KNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSR 119
             + +  +  E  +K + +  +++   + + + R +EK++  +E K         ++   
Sbjct: 650 TAETRESQQAEVTEKARTQDEQQQAPRRERQRRRNDEKRQAQQEAKALNVE---EQSVQE 706

Query: 120 KEEEEKKKEAEEKKKKR 136
            E+EE+ ++ + ++K+R
Sbjct: 707 TEQEERVQQVQPRRKQR 723

Length = 1068

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

 Score = 43.1 bits (102), Expect = 6e-05
 Identities = 26/76 (34%), Positives = 40/76 (52%)

Query: 100 EAEEEKKKTKNKEKNKNKSRKEEEEKKKEAEEKKKKRTKKKEKNKNKSRKEEEEEEKKKK 159
           E  E KKK K   +   K +KE EEK+K   +KKK + KK +    K  K++++ EKK +
Sbjct: 56  EYTEAKKKKKELAEEIEKVKKEYEEKQKWKWKKKKSKKKKDKDKDKKDDKKDDKSEKKDE 115

Query: 160 KKKKKKKRTKKKEEEK 175
           K+ + K     K   +
Sbjct: 116 KEAEDKLEDLTKSYSE 131

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

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

 Score = 44.5 bits (106), Expect = 7e-05
 Identities = 23/67 (34%), Positives = 42/67 (62%)

Query: 2   KNKKEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKK 61
           K KK  +K +KKR  +KKEK K     +++EE+  ++KEK ++ K +  +E E++K  ++
Sbjct: 411 KIKKIVEKAEKKREEEKKEKKKKAFAGKKKEEEEEEEKEKKEEEKEEEEEEAEEEKEEEE 470

Query: 62  KEKNKNK 68
           ++K K  
Sbjct: 471 EKKKKQA 477

Length = 482

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

 Score = 44.8 bits (107), Expect = 7e-05
 Identities = 38/181 (20%), Positives = 79/181 (43%), Gaps = 20/181 (11%)

Query: 15  RTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKKKEKNKNKNRKEEK 74
             + ++K +      +E EK  K++ + KK K +  +++  ++  K+ ++   + +KE  
Sbjct: 529 ERELEQKAEEAEALLKEAEK-LKEELEEKKEKLQEEEDKLLEEAEKEAQQAIKEAKKEAD 587

Query: 75  KKKKKRRTKKKEKNKNKSRKE--EKKKEAEEEKKKTKNKEKNKNKSRKEEEEKKKEAEEK 132
           +  K+ R  +K    +    E  E +K   +  +K + K+K +    KE++E+ K  +E 
Sbjct: 588 EIIKELRQLQKGGYASVKAHELIEARKRLNKANEKKEKKKKKQ----KEKQEELKVGDEV 643

Query: 133 KKKRTKKK----EKNKNK---------SRKEEEEEEKKKKKKKKKKKRTKKKEEEKRKNE 179
           K     +K        +K           K    + +K +K KKKKK+  K  + K +  
Sbjct: 644 KYLSLGQKGEVLSIPDDKEAIVQAGIMKMKVPLSDLEKIQKPKKKKKKKPKTVKPKPRTV 703

Query: 180 K 180
            
Sbjct: 704 S 704

Length = 782

>gnl|CDD|177089 CHL00189, infB, translation initiation factor 2; Provisional

 Score = 44.8 bits (106), Expect = 7e-05
 Identities = 31/127 (24%), Positives = 52/127 (40%)

Query: 37  KKKEKNKKNKNKSRKEEEKKKRTKKKEKNKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEE 96
           K + ++    +    +  KK   K  +KNK  N+ ++ K  KK + K+K+K K K   ++
Sbjct: 32  KIRLESDIKDSLLNLDINKKLHEKLDKKNKKFNKTDDLKDSKKTKLKQKKKIKKKLHIDD 91

Query: 97  KKKEAEEEKKKTKNKEKNKNKSRKEEEEKKKEAEEKKKKRTKKKEKNKNKSRKEEEEEEK 156
                 + K  +K        S   + + K E  +KK    K   K K K    ++E  K
Sbjct: 92  DYDNFFDSKNNSKQFAGPLAISLMRKPKPKTEKLKKKITVNKSTNKKKKKVLSSKDELIK 151

Query: 157 KKKKKKK 163
               K K
Sbjct: 152 YDNNKPK 158

Length = 742

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

 Score = 44.6 bits (105), Expect = 8e-05
 Identities = 42/183 (22%), Positives = 90/183 (49%), Gaps = 7/183 (3%)

Query: 2   KNKKEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKK 61
             K+EE+ K +  + ++++ +  +  KE E+E +  +KE  K+ +     E+E K+   K
Sbjct: 292 LAKEEEELKSELLKLERRKVDDEEKLKESEKELKKLEKELKKEKEEIEELEKELKELEIK 351

Query: 62  KEKNKNKN-------RKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKN 114
           +E  + +         K E+ +++    KK E  +  S  + K++E E + ++ K  +  
Sbjct: 352 REAEEEEEEQLEKLQEKLEQLEEELLAKKKLESERLSSAAKLKEEELELKNEEEKEAKLL 411

Query: 115 KNKSRKEEEEKKKEAEEKKKKRTKKKEKNKNKSRKEEEEEEKKKKKKKKKKKRTKKKEEE 174
              S +EE+  K+E +E+ K   + +E  + K  K  EE+E+ +K+  K  K   + ++ 
Sbjct: 412 LELSEQEEDLLKEEKKEELKIVEELEESLETKQGKLTEEKEELEKQALKLLKDKLELKKS 471

Query: 175 KRK 177
           +  
Sbjct: 472 EDL 474

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 = 44.3 bits (105), Expect = 8e-05
 Identities = 28/125 (22%), Positives = 50/125 (40%), Gaps = 4/125 (3%)

Query: 3   NKKEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKKK 62
           +      +K K +      +      +E     ++++ K      K  K+E+K   +KKK
Sbjct: 10  SFFSGTTQKSKLQPISYIYSNVLVLSKEILSTFSEEENKVATTSTKKDKKEDKNNESKKK 69

Query: 63  EKNKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKEE 122
            + K K +KE+K+ K     + + K   K+ K+ KK + +  K K      N      E 
Sbjct: 70  SEKKKKKKKEKKEPKS----EGETKLGFKTPKKSKKTKKKPPKPKPNEDVDNAFNKIAEL 125

Query: 123 EEKKK 127
            EK  
Sbjct: 126 AEKSN 130

Length = 413

>gnl|CDD|222447 pfam13904, DUF4207, Domain of unknown function (DUF4207)

 Score = 43.6 bits (103), Expect = 8e-05
 Identities = 33/131 (25%), Positives = 76/131 (58%), Gaps = 2/131 (1%)

Query: 5   KEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKKKEK 64
            + +KK +K   +K+++ + K R+E E  +R  K++  +  + K+++  +++    KKE 
Sbjct: 98  AQRQKKLQKLLEEKQKQEREKEREEAELRQRLAKEKYEEWCRQKAQQAAKQRTPKHKKEA 157

Query: 65  NKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKEEEE 124
            ++ +       K +R   + E+ K + ++ E KK  ++++K+ + + K + K ++EEEE
Sbjct: 158 AESASSSLSGSAKPERNVSQ-EEAKKRLQEWELKKLKQQQQKREEERRKQRKK-QQEEEE 215

Query: 125 KKKEAEEKKKK 135
           +K++AEE  +K
Sbjct: 216 RKQKAEEAWQK 226

This family is found in eukaryotes; it has several conserved tryptophan residues. The function is not known. Length = 261

>gnl|CDD|177089 CHL00189, infB, translation initiation factor 2; Provisional

 Score = 44.4 bits (105), Expect = 8e-05
 Identities = 37/156 (23%), Positives = 61/156 (39%), Gaps = 10/156 (6%)

Query: 32  EEKRTKKKEKNKKNKNKSRKEEEKKKRTKKKEKNKNKNRKEEKKKKKKRRTKKKEKNKNK 91
           E   +   E     KN    +  K    K + ++  K+        KK   K  +KNK  
Sbjct: 4   ENNISISSENTIDLKNPLFIKNLKHSSYKIRLESDIKDSLLNLDINKKLHEKLDKKNKKF 63

Query: 92  SRKEEKKKEAEEEKKKTKNKEKNKNKSRKEEEEKKKEAEEKKKKRTKK------KEKNKN 145
           ++ ++ K   + +K K K K+K K K   +++       +   K+           K K 
Sbjct: 64  NKTDDLK---DSKKTKLKQKKKIKKKLHIDDDYDNFFDSKNNSKQFAGPLAISLMRKPKP 120

Query: 146 KSRKEEEEE-EKKKKKKKKKKKRTKKKEEEKRKNEK 180
           K+ K +++    K   KKKKK  + K E  K  N K
Sbjct: 121 KTEKLKKKITVNKSTNKKKKKVLSSKDELIKYDNNK 156

Length = 742

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

 Score = 44.7 bits (106), Expect = 9e-05
 Identities = 34/186 (18%), Positives = 77/186 (41%), Gaps = 19/186 (10%)

Query: 23   KNKSRKEEEEE------KRTKKKEKNKKNKNKSRKEEEKKKRTKKKEKNKNKNRKEEKK- 75
             N  +K+  +E       R K   K K  K  + +EE  ++  +  +++  +        
Sbjct: 1029 TNAKKKDLVKELKKLGYVRFKDIIKKKSEKITAEEEEGAEEDDEADDEDDEEELGAAVSY 1088

Query: 76   ------------KKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKEEE 123
                        K+K  +   + + K K  ++ K    ++   +  +K +   + ++E E
Sbjct: 1089 DYLLSMPIWSLTKEKVEKLNAELEKKEKELEKLKNTTPKDMWLEDLDKFEEALEEQEEVE 1148

Query: 124  EKKKEAEEKKKKRTKKKEKNKNKSRKEEEEEEKKKKKKKKKKKRTKKKEEEKRKNEKAVR 183
            EK+   E++ K +TK K     K + +++E++KKK    K KK +     ++  +++  +
Sbjct: 1149 EKEIAKEQRLKSKTKGKASKLRKPKLKKKEKKKKKSSADKSKKASVVGNSKRVDSDEKRK 1208

Query: 184  LTKLSA 189
            L     
Sbjct: 1209 LDDKPD 1214

Length = 1388

>gnl|CDD|223496 COG0419, SbcC, ATPase involved in DNA repair [DNA replication, recombination, and repair]

 Score = 44.4 bits (105), Expect = 9e-05
 Identities = 27/177 (15%), Positives = 79/177 (44%), Gaps = 3/177 (1%)

Query: 2   KNKKEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKK 61
           + +KE  ++ K R  + +       +  EEE +  ++  +  + K +  +E E++     
Sbjct: 245 EEEKERLEELKARLLEIESLELEALKIREEELRELERLLEELEEKIERLEELEREIE--- 301

Query: 62  KEKNKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKE 121
           + + + +  +   ++ ++   K K   +   + EEK ++ E E ++   ++    K  +E
Sbjct: 302 ELEEELEGLRALLEELEELLEKLKSLEERLEKLEEKLEKLESELEELAEEKNELAKLLEE 361

Query: 122 EEEKKKEAEEKKKKRTKKKEKNKNKSRKEEEEEEKKKKKKKKKKKRTKKKEEEKRKN 178
             ++ +E  E+ +K  +K  +   +  +  +E +++  +     +  +++ EE  K 
Sbjct: 362 RLKELEERLEELEKELEKALERLKQLEEAIQELKEELAELSAALEEIQEELEELEKE 418

Length = 908

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

 Score = 44.5 bits (105), Expect = 9e-05
 Identities = 31/125 (24%), Positives = 63/125 (50%), Gaps = 2/125 (1%)

Query: 41  KNKKNKNKSRKEEEKKKRTKKKEKNKNKNRKEE-KKKKKKRRTKKKEKNKNKSRKEEKKK 99
           +N++  N +  +  ++K  +K+++      KE+   KK++  T   +    +   +E  K
Sbjct: 4   RNRREANINNNDRMQEKDDEKQDQKNRMELKEKVLDKKEEVVTDNVDSPVKEQSSQENLK 63

Query: 100 EAEEEKKKTKNKEKNKNKSRKEEEEKKKEAE-EKKKKRTKKKEKNKNKSRKEEEEEEKKK 158
            A+E KK TK + K   +  K +EE +KE + E  +K     E  ++  +K E+ + ++ 
Sbjct: 64  IADEVKKSTKEESKQLLEVLKTKEEHQKEIQYEILQKTIPSFEPKESILKKLEDIKPEQA 123

Query: 159 KKKKK 163
           KK+ K
Sbjct: 124 KKQTK 128

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|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 44.4 bits (104), Expect = 1e-04
 Identities = 44/164 (26%), Positives = 81/164 (49%), Gaps = 6/164 (3%)

Query: 23   KNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKKKEKNKNK----NRKEEKKKKK 78
            K  +R +E  E+   K E+ KK +    +E  K +  KKK ++  K     + E+ +K +
Sbjct: 1084 KEDNRADEATEEAFGKAEEAKKTETGKAEEARKAEEAKKKAEDARKAEEARKAEDARKAE 1143

Query: 79   KRRTKKKEKNKNKSRKEEKKKEAEEEKK--KTKNKEKNKNKSRKEEEEKKKEAEEKKKKR 136
            + R  +  K    +RK E  ++AEE +K    K  E  +      + E+ ++AE+ +K  
Sbjct: 1144 EARKAEDAKRVEIARKAEDARKAEEARKAEDAKKAEAARKAEEVRKAEELRKAEDARKAE 1203

Query: 137  TKKKEKNKNKSRKEEEEEEKKKKKKKKKKKRTKKKEEEKRKNEK 180
              +K + + K+ +  + E+ KK +  KK +  KK  EE +K E+
Sbjct: 1204 AARKAEEERKAEEARKAEDAKKAEAVKKAEEAKKDAEEAKKAEE 1247

Length = 2084

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

 Score = 44.0 bits (103), Expect = 1e-04
 Identities = 34/179 (18%), Positives = 88/179 (49%)

Query: 2    KNKKEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKK 61
            K  ++ +K ++ R+ +   K +   + E+ +     +K ++ +   ++RK E+ KK    
Sbjct: 1122 KKAEDARKAEEARKAEDARKAEEARKAEDAKRVEIARKAEDARKAEEARKAEDAKKAEAA 1181

Query: 62   KEKNKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKE 121
            ++  + +  +E +K +  R+ +   K + + + EE +K  + +K +   K +   K  +E
Sbjct: 1182 RKAEEVRKAEELRKAEDARKAEAARKAEEERKAEEARKAEDAKKAEAVKKAEEAKKDAEE 1241

Query: 122  EEEKKKEAEEKKKKRTKKKEKNKNKSRKEEEEEEKKKKKKKKKKKRTKKKEEEKRKNEK 180
             ++ ++E   ++ ++ ++        R+   + E+ +K  + KK   KKK +E +K E+
Sbjct: 1242 AKKAEEERNNEEIRKFEEARMAHFARRQAAIKAEEARKADELKKAEEKKKADEAKKAEE 1300

Length = 2084

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

 Score = 43.3 bits (102), Expect = 1e-04
 Identities = 24/103 (23%), Positives = 57/103 (55%), Gaps = 2/103 (1%)

Query: 83  KKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKEEEEKKKEAEEKKK--KRTKKK 140
             ++ N+ + +K+   K+ +E +KK + + +   K R  E+ ++KE E++    K  K+ 
Sbjct: 48  VAQQANRIQQQKKPAAKKEQERQKKLEQQAEEAEKQRAAEQARQKELEQRAAAEKAAKQA 107

Query: 141 EKNKNKSRKEEEEEEKKKKKKKKKKKRTKKKEEEKRKNEKAVR 183
           E+   ++ +++++ E+ K K+  + K   + E EK+  E+A +
Sbjct: 108 EQAAKQAEEKQKQAEEAKAKQAAEAKAKAEAEAEKKAKEEAKK 150

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|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]

 Score = 43.9 bits (104), Expect = 1e-04
 Identities = 24/171 (14%), Positives = 67/171 (39%), Gaps = 5/171 (2%)

Query: 2   KNKKEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNK-----KNKNKSRKEEEKK 56
           +   EE ++      + KE+ + K     EE +   +  + +         + R E E+ 
Sbjct: 343 ETLLEELEQLLAELEEAKEELEEKLSALLEELEELFEALREELAELEAELAEIRNELEEL 402

Query: 57  KRTKKKEKNKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKN 116
           KR  +  + + +   E  +  K+   + + + +    + E+  E  EE ++   + +++ 
Sbjct: 403 KREIESLEERLERLSERLEDLKEELKELEAELEELQTELEELNEELEELEEQLEELRDRL 462

Query: 117 KSRKEEEEKKKEAEEKKKKRTKKKEKNKNKSRKEEEEEEKKKKKKKKKKKR 167
           K  + E  + +E  ++ +K     E   ++   E+   +  +   +  +  
Sbjct: 463 KELERELAELQEELQRLEKELSSLEARLDRLEAEQRASQGVRAVLEALESG 513

Length = 1163

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

 Score = 44.2 bits (104), Expect = 1e-04
 Identities = 43/187 (22%), Positives = 99/187 (52%)

Query: 2   KNKKEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKK 61
              K ++ + K     K  + K K ++EEEE+ R KK+E+ ++    S KE+E  +  +K
Sbjct: 724 LADKVQEAQDKINEELKLLEQKIKEKEEEEEKSRLKKEEEEEEKSELSLKEKELAEEEEK 783

Query: 62  KEKNKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKE 121
            EK K +  KEEK K ++   +  E+   +  +  ++++   E+++   +E+ +  + + 
Sbjct: 784 TEKLKVEEEKEEKLKAQEEELRALEEELKEEAELLEEEQLLIEQEEKIKEEELEELALEL 843

Query: 122 EEEKKKEAEEKKKKRTKKKEKNKNKSRKEEEEEEKKKKKKKKKKKRTKKKEEEKRKNEKA 181
           +EE+K E   +++    ++E  K +  +E   +E++ +++K K +   K+E+EK + ++ 
Sbjct: 844 KEEQKLEKLAEEELERLEEEITKEELLQELLLKEEELEEQKLKDELESKEEKEKEEKKEL 903

Query: 182 VRLTKLS 188
              ++  
Sbjct: 904 EEESQKD 910

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|235334 PRK05035, PRK05035, electron transport complex protein RnfC; Provisional

 Score = 44.2 bits (105), Expect = 1e-04
 Identities = 35/166 (21%), Positives = 62/166 (37%), Gaps = 29/166 (17%)

Query: 33  EKRTKKKEKNKKNKNKSRKEEEKKKRTKKKEKNKNKNRKEEKKKKKKRRTKKKEKNKNK- 91
           E R  ++EK K  + K+R E  + +  ++K        +E + KK       K+K+    
Sbjct: 437 EIRAIEQEKKKAEEAKARFEARQARLEREKAA------REARHKKAAEARAAKDKDAVAA 490

Query: 92  --SRKEEKKKEAEEEKKKTKNKEKNKNKSRKEEEEKKKEAEEKK-----------KK--- 135
             +R + KK  A +          + +      E +K +A  ++           KK   
Sbjct: 491 ALARVKAKKAAATQPIVIKAGARPDNSAVIAAREARKAQARARQAEKQAAAAADPKKAAV 550

Query: 136 -----RTK-KKEKNKNKSRKEEEEEEKKKKKKKKKKKRTKKKEEEK 175
                R K KK   +  + + EEE + KK        R K K+  +
Sbjct: 551 AAAIARAKAKKAAQQAANAEAEEEVDPKKAAVAAAIARAKAKKAAQ 596

Length = 695

>gnl|CDD|223496 COG0419, SbcC, ATPase involved in DNA repair [DNA replication, recombination, and repair]

 Score = 44.4 bits (105), Expect = 1e-04
 Identities = 39/186 (20%), Positives = 85/186 (45%), Gaps = 7/186 (3%)

Query: 4   KKEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKKKE 63
           +  + ++++ R  ++  +   +  +  EE +R  ++ + +    ++  EE ++   K K 
Sbjct: 267 EALKIREEELRELERLLEELEEKIERLEELEREIEELEEELEGLRALLEELEELLEKLKS 326

Query: 64  KNKNKNRKEEKKKKKKRRTK--KKEKNKNKSRKEEKKKEAEE-----EKKKTKNKEKNKN 116
             +   + EEK +K +   +   +EKN+     EE+ KE EE     EK+  K  E+ K 
Sbjct: 327 LEERLEKLEEKLEKLESELEELAEEKNELAKLLEERLKELEERLEELEKELEKALERLKQ 386

Query: 117 KSRKEEEEKKKEAEEKKKKRTKKKEKNKNKSRKEEEEEEKKKKKKKKKKKRTKKKEEEKR 176
                +E K++ AE        ++E  + +   EE E E ++ +++ KK   +  + E +
Sbjct: 387 LEEAIQELKEELAELSAALEEIQEELEELEKELEELERELEELEEEIKKLEEQINQLESK 446

Query: 177 KNEKAV 182
           +   A 
Sbjct: 447 ELMIAE 452

Length = 908

>gnl|CDD|223496 COG0419, SbcC, ATPase involved in DNA repair [DNA replication, recombination, and repair]

 Score = 44.0 bits (104), Expect = 1e-04
 Identities = 30/183 (16%), Positives = 81/183 (44%)

Query: 2   KNKKEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKK 61
           K K EE + +     +  E       +E +E K+ ++ ++ ++ +   ++ E  ++R  +
Sbjct: 184 KAKIEELEGQLSELLEDIEDLLEALEEELKELKKLEEIQEEQEEEELEQEIEALEERLAE 243

Query: 62  KEKNKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKE 121
            E+ K +  + + +  +    + +     +    E ++  EE ++K +  E+ + +  + 
Sbjct: 244 LEEEKERLEELKARLLEIESLELEALKIREEELRELERLLEELEEKIERLEELEREIEEL 303

Query: 122 EEEKKKEAEEKKKKRTKKKEKNKNKSRKEEEEEEKKKKKKKKKKKRTKKKEEEKRKNEKA 181
           EEE +      ++     ++    + R E+ EE+ +K + + ++   +K E  K   E+ 
Sbjct: 304 EEELEGLRALLEELEELLEKLKSLEERLEKLEEKLEKLESELEELAEEKNELAKLLEERL 363

Query: 182 VRL 184
             L
Sbjct: 364 KEL 366

Length = 908

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

 Score = 43.8 bits (104), Expect = 1e-04
 Identities = 21/72 (29%), Positives = 34/72 (47%), Gaps = 2/72 (2%)

Query: 52  EEEKKKRTKKKEKNKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNK 111
           EE  K R   + + K K   E+K  K  ++   K   K +  KE++K + ++  + TKN 
Sbjct: 365 EEPLKARVIDELRPKTKAPSEKKTGKPSKKVLAKRAEKKE--KEKEKPKVKKRHRDTKNI 422

Query: 112 EKNKNKSRKEEE 123
            K +  S   EE
Sbjct: 423 GKRRKPSGTSEE 434

Length = 434

>gnl|CDD|115057 pfam06375, BLVR, Bovine leukaemia virus receptor (BLVR)

 Score = 43.5 bits (102), Expect = 1e-04
 Identities = 26/137 (18%), Positives = 59/137 (43%)

Query: 18  KKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKKKEKNKNKNRKEEKKKK 77
           +K +N   S+  E+ +    +K+  K  K + +++E+++ + KKKE    K+        
Sbjct: 176 QKHRNAETSKSPEKGDVPAVEKKSKKPKKKEKKEKEKERDKDKKKEVEGFKSLLLALDDS 235

Query: 78  KKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKEEEEKKKEAEEKKKKRT 137
                   E ++            + E  + K+ E  + K   + ++KK+  E+++KK+ 
Sbjct: 236 PASAASVAEADEASLANTVSGTAPDSEPDEPKDAEAEETKKSPKHKKKKQRKEKEEKKKK 295

Query: 138 KKKEKNKNKSRKEEEEE 154
           KK   ++        E+
Sbjct: 296 KKHHHHRCHHSDGGAEQ 312

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|214395 CHL00204, ycf1, Ycf1; Provisional

 Score = 43.9 bits (104), Expect = 1e-04
 Identities = 24/88 (27%), Positives = 43/88 (48%), Gaps = 1/88 (1%)

Query: 87   KNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKEEEEKKKEAEEKKKKRTKKKEKNKNK 146
            +N NK   ++KK      +KK+  + +N+N+  KE   + +   +K+KK   +   +  +
Sbjct: 1496 ENVNKKINQKKKGFIPSNEKKSI-EIENRNQEEKEPAGQGELESDKEKKGNLESVLSNQE 1554

Query: 147  SRKEEEEEEKKKKKKKKKKKRTKKKEEE 174
               EE+  E   KK+K KK+     E E
Sbjct: 1555 KNIEEDYAESDIKKRKNKKQYKSNTEAE 1582

Length = 1832

>gnl|CDD|236081 PRK07735, PRK07735, NADH dehydrogenase subunit C; Validated

 Score = 43.8 bits (103), Expect = 1e-04
 Identities = 48/183 (26%), Positives = 78/183 (42%), Gaps = 4/183 (2%)

Query: 3   NKKEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKN---KNKSRKEEEKKKRT 59
            K  E  KK+  R  K+E  K    K   E  + +++ + K+    KN     EE K+R 
Sbjct: 4   EKDLEDLKKEAARRAKEEARKRLVAKHGAEISKLEEENREKEKALPKNDDMTIEEAKRRA 63

Query: 60  KKKEKNKNKNRKEEKKKKKKRRT-KKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKS 118
               K K     ++K++  +  T ++K K K K+    K K A   K+K +  E+   + 
Sbjct: 64  AAAAKAKAAALAKQKREGTEEVTEEEKAKAKAKAAAAAKAKAAALAKQKREGTEEVTEEE 123

Query: 119 RKEEEEKKKEAEEKKKKRTKKKEKNKNKSRKEEEEEEKKKKKKKKKKKRTKKKEEEKRKN 178
           +   + K   A + K     K+++   +   EEEEE  K+K K K     K K     K 
Sbjct: 124 KAAAKAKAAAAAKAKAAALAKQKREGTEEVTEEEEETDKEKAKAKAAAAAKAKAAALAKQ 183

Query: 179 EKA 181
           + A
Sbjct: 184 KAA 186

Length = 430

>gnl|CDD|225606 COG3064, TolA, Membrane protein involved in colicin uptake [Cell envelope biogenesis, outer membrane]

 Score = 42.6 bits (100), Expect = 2e-04
 Identities = 35/124 (28%), Positives = 67/124 (54%), Gaps = 4/124 (3%)

Query: 70  RKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKEEEEKKKEA 129
           +K E+++KKK     +E    ++ ++E+ K+ E+E+ K + ++K   ++ K+ + ++K+ 
Sbjct: 75  KKGEQQRKKKEEQVAEELKPKQAAEQERLKQLEKERLKAQEQQKQAEEAEKQAQLEQKQQ 134

Query: 130 EEKKKK----RTKKKEKNKNKSRKEEEEEEKKKKKKKKKKKRTKKKEEEKRKNEKAVRLT 185
           EE+ +K    + KK E  K K+  E  + +   + KKK ++  K  EE K K E A    
Sbjct: 135 EEQARKAAAEQKKKAEAAKAKAAAEAAKLKAAAEAKKKAEEAAKAAEEAKAKAEAAAAKK 194

Query: 186 KLSA 189
           K  A
Sbjct: 195 KAEA 198

Length = 387

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

 Score = 43.8 bits (103), Expect = 2e-04
 Identities = 41/189 (21%), Positives = 88/189 (46%), Gaps = 2/189 (1%)

Query: 2   KNKKEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRT--KKKEKNKKNKNKSRKEEEKKKRT 59
           K K EE+K++K +  +++ +   +  KEE E         E+ +K K +  +E   + + 
Sbjct: 786 KLKVEEEKEEKLKAQEEELRALEEELKEEAELLEEEQLLIEQEEKIKEEELEELALELKE 845

Query: 60  KKKEKNKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSR 119
           ++K +   +   E  +++  +    +E    +   EE+K + E E K+ K KE+ K    
Sbjct: 846 EQKLEKLAEEELERLEEEITKEELLQELLLKEEELEEQKLKDELESKEEKEKEEKKELEE 905

Query: 120 KEEEEKKKEAEEKKKKRTKKKEKNKNKSRKEEEEEEKKKKKKKKKKKRTKKKEEEKRKNE 179
           + +++   E +E + +    +E       + E EE   ++  +K+K+   K+EEE+R   
Sbjct: 906 ESQKDNLLEEKENEIEERIAEEAIILLKYESEPEELLLEEADEKEKEEDNKEEEEERNKR 965

Query: 180 KAVRLTKLS 188
             +   +L 
Sbjct: 966 LLLAKEELG 974

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 = 43.4 bits (102), Expect = 2e-04
 Identities = 40/189 (21%), Positives = 95/189 (50%), Gaps = 2/189 (1%)

Query: 2   KNKKEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKK 61
           K ++E K +  K   +K +  +     E+E +K  K+ +K K+   +  KE ++ +  ++
Sbjct: 294 KEEEELKSELLKLERRKVDDEEKLKESEKELKKLEKELKKEKEEIEELEKELKELEIKRE 353

Query: 62  KEKNKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKE 121
            E+ + +  ++ ++K ++   +   K K +S +     + +EE+ + KN+E+ + K   E
Sbjct: 354 AEEEEEEQLEKLQEKLEQLEEELLAKKKLESERLSSAAKLKEEELELKNEEEKEAKLLLE 413

Query: 122 EEEKKKEA--EEKKKKRTKKKEKNKNKSRKEEEEEEKKKKKKKKKKKRTKKKEEEKRKNE 179
             E++++   EEKK++    +E  ++   K+ +  E+K++ +K+  K  K K E K+  +
Sbjct: 414 LSEQEEDLLKEEKKEELKIVEELEESLETKQGKLTEEKEELEKQALKLLKDKLELKKSED 473

Query: 180 KAVRLTKLS 188
                  + 
Sbjct: 474 LLKETKLVK 482

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 = 43.0 bits (101), Expect = 2e-04
 Identities = 46/201 (22%), Positives = 99/201 (49%), Gaps = 13/201 (6%)

Query: 2   KNKKEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKK 61
           K  KEE+K+KK +  + K   K +   + E  K  ++K  +++   +S KE +K ++  K
Sbjct: 273 KENKEEEKEKKLQEEELKLLAKEEEELKSELLKLERRKVDDEEKLKESEKELKKLEKELK 332

Query: 62  KEKNKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKE 121
           KEK + +  ++E K+ + +R  ++E+ +   + +EK ++ EEE    K  E  +  S  +
Sbjct: 333 KEKEEIEELEKELKELEIKREAEEEEEEQLEKLQEKLEQLEEELLAKKKLESERLSSAAK 392

Query: 122 EEEKKKEAEEKKKKR-------------TKKKEKNKNKSRKEEEEEEKKKKKKKKKKKRT 168
            +E++ E + +++K                K+EK +     EE EE  + K+ K  +++ 
Sbjct: 393 LKEEELELKNEEEKEAKLLLELSEQEEDLLKEEKKEELKIVEELEESLETKQGKLTEEKE 452

Query: 169 KKKEEEKRKNEKAVRLTKLSA 189
           + +++  +  +  + L K   
Sbjct: 453 ELEKQALKLLKDKLELKKSED 473

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

 Score = 43.3 bits (103), Expect = 2e-04
 Identities = 41/185 (22%), Positives = 79/185 (42%), Gaps = 31/185 (16%)

Query: 5   KEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKKKEK 64
            E + ++K    +   K   K ++E EE          KK K +  +++  ++  K+ ++
Sbjct: 528 LERELEQKAEEAEALLKEAEKLKEELEE----------KKEKLQEEEDKLLEEAEKEAQQ 577

Query: 65  NKNKNRKEEKKKKKKRRTKKKEK---NKNKSRKEEKKK--EAEEEKKKTKNKEKNKNKSR 119
              + +KE  +  K+ R  +K      K     E +K+  +A E+K+K K K+K K +  
Sbjct: 578 AIKEAKKEADEIIKELRQLQKGGYASVKAHELIEARKRLNKANEKKEKKKKKQKEKQEEL 637

Query: 120 KEEEE-------KKKEAEEKKKKRT--------KKKEKNKN-KSRKEEEEEEKKKKKKKK 163
           K  +E       +K E       +         K K    + +  ++ ++++KKK K  K
Sbjct: 638 KVGDEVKYLSLGQKGEVLSIPDDKEAIVQAGIMKMKVPLSDLEKIQKPKKKKKKKPKTVK 697

Query: 164 KKKRT 168
            K RT
Sbjct: 698 PKPRT 702

Length = 782

>gnl|CDD|235334 PRK05035, PRK05035, electron transport complex protein RnfC; Provisional

 Score = 43.4 bits (103), Expect = 2e-04
 Identities = 34/201 (16%), Positives = 75/201 (37%), Gaps = 19/201 (9%)

Query: 2   KNKKEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKS------------ 49
           +  ++EKKK ++ + + + +     R++   E R KK  + +  K+K             
Sbjct: 439 RAIEQEKKKAEEAKARFEARQARLEREKAAREARHKKAAEARAAKDKDAVAAALARVKAK 498

Query: 50  RKEEEKKKRTKKKEKNKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKE-----AEEE 104
           +    +    K   +  N      ++ +K +   ++ + +  +  + KK       A  +
Sbjct: 499 KAAATQPIVIKAGARPDNSAVIAAREARKAQARARQAEKQAAAAADPKKAAVAAAIARAK 558

Query: 105 KKKTKNKEKNKNKSRKEEEEKKKEAEEKKKKRTKKKEKNKNKSRKEEEEEEKKKKKKKKK 164
            KK   +  N     + + +K   A    + + KK  +    +  EE+  E   KK    
Sbjct: 559 AKKAAQQAANAEAEEEVDPKKAAVAAAIARAKAKKAAQQAASAEPEEQVAEVDPKKAAVA 618

Query: 165 K--KRTKKKEEEKRKNEKAVR 183
               R K K+ E++ N +   
Sbjct: 619 AAIARAKAKKAEQQANAEPEE 639

Length = 695

>gnl|CDD|223496 COG0419, SbcC, ATPase involved in DNA repair [DNA replication, recombination, and repair]

 Score = 43.2 bits (102), Expect = 2e-04
 Identities = 36/189 (19%), Positives = 87/189 (46%), Gaps = 10/189 (5%)

Query: 2   KNKKEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSR----KEEEKKK 57
           + + +E KK ++ + +++E+   +  +  EE     ++EK +  + K+R    +  E + 
Sbjct: 209 EEELKELKKLEEIQEEQEEEELEQEIEALEERLAELEEEKERLEELKARLLEIESLELEA 268

Query: 58  RTKKKEKNKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNK 117
              ++E+ +   R  E+ ++K  R ++ E+   +  +E +   A  E+ +   ++    +
Sbjct: 269 LKIREEELRELERLLEELEEKIERLEELEREIEELEEELEGLRALLEELEELLEKLKSLE 328

Query: 118 SRKEEEEKKKEA------EEKKKKRTKKKEKNKNKSRKEEEEEEKKKKKKKKKKKRTKKK 171
            R E+ E+K E       E  ++K    K   +     EE  EE +K+ +K  ++  + +
Sbjct: 329 ERLEKLEEKLEKLESELEELAEEKNELAKLLEERLKELEERLEELEKELEKALERLKQLE 388

Query: 172 EEEKRKNEK 180
           E  +   E+
Sbjct: 389 EAIQELKEE 397

Length = 908

>gnl|CDD|188306 TIGR03319, RNase_Y, ribonuclease Y

 Score = 43.4 bits (103), Expect = 2e-04
 Identities = 40/167 (23%), Positives = 77/167 (46%), Gaps = 6/167 (3%)

Query: 2   KNKKEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKN------KSRKEEEK 55
           K   E+K    +   K+  +   K  +  ++E   + KE+  K +       K R+ E +
Sbjct: 20  KRIAEKKLGSAEELAKRIIEEAKKEAETLKKEALLEAKEEVHKLRAELERELKERRNELQ 79

Query: 56  KKRTKKKEKNKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNK 115
           +   +  ++ +  +RK E   KK+   +KKEK  +   K   +KE E E+   + +E+ +
Sbjct: 80  RLERRLLQREETLDRKMESLDKKEENLEKKEKELSNKEKNLDEKEEELEELIAEQREELE 139

Query: 116 NKSRKEEEEKKKEAEEKKKKRTKKKEKNKNKSRKEEEEEEKKKKKKK 162
             S   +EE K+   E+ ++  + +     K  +EE +EE  KK K+
Sbjct: 140 RISGLTQEEAKEILLEEVEEEARHEAAKLIKEIEEEAKEEADKKAKE 186

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

 Score = 43.0 bits (102), Expect = 2e-04
 Identities = 16/56 (28%), Positives = 29/56 (51%)

Query: 46  KNKSRKEEEKKKRTKKKEKNKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEA 101
           K K+  E++  K +KK    + + +++EK+K K ++  +  KN  K RK     E 
Sbjct: 379 KTKAPSEKKTGKPSKKVLAKRAEKKEKEKEKPKVKKRHRDTKNIGKRRKPSGTSEE 434

Length = 434

>gnl|CDD|172341 PRK13808, PRK13808, adenylate kinase; Provisional

 Score = 43.0 bits (101), Expect = 2e-04
 Identities = 29/132 (21%), Positives = 50/132 (37%), Gaps = 2/132 (1%)

Query: 51  KEEEKKKRTKKKEKNKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKN 110
           K+  K    K   K  +   K   KK  K++  K   +  K+ K   K   + +K   K 
Sbjct: 200 KKAAKTPAAKSGAKKASAKAKSAAKKVSKKKAAKTAVSAKKAAKTAAKAAKKAKKTAKKA 259

Query: 111 KEKNKNKSRKEEEEKKKEAEE--KKKKRTKKKEKNKNKSRKEEEEEEKKKKKKKKKKKRT 168
            +K     +K  ++  K A +  K   +  K +    K   ++     K K   K  KR 
Sbjct: 260 LKKAAKAVKKAAKKAAKAAAKAAKGAAKATKGKAKAKKKAGKKAAAGSKAKATAKAPKRG 319

Query: 169 KKKEEEKRKNEK 180
            K ++ K+  +K
Sbjct: 320 AKGKKAKKVTKK 331

Length = 333

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

 Score = 43.4 bits (103), Expect = 2e-04
 Identities = 20/71 (28%), Positives = 32/71 (45%), Gaps = 2/71 (2%)

Query: 88  NKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKEEEEKKKEAEEKKKKRTKKKEKNKNKS 147
           +      E +++E E        ++K + K RK E++ +KE  EK     KKK +   K 
Sbjct: 388 HDKPLLAEGEEEEGENGNLSPAERKKLRKKQRKAEKKAEKEEAEKAAA--KKKAEAAAKK 445

Query: 148 RKEEEEEEKKK 158
            K  + E KK 
Sbjct: 446 AKGPDGETKKV 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|236944 PRK11642, PRK11642, exoribonuclease R; Provisional

 Score = 43.6 bits (103), Expect = 2e-04
 Identities = 21/85 (24%), Positives = 30/85 (35%)

Query: 4   KKEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKKKE 63
           +      K  R   KK     K  K  +  K+   +  +     K  K +  KK  +K +
Sbjct: 729 RAPRNVGKTAREKAKKGDAGKKGGKRRQVGKKVNFEPDSAFRGEKKAKPKAAKKDARKAK 788

Query: 64  KNKNKNRKEEKKKKKKRRTKKKEKN 88
           K   K +K     K KR  KKK   
Sbjct: 789 KPSAKTQKIAAATKAKRAAKKKVAE 813

Length = 813

>gnl|CDD|236944 PRK11642, PRK11642, exoribonuclease R; Provisional

 Score = 43.6 bits (103), Expect = 2e-04
 Identities = 18/84 (21%), Positives = 33/84 (39%)

Query: 26  SRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKKKEKNKNKNRKEEKKKKKKRRTKKK 85
            R      K  ++K K      K  K  +  K+   +  +  +  K+ K K  K+  +K 
Sbjct: 728 ERAPRNVGKTAREKAKKGDAGKKGGKRRQVGKKVNFEPDSAFRGEKKAKPKAAKKDARKA 787

Query: 86  EKNKNKSRKEEKKKEAEEEKKKTK 109
           +K   K++K     +A+   KK  
Sbjct: 788 KKPSAKTQKIAAATKAKRAAKKKV 811

Length = 813

>gnl|CDD|219408 pfam07423, DUF1510, Protein of unknown function (DUF1510)

 Score = 42.0 bits (99), Expect = 2e-04
 Identities = 17/79 (21%), Positives = 49/79 (62%)

Query: 83  KKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKEEEEKKKEAEEKKKKRTKKKEK 142
            +   ++ +++K + ++ AE E+ K + KE   ++ ++++ + +KE EE +++  ++ E+
Sbjct: 42  DQAAADEQEAKKSDDQETAEIEEVKEEEKEAANSEDKEDKGDAEKEDEESEEENEEEDEE 101

Query: 143 NKNKSRKEEEEEEKKKKKK 161
           + +++ KE EE+ +   +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|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 42.8 bits (100), Expect = 3e-04
 Identities = 49/181 (27%), Positives = 84/181 (46%), Gaps = 9/181 (4%)

Query: 4    KKEEKKKKKKRRTKKKEKNKNKS----RKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRT 59
            KK E+ +KK     KKE  + K     +K+E EEK+  ++ K  + +NK + EE KK+  
Sbjct: 1681 KKAEEDEKKAAEALKKEAEEAKKAEELKKKEAEEKKKAEELKKAEEENKIKAEEAKKEAE 1740

Query: 60   KKKEKNKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSR 119
            + K+K +   + EE+KKK     K++EK   + RKE++    EE  ++ + +    +K  
Sbjct: 1741 EDKKKAEEAKKDEEEKKKIAHLKKEEEKKAEEIRKEKEAVIEEELDEEDEKRRMEVDKKI 1800

Query: 120  KEEEEKKKEAEEKKKKRTKKKEKNKNKSRKEEEEEEKKKKKKKKKKKRTKKKEEEKRKNE 179
            K+  +      E  K+       +     KE E+   K+    K  +  +    EK K  
Sbjct: 1801 KDIFDNFANIIEGGKEGNLVINDS-----KEMEDSAIKEVADSKNMQLEEADAFEKHKFN 1855

Query: 180  K 180
            K
Sbjct: 1856 K 1856

Length = 2084

>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]

 Score = 42.8 bits (101), Expect = 3e-04
 Identities = 31/186 (16%), Positives = 91/186 (48%), Gaps = 6/186 (3%)

Query: 2   KNKKEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKK 61
             K EE+ K  K   +  E    + R++ EE +R  ++ K +    +   E+ + +  + 
Sbjct: 683 LEKLEEELKSLKNELRSLEDLLEELRRQLEELERQLEELKRELAALEEELEQLQSRLEEL 742

Query: 62  KEK------NKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNK 115
           +E+         + ++  ++ +++  + ++   K K   EE +++ +  +++ +  E+  
Sbjct: 743 EEELEELEEELEELQERLEELEEELESLEEALAKLKEEIEELEEKRQALQEELEELEEEL 802

Query: 116 NKSRKEEEEKKKEAEEKKKKRTKKKEKNKNKSRKEEEEEEKKKKKKKKKKKRTKKKEEEK 175
            ++ +  +  ++E E  +++R + +++ +    + EE EEK  + +++ ++  K+ EE K
Sbjct: 803 EEAERRLDALERELESLEQRRERLEQEIEELEEEIEELEEKLDELEEELEELEKELEELK 862

Query: 176 RKNEKA 181
            + E+ 
Sbjct: 863 EELEEL 868

Length = 1163

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

 Score = 42.8 bits (101), Expect = 3e-04
 Identities = 21/83 (25%), Positives = 36/83 (43%)

Query: 101 AEEEKKKTKNKEKNKNKSRKEEEEKKKEAEEKKKKRTKKKEKNKNKSRKEEEEEEKKKKK 160
            ++ K +  +   +      +E       EE K   T  K+  K     E +++ +KKKK
Sbjct: 16  TQKSKLQPISYIYSNVLVLSKEILSTFSEEENKVATTSTKKDKKEDKNNESKKKSEKKKK 75

Query: 161 KKKKKKRTKKKEEEKRKNEKAVR 183
           KKK+KK  K + E K   +   +
Sbjct: 76  KKKEKKEPKSEGETKLGFKTPKK 98

Length = 413

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

 Score = 42.4 bits (100), Expect = 3e-04
 Identities = 23/89 (25%), Positives = 39/89 (43%), Gaps = 3/89 (3%)

Query: 102 EEEKKKTKNKEKNKNKSRKEEEEKKKEAEEKKKKRTKKKEKNKNK---SRKEEEEEEKKK 158
           + + +       N     KE      E E K    + KK+K ++K   S+K+ E+++KKK
Sbjct: 18  KSKLQPISYIYSNVLVLSKEILSTFSEEENKVATTSTKKDKKEDKNNESKKKSEKKKKKK 77

Query: 159 KKKKKKKKRTKKKEEEKRKNEKAVRLTKL 187
           K+KK+ K   + K   K   +      K 
Sbjct: 78  KEKKEPKSEGETKLGFKTPKKSKKTKKKP 106

Length = 413

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

 Score = 42.2 bits (100), Expect = 3e-04
 Identities = 16/67 (23%), Positives = 41/67 (61%)

Query: 2   KNKKEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKK 61
             K ++  +K +++ ++++K K K     ++++  +++EK KK + K  +EEE ++  ++
Sbjct: 409 TKKIKKIVEKAEKKREEEKKEKKKKAFAGKKKEEEEEEEKEKKEEEKEEEEEEAEEEKEE 468

Query: 62  KEKNKNK 68
           +E+ K K
Sbjct: 469 EEEKKKK 475

Length = 482

>gnl|CDD|220271 pfam09507, CDC27, DNA polymerase subunit Cdc27

 Score = 42.5 bits (100), Expect = 3e-04
 Identities = 25/156 (16%), Positives = 73/156 (46%)

Query: 2   KNKKEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKK 61
                ++   K  ++    + K KS K+ ++  +    EK +   +      ++    K 
Sbjct: 156 PTANGKRPSSKPPKSIMSPEVKVKSAKKTQDTSKETTTEKTEGKTSVKAASLKRNPPKKS 215

Query: 62  KEKNKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKE 121
              +    +K ++KK+KK  ++   K +++    ++    E+E  +    ++++++   +
Sbjct: 216 NIMSSFFKKKTKEKKEKKEASESTVKEESEEESGKRDVILEDESAEPTGLDEDEDEDEPK 275

Query: 122 EEEKKKEAEEKKKKRTKKKEKNKNKSRKEEEEEEKK 157
              ++ ++EE+ +++ K+K K   K  ++E+E+E+ 
Sbjct: 276 PSGERSDSEEETEEKEKEKRKRLKKMMEDEDEDEEM 311

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|227446 COG5116, RPN2, 26S proteasome regulatory complex component [Posttranslational modification, protein turnover, chaperones]

 Score = 43.0 bits (101), Expect = 3e-04
 Identities = 20/72 (27%), Positives = 28/72 (38%), Gaps = 7/72 (9%)

Query: 77  KKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKEEEEKKKEAEEKKKKR 136
           K   R K+K K K     +E K E       +   E  +    K+ EEK  +A      +
Sbjct: 792 KAAARAKQKPKEKG-PNDKEIKIE-----SPSVETEGERCT-IKQREEKGIDAPAILNVK 844

Query: 137 TKKKEKNKNKSR 148
            KK  K  N +R
Sbjct: 845 KKKPYKVDNMTR 856

Length = 926

>gnl|CDD|220684 pfam10310, DUF2413, Protein of unknown function (DUF2413)

 Score = 42.5 bits (100), Expect = 3e-04
 Identities = 22/112 (19%), Positives = 38/112 (33%), Gaps = 12/112 (10%)

Query: 30  EEEEKRTKKKEKNKKNKNKSRKEE------------EKKKRTKKKEKNKNKNRKEEKKKK 77
            +E+  TKK +K   +K+ +  +E            EK K  KK ++          KK 
Sbjct: 9   PDEKAPTKKPKKGDASKDSTEDDEDILEFLDELEQSEKAKPPKKPKEASRPGTPRNPKKS 68

Query: 78  KKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKEEEEKKKEA 129
            K        ++ K  K  K  E+             +++  +E EE     
Sbjct: 69  SKPTESSAASSEEKPAKPRKSAESTRSSHPKSKAPSTESEEEEEPEETPDPI 120

This is a family of proteins conserved in fungi. The function is not known. Length = 436

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

 Score = 42.8 bits (100), Expect = 4e-04
 Identities = 47/178 (26%), Positives = 91/178 (51%), Gaps = 2/178 (1%)

Query: 2    KNKKEEKKKKKK-RRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTK 60
            K + EE KK ++ ++ + +EK K +  K+ EEE + K +E  K+ +   +K EE KK  +
Sbjct: 1695 KKEAEEAKKAEELKKKEAEEKKKAEELKKAEEENKIKAEEAKKEAEEDKKKAEEAKKDEE 1754

Query: 61   KKEKNKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKK-EAEEEKKKTKNKEKNKNKSR 119
            +K+K  +  ++EEKK ++ R+ K+    +    ++EK++ E +++ K   +   N  +  
Sbjct: 1755 EKKKIAHLKKEEEKKAEEIRKEKEAVIEEELDEEDEKRRMEVDKKIKDIFDNFANIIEGG 1814

Query: 120  KEEEEKKKEAEEKKKKRTKKKEKNKNKSRKEEEEEEKKKKKKKKKKKRTKKKEEEKRK 177
            KE      +++E +    K+   +KN   +E +  EK K  K  +      KE +  K
Sbjct: 1815 KEGNLVINDSKEMEDSAIKEVADSKNMQLEEADAFEKHKFNKNNENGEDGNKEADFNK 1872

Length = 2084

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

 Score = 42.3 bits (99), Expect = 4e-04
 Identities = 45/187 (24%), Positives = 86/187 (45%), Gaps = 3/187 (1%)

Query: 1   CKNKKEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTK 60
               K+ +  K     K KE    K    EE      + + +     K    E++ +   
Sbjct: 627 EGILKDTELTKLLESAKAKESGLRKGVSLEEGLAEKSELKASLSELTKELLAEQELQEKA 686

Query: 61  KKEKNKNKNRKEEKKKKKKRRTKKKEKNKNK---SRKEEKKKEAEEEKKKTKNKEKNKNK 117
           + E  KN+  + +++ KKK +  K+E  K K         K +  ++K   + K   +  
Sbjct: 687 ESELAKNEILRRQEEIKKKEQRIKEELKKLKLEKEELLADKVQEAQDKINEELKLLEQKI 746

Query: 118 SRKEEEEKKKEAEEKKKKRTKKKEKNKNKSRKEEEEEEKKKKKKKKKKKRTKKKEEEKRK 177
             KEEEE+K   ++++++  K +   K K   EEEE+ +K K +++K+++ K +EEE R 
Sbjct: 747 KEKEEEEEKSRLKKEEEEEEKSELSLKEKELAEEEEKTEKLKVEEEKEEKLKAQEEELRA 806

Query: 178 NEKAVRL 184
            E+ ++ 
Sbjct: 807 LEEELKE 813

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

 Score = 41.9 bits (99), Expect = 4e-04
 Identities = 20/51 (39%), Positives = 28/51 (54%), Gaps = 3/51 (5%)

Query: 2   KNKKEEKKKKKKRRTKKKEKNKNKSRKEEEEEK-RTKKKEKNKKNKNKSRK 51
           K K   +KK  K    KK   K   +KE+E+EK + KK+ ++ KN  K RK
Sbjct: 379 KTKAPSEKKTGK--PSKKVLAKRAEKKEKEKEKPKVKKRHRDTKNIGKRRK 427

Length = 434

>gnl|CDD|233757 TIGR02168, SMC_prok_B, chromosome segregation protein SMC, common bacterial type

 Score = 42.4 bits (100), Expect = 4e-04
 Identities = 29/185 (15%), Positives = 82/185 (44%), Gaps = 4/185 (2%)

Query: 5   KEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKE--KNKKNKNKSRKEEEKKKRTKKK 62
           +E   + ++   K +E     S  EEE E+  K+     N+ ++ + +K+  +++    +
Sbjct: 256 EELTAELQELEEKLEELRLEVSELEEEIEELQKELYALANEISRLEQQKQILRERLANLE 315

Query: 63  EKNKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKEE 122
            + +    + E+ + K      +E  + + + EE K+E E  + + +  E    +     
Sbjct: 316 RQLEELEAQLEELESKLDE-LAEELAELEEKLEELKEELESLEAELEELEAELEELESRL 374

Query: 123 EEKKKEAEEKKKKRTK-KKEKNKNKSRKEEEEEEKKKKKKKKKKKRTKKKEEEKRKNEKA 181
           EE +++ E  + K  + + +     +  E  E   ++ + ++++ + + +E  K+  E  
Sbjct: 375 EELEEQLETLRSKVAQLELQIASLNNEIERLEARLERLEDRRERLQQEIEELLKKLEEAE 434

Query: 182 VRLTK 186
           ++  +
Sbjct: 435 LKELQ 439

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|237258 PRK12903, secA, preprotein translocase subunit SecA; Reviewed

 Score = 42.3 bits (100), Expect = 4e-04
 Identities = 25/134 (18%), Positives = 50/134 (37%)

Query: 18  KKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKKKEKNKNKNRKEEKKKK 77
             +   N    +  +E   +  E  ++     R + E+     ++ +  N+ +K  K++ 
Sbjct: 791 LSDGINNSDINDRPQELIDQIIESEEERLKALRIQREEMLMRPEELELINEEQKNLKQEI 850

Query: 78  KKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKEEEEKKKEAEEKKKKRT 137
           K   ++ +E  +      E K E  E K   K   K         +      E K+ ++T
Sbjct: 851 KLELSEIQEAEEEIQNINENKNEFVEFKNDPKKLNKLIIAKDVLIKLVISSDEIKQDEKT 910

Query: 138 KKKEKNKNKSRKEE 151
            KK+K   +   EE
Sbjct: 911 TKKKKKDLEKTDEE 924

Length = 925

>gnl|CDD|115057 pfam06375, BLVR, Bovine leukaemia virus receptor (BLVR)

 Score = 42.0 bits (98), Expect = 4e-04
 Identities = 40/152 (26%), Positives = 62/152 (40%), Gaps = 6/152 (3%)

Query: 7   EKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKKKEKNK 66
           EK   +K R  +  K+  K      E+K  K K+K KK K K R +++KK+    K    
Sbjct: 171 EKLPVQKHRNAETSKSPEKGDVPAVEKKSKKPKKKEKKEKEKERDKDKKKEVEGFKSLLL 230

Query: 67  NKNRKEEKKKKKKRRTKKKEKN------KNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRK 120
             +             +    N       +    E K  EAEE KK  K+K+K + K ++
Sbjct: 231 ALDDSPASAASVAEADEASLANTVSGTAPDSEPDEPKDAEAEETKKSPKHKKKKQRKEKE 290

Query: 121 EEEEKKKEAEEKKKKRTKKKEKNKNKSRKEEE 152
           E+++KKK    +        E+       EEE
Sbjct: 291 EKKKKKKHHHHRCHHSDGGAEQPVQNGAVEEE 322

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|221641 pfam12569, NARP1, NMDA receptor-regulated protein 1

 Score = 41.8 bits (99), Expect = 4e-04
 Identities = 15/70 (21%), Positives = 35/70 (50%)

Query: 84  KKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKEEEEKKKEAEEKKKKRTKKKEKN 143
           K    + +  + E    +  E+KK + K++   K  ++EE +K  A++K +   KK +  
Sbjct: 390 KPLLAEGEEEEGENGNLSPAERKKLRKKQRKAEKKAEKEEAEKAAAKKKAEAAAKKAKGP 449

Query: 144 KNKSRKEEEE 153
             +++K + +
Sbjct: 450 DGETKKVDPD 459

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|215774 pfam00183, HSP90, Hsp90 protein

 Score = 42.1 bits (99), Expect = 4e-04
 Identities = 23/62 (37%), Positives = 39/62 (62%)

Query: 121 EEEEKKKEAEEKKKKRTKKKEKNKNKSRKEEEEEEKKKKKKKKKKKRTKKKEEEKRKNEK 180
           E+E   +E EE+K+++ +++EK  +K  + +EEEEK++KKKK KK +    E E     K
Sbjct: 32  EKEVPDEEEEEEKEEKKEEEEKTTDKEEEVDEEEEKEEKKKKTKKVKETTTEWELLNKTK 91

Query: 181 AV 182
            +
Sbjct: 92  PI 93

Length = 529

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

 Score = 41.9 bits (99), Expect = 4e-04
 Identities = 18/71 (25%), Positives = 42/71 (59%), Gaps = 3/71 (4%)

Query: 39  KEKNKKNKNKSRKEEEKKKRTKKKEKNKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKK 98
             +  +  +K+R+EEE+K     K   + +  + ++KK++K++ +++ K    S +E++K
Sbjct: 254 SPEVLRKVDKTREEEEEKIL---KAAEEERQEEAQEKKEEKKKEEREAKLAKLSPEEQRK 310

Query: 99  KEAEEEKKKTK 109
            E +E KK+ +
Sbjct: 311 LEEKERKKQAR 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|235640 PRK05901, PRK05901, RNA polymerase sigma factor; Provisional

 Score = 41.9 bits (99), Expect = 5e-04
 Identities = 24/102 (23%), Positives = 37/102 (36%), Gaps = 2/102 (1%)

Query: 88  NKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKEEEEKKKEAEEKKKKRTKKKEKNKNKS 147
               S K E   E E +KK  K   K+K+K    +EE K+  E KKK   +  +      
Sbjct: 1   MTTASTKAELAAEEEAKKKLKKLAAKSKSKGFITKEEIKEALESKKKTPEQIDQVLIFL- 59

Query: 148 RKEEEEEEKKKKKKKKKKKRTKKKEEEKRKNEKAVRLTKLSA 189
                ++     +    KK+TK   +       A +  K   
Sbjct: 60  -SGMVKDTDDATESDIPKKKTKTAAKAAAAKAPAKKKLKDEL 100

Length = 509

>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]

 Score = 42.0 bits (99), Expect = 5e-04
 Identities = 27/181 (14%), Positives = 89/181 (49%), Gaps = 4/181 (2%)

Query: 2   KNKKEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKK 61
             ++  ++ +++    ++E  + + + +E EE+  + +++ ++ K +  + E +K+  + 
Sbjct: 818 SLEQRRERLEQEIEELEEEIEELEEKLDELEEELEELEKELEELKEELEELEAEKEELED 877

Query: 62  KEKNKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKE 121
           + K   + ++E +++ ++  ++  E  +   +  E+ +E E + ++ + +     +  +E
Sbjct: 878 ELKELEEEKEELEEELRELESELAELKEEIEKLRERLEELEAKLERLEVELPELEEELEE 937

Query: 122 EEEKKKEAEEKKKKRTKKKEKNK----NKSRKEEEEEEKKKKKKKKKKKRTKKKEEEKRK 177
           E E   E E +++    ++E       N    EE EE +++ ++ K ++   ++ +EK  
Sbjct: 938 EYEDTLETELEREIERLEEEIEALGPVNLRAIEEYEEVEERYEELKSQREDLEEAKEKLL 997

Query: 178 N 178
            
Sbjct: 998 E 998

Length = 1163

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

 Score = 41.8 bits (99), Expect = 5e-04
 Identities = 20/75 (26%), Positives = 45/75 (60%)

Query: 27  RKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKKKEKNKNKNRKEEKKKKKKRRTKKKE 86
              ++  K+ KK  +  + K +  K+E+KKK    K+K + +  ++EKK+++K   +++ 
Sbjct: 403 TGSKKATKKIKKIVEKAEKKREEEKKEKKKKAFAGKKKEEEEEEEKEKKEEEKEEEEEEA 462

Query: 87  KNKNKSRKEEKKKEA 101
           + + +  +E+KKK+A
Sbjct: 463 EEEKEEEEEKKKKQA 477

Length = 482

>gnl|CDD|220271 pfam09507, CDC27, DNA polymerase subunit Cdc27

 Score = 41.7 bits (98), Expect = 5e-04
 Identities = 34/157 (21%), Positives = 64/157 (40%), Gaps = 4/157 (2%)

Query: 30  EEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKKKEKNKNKNRKEEKKKKKKRRTKKKEKNK 89
                  K     K+  +K  K     +   K  K      KE   +K + +T  K  + 
Sbjct: 148 PAASPALKPTANGKRPSSKPPKSIMSPEVKVKSAKKTQDTSKETTTEKTEGKTSVKAASL 207

Query: 90  NKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKEEEEKKKEAEEKKKKRTKKKEKNK-NKSR 148
            ++  ++    +   KKKTK K   K K    E   K+E+EE+  KR    E      + 
Sbjct: 208 KRNPPKKSNIMSSFFKKKTKEK---KEKKEASESTVKEESEEESGKRDVILEDESAEPTG 264

Query: 149 KEEEEEEKKKKKKKKKKKRTKKKEEEKRKNEKAVRLT 185
            +E+E+E + K   ++    ++ EE++++  K ++  
Sbjct: 265 LDEDEDEDEPKPSGERSDSEEETEEKEKEKRKRLKKM 301

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|218177 pfam04615, Utp14, Utp14 protein

 Score = 42.0 bits (99), Expect = 5e-04
 Identities = 43/181 (23%), Positives = 91/181 (50%), Gaps = 5/181 (2%)

Query: 4   KKEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKKKE 63
           ++ E+ ++K       E+++++    EEE++   + + + +N    RK+  K K  +  E
Sbjct: 309 RQGEELRRKIEGKSVSEEDEDEDSDSEEEDEDDDEDDDDGENPWMLRKKLGKLKEGEDDE 368

Query: 64  KNKN----KNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSR 119
           +N      K  +  + +KK+    + E+ + +   EE+  E E E+   KN  + K    
Sbjct: 369 ENSGLLSMKFMQRAEARKKEENDAEIEELRRELEGEEESDEEENEEPSKKNVGRRKFGPE 428

Query: 120 KEEEEKKKEAEEKKKKRTKKKEKNKNKSRKEEEEEEKK-KKKKKKKKKRTKKKEEEKRKN 178
             E+E + +  +K+ K   K++K  ++  + E+EEE K +K   K  KR++K ++E+ + 
Sbjct: 429 NGEKEAESKKLKKENKNEFKEKKESDEEEELEDEEEAKVEKVANKLLKRSEKAQKEEEEE 488

Query: 179 E 179
           E
Sbjct: 489 E 489

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|223496 COG0419, SbcC, ATPase involved in DNA repair [DNA replication, recombination, and repair]

 Score = 42.1 bits (99), Expect = 5e-04
 Identities = 35/187 (18%), Positives = 89/187 (47%), Gaps = 4/187 (2%)

Query: 7   EKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKKKEKNK 66
           E  K+ K + ++ E   ++  ++ E+     ++E  +  K +  +EE++++  +++ +  
Sbjct: 178 EVIKEAKAKIEELEGQLSELLEDIEDLLEALEEELKELKKLEEIQEEQEEEELEQEIEAL 237

Query: 67  NKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKEEEEKK 126
            +   E +++K++    K    + +S + E  K  EEE ++ +   +   +  +  EE +
Sbjct: 238 EERLAELEEEKERLEELKARLLEIESLELEALKIREEELRELERLLEELEEKIERLEELE 297

Query: 127 KEAEEKKKKRTKKKEKNKNKSRKEEE----EEEKKKKKKKKKKKRTKKKEEEKRKNEKAV 182
           +E EE +++    +   +      E+    EE  +K ++K +K  ++ +E  + KNE A 
Sbjct: 298 REIEELEEELEGLRALLEELEELLEKLKSLEERLEKLEEKLEKLESELEELAEEKNELAK 357

Query: 183 RLTKLSA 189
            L +   
Sbjct: 358 LLEERLK 364

Length = 908

>gnl|CDD|240246 PTZ00053, PTZ00053, methionine aminopeptidase 2; Provisional

 Score = 42.0 bits (99), Expect = 5e-04
 Identities = 19/92 (20%), Positives = 41/92 (44%), Gaps = 5/92 (5%)

Query: 88  NKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKEE-----EEKKKEAEEKKKKRTKKKEK 142
             N++ + E K++ ++ K+K   K+  K+K   ++      E   E +E + K+  KK+K
Sbjct: 1   AMNENGENEVKQQKQQNKQKGTKKKNKKSKKDVDDDDAFLAELISENQEAENKQNNKKKK 60

Query: 143 NKNKSRKEEEEEEKKKKKKKKKKKRTKKKEEE 174
            K K +K++   E            +    ++
Sbjct: 61  KKKKKKKKKNLGEAYDLAYDLPVVWSSAAFQD 92

Length = 470

>gnl|CDD|235175 PRK03918, PRK03918, chromosome segregation protein; Provisional

 Score = 42.0 bits (99), Expect = 5e-04
 Identities = 39/181 (21%), Positives = 88/181 (48%), Gaps = 1/181 (0%)

Query: 2   KNKKEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKK 61
           K K EEK ++ + R ++ +K   +  ++ +E K  K+K +     ++  +E   + R  +
Sbjct: 254 KRKLEEKIRELEERIEELKKEIEELEEKVKELKELKEKAEEYIKLSEFYEEYLDELREIE 313

Query: 62  KEKNKNKNRKEE-KKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRK 120
           K  ++ +      +++ K+   K++   + K + +E +K  EE +++ +  E+ K K  +
Sbjct: 314 KRLSRLEEEINGIEERIKELEEKEERLEELKKKLKELEKRLEELEERHELYEEAKAKKEE 373

Query: 121 EEEEKKKEAEEKKKKRTKKKEKNKNKSRKEEEEEEKKKKKKKKKKKRTKKKEEEKRKNEK 180
            E  KK+      +K  K+ E+ +    + EEE  K   +  + KK  K+ ++   + +K
Sbjct: 374 LERLKKRLTGLTPEKLEKELEELEKAKEEIEEEISKITARIGELKKEIKELKKAIEELKK 433

Query: 181 A 181
           A
Sbjct: 434 A 434

Length = 880

>gnl|CDD|233467 TIGR01554, major_cap_HK97, phage major capsid protein, HK97 family

 Score = 41.6 bits (98), Expect = 5e-04
 Identities = 11/98 (11%), Positives = 36/98 (36%), Gaps = 1/98 (1%)

Query: 6   EEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKE-KNKKNKNKSRKEEEKKKRTKKKEK 64
           +E ++      K+  K     +  E EE++ +    K + +K  +  +  ++   + + K
Sbjct: 2   KELREALAELAKELRKLTEDEKLAEAEEEKAEYDALKEEIDKLDAEIDRLEELLDELEAK 61

Query: 65  NKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAE 102
                     +++++    +  + +   R  +     E
Sbjct: 62  PAASGEGGGGEEEEEEAKAEAAEFRAYLRGGDDALAEE 99

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|115057 pfam06375, BLVR, Bovine leukaemia virus receptor (BLVR)

 Score = 42.0 bits (98), Expect = 5e-04
 Identities = 37/136 (27%), Positives = 67/136 (49%), Gaps = 9/136 (6%)

Query: 51  KEEEKKKRTKKKEKNKNKNRKEEKKKKKKRR-----TKKKEKNKNKSRKEEKKKEAEEEK 105
           K EE+++  ++ EK+K + +K EK+K+ +RR     T+  E        +   +E  E  
Sbjct: 83  KLEEERRHRQRLEKDKREKKKREKEKRGRRRHHSLGTESDEDIAPAQMVDIVTEEMPENA 142

Query: 106 KKTKNKEKNKNKSRKEEEEKKKEAEEKKKKRTKKKEKNKNKSRKEEEEE----EKKKKKK 161
             +   +K+ N   +  +    +     +K   +K +N   S+  E+ +    EKK KK 
Sbjct: 143 LPSDEDDKDPNDPYRALDIDLDKPLADSEKLPVQKHRNAETSKSPEKGDVPAVEKKSKKP 202

Query: 162 KKKKKRTKKKEEEKRK 177
           KKK+K+ K+KE +K K
Sbjct: 203 KKKEKKEKEKERDKDK 218

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|236081 PRK07735, PRK07735, NADH dehydrogenase subunit C; Validated

 Score = 41.9 bits (98), Expect = 5e-04
 Identities = 45/178 (25%), Positives = 73/178 (41%), Gaps = 13/178 (7%)

Query: 2   KNKKEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKE-------EE 54
           K+  E  K +++ R K+K   KN     EE ++R     K K      +K        EE
Sbjct: 29  KHGAEISKLEEENREKEKALPKNDDMTIEEAKRRAAAAAKAKAAALAKQKREGTEEVTEE 88

Query: 55  KKKRTKKKEKNKNKNRKEEKKKKKKR-----RTKKKEKNKNKSRKEEKKKEAEEEKKKTK 109
           +K + K K     K +     K+K+        ++K   K K+    K K A   K+K +
Sbjct: 89  EKAKAKAKAAAAAKAKAAALAKQKREGTEEVTEEEKAAAKAKAAAAAKAKAAALAKQKRE 148

Query: 110 NKEKNKNKSRKEEEEK-KKEAEEKKKKRTKKKEKNKNKSRKEEEEEEKKKKKKKKKKK 166
             E+   +  + ++EK K +A    K +     K K     E  EE  +++K K K K
Sbjct: 149 GTEEVTEEEEETDKEKAKAKAAAAAKAKAAALAKQKAAEAGEGTEEVTEEEKAKAKAK 206

Length = 430

>gnl|CDD|236944 PRK11642, PRK11642, exoribonuclease R; Provisional

 Score = 42.0 bits (99), Expect = 5e-04
 Identities = 19/87 (21%), Positives = 39/87 (44%)

Query: 16  TKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKKKEKNKNKNRKEEKK 75
           +++  +N  K+ +E+ ++    KK   ++   K    E       +K+      +K+ +K
Sbjct: 727 SERAPRNVGKTAREKAKKGDAGKKGGKRRQVGKKVNFEPDSAFRGEKKAKPKAAKKDARK 786

Query: 76  KKKKRRTKKKEKNKNKSRKEEKKKEAE 102
            KK     +K     K+++  KKK AE
Sbjct: 787 AKKPSAKTQKIAAATKAKRAAKKKVAE 813

Length = 813

>gnl|CDD|219408 pfam07423, DUF1510, Protein of unknown function (DUF1510)

 Score = 40.9 bits (96), Expect = 5e-04
 Identities = 18/87 (20%), Positives = 44/87 (50%)

Query: 59  TKKKEKNKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKS 118
              +     +  K+   ++     + KE+ K  +  E+K+ + + EK+  +++E+N+ + 
Sbjct: 40  PSDQAAADEQEAKKSDDQETAEIEEVKEEEKEAANSEDKEDKGDAEKEDEESEEENEEED 99

Query: 119 RKEEEEKKKEAEEKKKKRTKKKEKNKN 145
            +  +E +KE EEK +   +K+  N +
Sbjct: 100 EESSDENEKETEEKTESNVEKEITNPS 126

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|219655 pfam07946, DUF1682, Protein of unknown function (DUF1682)

 Score = 41.5 bits (98), Expect = 5e-04
 Identities = 21/68 (30%), Positives = 43/68 (63%)

Query: 73  EKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKEEEEKKKEAEEK 132
            +  +K  +T+++E+ K     EE+++E  +EKK+ K KE+ + K  K   E++++ EEK
Sbjct: 255 PEVLRKVDKTREEEEEKILKAAEEERQEEAQEKKEEKKKEEREAKLAKLSPEEQRKLEEK 314

Query: 133 KKKRTKKK 140
           ++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|224495 COG1579, COG1579, Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]

 Score = 41.2 bits (97), Expect = 5e-04
 Identities = 29/148 (19%), Positives = 69/148 (46%), Gaps = 3/148 (2%)

Query: 27  RKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKKKEKNKNKNRKEEKKKKKKRRTKKKE 86
            KE  +  +  K E    NK     E E +    +  + +++ ++  ++ K+        
Sbjct: 26  IKEIRKALKKAKAELEALNKALEALEIELEDLENQVSQLESEIQEIRERIKRAEEKLSAV 85

Query: 87  KNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKEEEEKKKEAEEKKKKRTK-KKEKNKN 145
           K++ + R    + +  +E+  +   E  +    +E E+ +KE E+ K++  + +K   + 
Sbjct: 86  KDERELRALNIEIQIAKERINSLEDELAE--LMEEIEKLEKEIEDLKERLERLEKNLAEA 143

Query: 146 KSRKEEEEEEKKKKKKKKKKKRTKKKEE 173
           ++R EEE  E +++ ++   KR + KE+
Sbjct: 144 EARLEEEVAEIREEGQELSSKREELKEK 171

Length = 239

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

 Score = 41.9 bits (98), Expect = 6e-04
 Identities = 31/173 (17%), Positives = 86/173 (49%)

Query: 2    KNKKEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKK 61
              + +E++K +K   ++ E+ + +  KEE  ++   K+E+ ++ K K   E +++K  ++
Sbjct: 840  ALELKEEQKLEKLAEEELERLEEEITKEELLQELLLKEEELEEQKLKDELESKEEKEKEE 899

Query: 62   KEKNKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKE 121
            K++ + +++K+   ++K+   +++   +     + + +  E   ++   KEK ++   +E
Sbjct: 900  KKELEEESQKDNLLEEKENEIEERIAEEAIILLKYESEPEELLLEEADEKEKEEDNKEEE 959

Query: 122  EEEKKKEAEEKKKKRTKKKEKNKNKSRKEEEEEEKKKKKKKKKKKRTKKKEEE 174
            EE  K+    K++              KEE   + + KK++ ++++ +   E 
Sbjct: 960  EERNKRLLLAKEELGNVNLMAIAEFEEKEERYNKDELKKERLEEEKKELLREI 1012

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 = 6e-04
 Identities = 41/169 (24%), Positives = 87/169 (51%)

Query: 6    EEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKKKEKN 65
            EE ++ ++  TK++   +   ++EE EE++ K + ++K+ K K  K+E +++  K     
Sbjct: 855  EELERLEEEITKEELLQELLLKEEELEEQKLKDELESKEEKEKEEKKELEEESQKDNLLE 914

Query: 66   KNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKEEEEK 125
            + +N  EE+  ++     K E    +   EE  ++ +EE  K + +E+NK     +EE  
Sbjct: 915  EKENEIEERIAEEAIILLKYESEPEELLLEEADEKEKEEDNKEEEEERNKRLLLAKEELG 974

Query: 126  KKEAEEKKKKRTKKKEKNKNKSRKEEEEEEKKKKKKKKKKKRTKKKEEE 174
                    +   K++  NK++ +KE  EEEKK+  ++  ++  ++ +E 
Sbjct: 975  NVNLMAIAEFEEKEERYNKDELKKERLEEEKKELLREIIEETCQRFKEF 1023

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 = 6e-04
 Identities = 20/90 (22%), Positives = 37/90 (41%)

Query: 52  EEEKKKRTKKKEKNKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNK 111
           +EE  +     +K   ++ K   KK     ++  E+       E+   + E +K   + +
Sbjct: 59  DEEPDENGAVSKKKPTRSVKRATKKTVVEISEPLEEGSELVVNEDAALDKESKKTPRRTR 118

Query: 112 EKNKNKSRKEEEEKKKEAEEKKKKRTKKKE 141
            K    S   EEEK ++   K++K  K  E
Sbjct: 119 RKAAAASSDVEEEKTEKKVRKRRKVKKMDE 148

Length = 581

>gnl|CDD|178945 PRK00247, PRK00247, putative inner membrane protein translocase component YidC; Validated

 Score = 41.4 bits (97), Expect = 6e-04
 Identities = 19/134 (14%), Positives = 48/134 (35%), Gaps = 8/134 (5%)

Query: 50  RKEEEKKKRTKKKEKNKNKNR------KEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEE 103
            +E++K+K+       +N+ R      +  +   +    KK    +    K  KK+ A++
Sbjct: 294 YREKQKEKKAFLWTLRRNRLRMIITPWRAPELHAENAEIKKTRTAEKNEAKARKKEIAQK 353

Query: 104 EKKKTKNKEKNKNKSRKEEEEKKKEAEEKKKKRTKKKEKNKNKSRKEEEEEEKKKKKKKK 163
            +   +   +   + R     + +    +   + KKK        ++   E ++ K    
Sbjct: 354 RRAAEREINREARQERAAAMARAR--ARRAAVKAKKKGLIDASPNEDTPSENEESKGSPP 411

Query: 164 KKKRTKKKEEEKRK 177
           + + T   E  +  
Sbjct: 412 QVEATTTAEPNREP 425

Length = 429

>gnl|CDD|219563 pfam07767, Nop53, Nop53 (60S ribosomal biogenesis)

 Score = 41.2 bits (97), Expect = 6e-04
 Identities = 36/158 (22%), Positives = 85/158 (53%), Gaps = 4/158 (2%)

Query: 24  NKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKKKEKNKNKNRKEEKKKKKKRRTK 83
           N S ++ +E  + + +++ K  K +   E  ++K+ +K     ++  +  +   ++    
Sbjct: 189 NPSFEDHQELLQEEYEKEVKAEKKRQELERVEEKKLEKMAPEASRLDEMSEGLLEESDDD 248

Query: 84  KKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKEEEEKKKEAEEKKKKRTKKKEKN 143
            +E++ ++S  E  + E E   K  + K K K +  KE+  K+ E E K++K+ KKK   
Sbjct: 249 GEEESDDESAWEGFESEYEPINKPVRPKRKTKAQRNKEKRRKELEREAKEEKQLKKKLAQ 308

Query: 144 KNK----SRKEEEEEEKKKKKKKKKKKRTKKKEEEKRK 177
             +    +++  ++E+ + +KK+++K+R +KK+ ++RK
Sbjct: 309 LARLKEIAKEVAQKEKARARKKEQRKERGEKKKLKRRK 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|219838 pfam08432, DUF1742, Fungal protein of unknown function (DUF1742)

 Score = 40.1 bits (94), Expect = 6e-04
 Identities = 31/117 (26%), Positives = 54/117 (46%), Gaps = 5/117 (4%)

Query: 6   EEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKKKEKN 65
            E KKKKK   ++ EK     +KE EE+++ K K+K  K K    K+++  K+  K EK 
Sbjct: 58  TEAKKKKKELAEEIEK----VKKEYEEKQKWKWKKKKSKKKKDKDKDKKDDKKDDKSEKK 113

Query: 66  KNKNRKEEKKKKKKRRTKKKEKNKN-KSRKEEKKKEAEEEKKKTKNKEKNKNKSRKE 121
             K  +++ +   K  ++        K RK    K+  + +   K + +   K  +E
Sbjct: 114 DEKEAEDKLEDLTKSYSETLSTLSELKPRKYALHKDIYQSRLDRKRRAEVAKKEAEE 170

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

>gnl|CDD|177089 CHL00189, infB, translation initiation factor 2; Provisional

 Score = 41.7 bits (98), Expect = 6e-04
 Identities = 28/113 (24%), Positives = 47/113 (41%), Gaps = 1/113 (0%)

Query: 7   EKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKKKEKNK 66
           +  KK   +  KK K  NK+   ++ +K   K++K  K K     + +    +K   K  
Sbjct: 47  DINKKLHEKLDKKNKKFNKTDDLKDSKKTKLKQKKKIKKKLHIDDDYDNFFDSKNNSKQF 106

Query: 67  NKNRKEEKKKKKKRRTKK-KEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKS 118
                    +K K +T+K K+K        +KKK+    K +    + NK KS
Sbjct: 107 AGPLAISLMRKPKPKTEKLKKKITVNKSTNKKKKKVLSSKDELIKYDNNKPKS 159

Length = 742

>gnl|CDD|219408 pfam07423, DUF1510, Protein of unknown function (DUF1510)

 Score = 40.5 bits (95), Expect = 6e-04
 Identities = 20/88 (22%), Positives = 44/88 (50%)

Query: 84  KKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKEEEEKKKEAEEKKKKRTKKKEKN 143
                     +E KK + +E  +  + KE+ K  +  E++E K +AE++ ++  ++ E+ 
Sbjct: 39  SPSDQAAADEQEAKKSDDQETAEIEEVKEEEKEAANSEDKEDKGDAEKEDEESEEENEEE 98

Query: 144 KNKSRKEEEEEEKKKKKKKKKKKRTKKK 171
             +S  E E+E ++K +   +K+ T   
Sbjct: 99  DEESSDENEKETEEKTESNVEKEITNPS 126

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|130141 TIGR01069, mutS2, MutS2 family protein

 Score = 41.7 bits (98), Expect = 6e-04
 Identities = 38/184 (20%), Positives = 75/184 (40%), Gaps = 14/184 (7%)

Query: 3   NKKEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKKK 62
           N   EK    ++  ++K ++  K  KE+E+ K   K+ + +  + K R+  +K +  K+ 
Sbjct: 514 NVLIEKLSALEKELEQKNEHLEKLLKEQEKLK---KELEQEMEELKERERNKKLELEKEA 570

Query: 63  EKNKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKEE 122
           ++     +KE +   ++ + KK  K K     E+  K  +E K+K   K  N    +  +
Sbjct: 571 QEALKALKKEVESIIRELKEKKIHKAKEIKSIEDLVKL-KETKQKIPQKPTNFQADKIGD 629

Query: 123 EEKKKEAEEKKKKRTKKKEKNKN----------KSRKEEEEEEKKKKKKKKKKKRTKKKE 172
           + + +   +K K          N             + E+  +    KK K  K TK + 
Sbjct: 630 KVRIRYFGQKGKIVQILGGNKWNVTVGGMRMKVHGSELEKINKAPPPKKFKVPKTTKPEP 689

Query: 173 EEKR 176
           +E  
Sbjct: 690 KEAS 693

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|240388 PTZ00372, PTZ00372, endonuclease 4-like protein; Provisional

 Score = 41.2 bits (97), Expect = 7e-04
 Identities = 21/88 (23%), Positives = 40/88 (45%)

Query: 94  KEEKKKEAEEEKKKTKNKEKNKNKSRKEEEEKKKEAEEKKKKRTKKKEKNKNKSRKEEEE 153
           ++ K +             K    +  EEE K      KK K+  K  ++K KS K++++
Sbjct: 17  QKSKLQPISYIYSNVLVLSKEILSTFSEEENKVATTSTKKDKKEDKNNESKKKSEKKKKK 76

Query: 154 EEKKKKKKKKKKKRTKKKEEEKRKNEKA 181
           +++KK+ K + + +   K  +K K  K 
Sbjct: 77  KKEKKEPKSEGETKLGFKTPKKSKKTKK 104

Length = 413

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

 Score = 41.1 bits (97), Expect = 7e-04
 Identities = 15/54 (27%), Positives = 27/54 (50%)

Query: 51  KEEEKKKRTKKKEKNKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEE 104
           K   +KK  K  +K   K  ++++K+K+K + KK+ ++     K  K     EE
Sbjct: 381 KAPSEKKTGKPSKKVLAKRAEKKEKEKEKPKVKKRHRDTKNIGKRRKPSGTSEE 434

Length = 434

>gnl|CDD|172341 PRK13808, PRK13808, adenylate kinase; Provisional

 Score = 41.0 bits (96), Expect = 7e-04
 Identities = 34/143 (23%), Positives = 48/143 (33%), Gaps = 13/143 (9%)

Query: 52  EEEKKKRTKKKEKNKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNK 111
               KK  K         +   K K   ++  KK   K        KK A+   K  K  
Sbjct: 196 AANAKKAAKTPAAKSGAKKASAKAKSAAKKVSKK---KAAKTAVSAKKAAKTAAKAAKKA 252

Query: 112 EKNKNKSRKEEEEKKKEAEEKKKKRTKKKEKNKNKSRKEEEEEEKKKKKKKKKKKRTKKK 171
           +K   K+ K+  +  K+A +K  K   K  K   K+           K K K KK+  KK
Sbjct: 253 KKTAKKALKKAAKAVKKAAKKAAKAAAKAAKGAAKA----------TKGKAKAKKKAGKK 302

Query: 172 EEEKRKNEKAVRLTKLSAFGISG 194
                K +   +  K  A G   
Sbjct: 303 AAAGSKAKATAKAPKRGAKGKKA 325

Length = 333

>gnl|CDD|233758 TIGR02169, SMC_prok_A, chromosome segregation protein SMC, primarily archaeal type

 Score = 41.6 bits (98), Expect = 7e-04
 Identities = 26/179 (14%), Positives = 76/179 (42%), Gaps = 6/179 (3%)

Query: 2   KNKKEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKK 61
           K K+  ++ ++   + ++E    KS  +E E +  + +E      +K  +     +    
Sbjct: 734 KLKERLEELEEDLSSLEQEIENVKSELKELEARIEELEED----LHKLEEALNDLEARLS 789

Query: 62  KEKNKNKNRKEEKKKKKKRRTKKKEKNKNKS-RKEEKKKEAEEEKKKTKNKEKNKNKSRK 120
             +      +  K +++  R + + +   +   +   +KE  E++ +   +++   K + 
Sbjct: 790 HSRIPEIQAELSKLEEEVSRIEARLREIEQKLNRLTLEKEYLEKEIQELQEQRIDLKEQI 849

Query: 121 EEEEKKKEAEEKKKKRTKKKEKNKNKSRKEEEEEEKKKKKKKKKKKRTKKKEEEKRKNE 179
           +  EK+ E    KK+  +++ +   ++   + E      KK++ +   + +E E++  E
Sbjct: 850 KSIEKEIENLNGKKEELEEELEEL-EAALRDLESRLGDLKKERDELEAQLRELERKIEE 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|218752 pfam05793, TFIIF_alpha, Transcription initiation factor IIF, alpha subunit (TFIIF-alpha)

 Score = 41.5 bits (97), Expect = 7e-04
 Identities = 31/198 (15%), Positives = 78/198 (39%), Gaps = 16/198 (8%)

Query: 2   KNKKEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKK 61
             + ++ K K      + + +++    E+ +E+++KKK+K      K   +++K KR   
Sbjct: 207 GGRGKDLKIKDLEGDDEDDGDESDKGGEDGDEEKSKKKKKKLAKNKKKLDDDKKGKRGGD 266

Query: 62  KEKNKNKNRKEEKKKKKKRRTKKKEKNKNK-SRKEEKKKEAEEEKKKTKNKEKNKNKSRK 120
            + ++  +   + + +++        + N    +E+K       K + +  E ++    +
Sbjct: 267 DDADEYDSDDGDDEGREEDYISDSSASGNDPEEREDKLSPEIPAKPEIEQDEDSEESEEE 326

Query: 121 EEEEKKKEAEEKKKKRTKKKEKNKNKSRKEEEEEE---------------KKKKKKKKKK 165
           + EE+   +++ KK +  K +KN       +  ++                 KK+K+ KK
Sbjct: 327 KNEEEGGLSKKGKKLKKLKGKKNGLDKDDSDSGDDSDDSDIDGEDSVSLVTAKKQKEPKK 386

Query: 166 KRTKKKEEEKRKNEKAVR 183
           +           N    R
Sbjct: 387 EEPVDSNPSSPGNSGPAR 404

Transcription initiation factor IIF, alpha subunit (TFIIF-alpha) or RNA polymerase II-associating protein 74 (RAP74) is the large subunit of transcription factor IIF (TFIIF), which is essential for accurate initiation and stimulates elongation by RNA polymerase II. Length = 528

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

 Score = 41.3 bits (97), Expect = 7e-04
 Identities = 19/82 (23%), Positives = 46/82 (56%)

Query: 99  KEAEEEKKKTKNKEKNKNKSRKEEEEKKKEAEEKKKKRTKKKEKNKNKSRKEEEEEEKKK 158
           K  EE K  T      + +  KE  +K ++  +K  +   + + ++    K +EE+ K++
Sbjct: 351 KLYEEVKSNTDLSGDKRQELLKEYNKKLQDYTKKLGEVKDETDASEEAEAKAKEEKLKQE 410

Query: 159 KKKKKKKKRTKKKEEEKRKNEK 180
           + +KK+K++  + +E+++K+E+
Sbjct: 411 ENEKKQKEQADEDKEKRQKDER 432

Length = 434

>gnl|CDD|236944 PRK11642, PRK11642, exoribonuclease R; Provisional

 Score = 41.7 bits (98), Expect = 7e-04
 Identities = 23/89 (25%), Positives = 38/89 (42%), Gaps = 5/89 (5%)

Query: 54  EKKKRTKKKEKNKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEK 113
           E+  R   K   +   + +  KK  KRR   K+ N         +K+A+ +  K     K
Sbjct: 728 ERAPRNVGKTAREKAKKGDAGKKGGKRRQVGKKVNFEPDSAFRGEKKAKPKAAK-----K 782

Query: 114 NKNKSRKEEEEKKKEAEEKKKKRTKKKEK 142
           +  K++K   + +K A   K KR  KK+ 
Sbjct: 783 DARKAKKPSAKTQKIAAATKAKRAAKKKV 811

Length = 813

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

 Score = 40.5 bits (95), Expect = 7e-04
 Identities = 21/128 (16%), Positives = 39/128 (30%), Gaps = 3/128 (2%)

Query: 51  KEEEKKKRTKKKEKNKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKN 110
             EE +   +  E+      + E   +      K++    K  K+ K K   + K K K 
Sbjct: 52  PTEEPQPEPEPPEEQPKPPTEPETPPEPTPPKPKEKPKPEKKPKKPKPKPKPKPKPKPKV 111

Query: 111 KEKNKNKSRKEEEEKKKEAEEKKKKRTKKKEKNKNKSRKEEEEEEKKKKKKKKKKKRTKK 170
           K + K K    +   K  A   +  R        + S              ++  +R  +
Sbjct: 112 KPQPKPKKPPSKTAAKAPAAPNQPARP---PSAASASGAATGPSASYLSGLRRAIRRAPR 168

Query: 171 KEEEKRKN 178
              + R  
Sbjct: 169 YPAQARAR 176

Length = 244

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

 Score = 41.6 bits (98), Expect = 8e-04
 Identities = 41/203 (20%), Positives = 76/203 (37%), Gaps = 34/203 (16%)

Query: 6    EEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEE------------ 53
            +E KK    R K   K K++    EEEE   +  E + ++  +                 
Sbjct: 1038 KELKKLGYVRFKDIIKKKSEKITAEEEEGAEEDDEADDEDDEEELGAAVSYDYLLSMPIW 1097

Query: 54   ----------EKKKRTKKKEKNKNKNR------KEEKKKKKKRRTKKKEKNKNKSRKEEK 97
                        +   K+KE  K KN        E+  K ++   +++E  + +  KE++
Sbjct: 1098 SLTKEKVEKLNAELEKKEKELEKLKNTTPKDMWLEDLDKFEEALEEQEEVEEKEIAKEQR 1157

Query: 98   KKEAEEEKKKTKNKEKNKNKSRKEEEEKKKEAEEKKKKRTKKKEKNKNKSRKEEEEEEKK 157
                   K KTK K     K + +++EKKK+     K +      N  +   +E+ +   
Sbjct: 1158 L------KSKTKGKASKLRKPKLKKKEKKKKKSSADKSKKASVVGNSKRVDSDEKRKLDD 1211

Query: 158  KKKKKKKKKRTKKKEEEKRKNEK 180
            K   KK       +E+++ +  K
Sbjct: 1212 KPDNKKSNSSGSDQEDDEEQKTK 1234

Length = 1388

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

 Score = 41.5 bits (97), Expect = 8e-04
 Identities = 42/186 (22%), Positives = 86/186 (46%), Gaps = 1/186 (0%)

Query: 2   KNKKEEKKKKKKR-RTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTK 60
           K +KE KK+K++    +K+ K     R+ EEEE+   +K + K  + +     +KK  ++
Sbjct: 326 KLEKELKKEKEEIEELEKELKELEIKREAEEEEEEQLEKLQEKLEQLEEELLAKKKLESE 385

Query: 61  KKEKNKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRK 120
           +         +E + K ++ +  K     ++  ++  K+E +EE K  +  E++    + 
Sbjct: 386 RLSSAAKLKEEELELKNEEEKEAKLLLELSEQEEDLLKEEKKEELKIVEELEESLETKQG 445

Query: 121 EEEEKKKEAEEKKKKRTKKKEKNKNKSRKEEEEEEKKKKKKKKKKKRTKKKEEEKRKNEK 180
           +  E+K+E E++  K  K K + K      +E +  K  ++ +     +K EE  +K  K
Sbjct: 446 KLTEEKEELEKQALKLLKDKLELKKSEDLLKETKLVKLLEQLELLLLRQKLEEASQKESK 505

Query: 181 AVRLTK 186
           A     
Sbjct: 506 AREGLA 511

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|235250 PRK04195, PRK04195, replication factor C large subunit; Provisional

 Score = 41.1 bits (97), Expect = 8e-04
 Identities = 20/75 (26%), Positives = 45/75 (60%), Gaps = 6/75 (8%)

Query: 2   KNKKEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKK 61
           K  K+ KK  +K   K++E+      K+E+++K    K+K ++ + +  K+EE+K+  ++
Sbjct: 407 KATKKIKKIVEKAEKKREEE------KKEKKKKAFAGKKKEEEEEEEKEKKEEEKEEEEE 460

Query: 62  KEKNKNKNRKEEKKK 76
           + + + +  +E+KKK
Sbjct: 461 EAEEEKEEEEEKKKK 475

Length = 482

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

 Score = 41.1 bits (97), Expect = 8e-04
 Identities = 23/78 (29%), Positives = 33/78 (42%), Gaps = 4/78 (5%)

Query: 26  SRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKKKEKNKNKNRKEEKKKKKKRRTKKK 85
            R  EE  K     E   K K  S K   K  +  KK   K   +KE K+K+K +  K+ 
Sbjct: 361 ERYIEEPLKARVIDELRPKTKAPSEK---KTGKPSKKVLAKRAEKKE-KEKEKPKVKKRH 416

Query: 86  EKNKNKSRKEEKKKEAEE 103
              KN  ++ +    +EE
Sbjct: 417 RDTKNIGKRRKPSGTSEE 434

Length = 434

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

 Score = 41.1 bits (97), Expect = 8e-04
 Identities = 12/54 (22%), Positives = 26/54 (48%)

Query: 98  KKEAEEEKKKTKNKEKNKNKSRKEEEEKKKEAEEKKKKRTKKKEKNKNKSRKEE 151
           K  +E++  K   K   K   +KE+E++K + +++ +      ++ K     EE
Sbjct: 381 KAPSEKKTGKPSKKVLAKRAEKKEKEKEKPKVKKRHRDTKNIGKRRKPSGTSEE 434

Length = 434

>gnl|CDD|215521 PLN02967, PLN02967, kinase

 Score = 41.2 bits (96), Expect = 8e-04
 Identities = 28/127 (22%), Positives = 54/127 (42%), Gaps = 4/127 (3%)

Query: 5   KEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKKKEK 64
               KKK  R  K+  K       E  EE       ++     +S+K   + +R      
Sbjct: 66  GAVSKKKPTRSVKRATKKTVVEISEPLEEGSELVVNEDAALDKESKKTPRRTRRKAAAAS 125

Query: 65  NKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKEEEE 124
           +  +  K EKK +K+R+ KK +++      E +  + EE    ++     +N+S +E + 
Sbjct: 126 SDVEEEKTEKKVRKRRKVKKMDEDVEDQGSESEVSDVEE----SEFVTSLENESEEELDL 181

Query: 125 KKKEAEE 131
           +K + E+
Sbjct: 182 EKDDGED 188

Length = 581

>gnl|CDD|233758 TIGR02169, SMC_prok_A, chromosome segregation protein SMC, primarily archaeal type

 Score = 41.6 bits (98), Expect = 8e-04
 Identities = 33/180 (18%), Positives = 81/180 (45%), Gaps = 7/180 (3%)

Query: 1   CKNKKEEKKKKKKR---RTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKK 57
            + + E  K + K    R ++ E++ +K  +   + +      +  + + +  K EE+  
Sbjct: 749 LEQEIENVKSELKELEARIEELEEDLHKLEEALNDLEARLSHSRIPEIQAELSKLEEEVS 808

Query: 58  RTKKK----EKNKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEK 113
           R + +    E+  N+   E++  +K+ +  ++++   K + +  +KE E    K +  E+
Sbjct: 809 RIEARLREIEQKLNRLTLEKEYLEKEIQELQEQRIDLKEQIKSIEKEIENLNGKKEELEE 868

Query: 114 NKNKSRKEEEEKKKEAEEKKKKRTKKKEKNKNKSRKEEEEEEKKKKKKKKKKKRTKKKEE 173
              +      + +    + KK+R + + + +   RK EE E + +KK+K+  +   K E 
Sbjct: 869 ELEELEAALRDLESRLGDLKKERDELEAQLRELERKIEELEAQIEKKRKRLSELKAKLEA 928

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|221641 pfam12569, NARP1, NMDA receptor-regulated protein 1

 Score = 41.1 bits (97), Expect = 8e-04
 Identities = 17/71 (23%), Positives = 32/71 (45%), Gaps = 1/71 (1%)

Query: 104 EKKKTKNKEKNKNKSRKEEEEKKKEAEEKKKKRTKKKEKNKNKSRKEEEEEEKKKKKKKK 163
           +    + +E+          E+KK   +K++K  KK EK + +    +++ E   KK K 
Sbjct: 390 KPLLAEGEEEEGENGNLSPAERKK-LRKKQRKAEKKAEKEEAEKAAAKKKAEAAAKKAKG 448

Query: 164 KKKRTKKKEEE 174
               TKK + +
Sbjct: 449 PDGETKKVDPD 459

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 = 41.2 bits (97), Expect = 9e-04
 Identities = 29/178 (16%), Positives = 90/178 (50%), Gaps = 1/178 (0%)

Query: 4   KKEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKKKE 63
           + + +K +++ ++ K E    +   EE   +  + + + ++ K +    EE+ ++ + + 
Sbjct: 680 EAQLEKLEEELKSLKNELRSLEDLLEELRRQLEELERQLEELKRELAALEEELEQLQSRL 739

Query: 64  KNKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKEEE 123
           +   +  +E +++ ++ + + +E  +     EE   + +EE ++ + K +   +  +E E
Sbjct: 740 EELEEELEELEEELEELQERLEELEEELESLEEALAKLKEEIEELEEKRQALQEELEELE 799

Query: 124 EKKKEAEEKK-KKRTKKKEKNKNKSRKEEEEEEKKKKKKKKKKKRTKKKEEEKRKNEK 180
           E+ +EAE +      + +   + + R E+E EE +++ ++ ++K  + +EE +   ++
Sbjct: 800 EELEEAERRLDALERELESLEQRRERLEQEIEELEEEIEELEEKLDELEEELEELEKE 857

Length = 1163

>gnl|CDD|233758 TIGR02169, SMC_prok_A, chromosome segregation protein SMC, primarily archaeal type

 Score = 41.2 bits (97), Expect = 9e-04
 Identities = 44/179 (24%), Positives = 89/179 (49%), Gaps = 13/179 (7%)

Query: 9   KKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKKKEKNKNK 68
           K+K+    +K+   +  +  EEE EK T++  + +K     R EE ++   +  +K K+ 
Sbjct: 230 KEKEALERQKEAIERQLASLEEELEKLTEEISELEK-----RLEEIEQLLEELNKKIKDL 284

Query: 69  NRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKEEEEKKKE 128
             +E+ + K+K    + E    +    EK++E E+ +++    E   +K   E EE ++E
Sbjct: 285 GEEEQLRVKEKIGELEAEIASLERSIAEKERELEDAEERLAKLEAEIDKLLAEIEELERE 344

Query: 129 AEEKKKKRTK--------KKEKNKNKSRKEEEEEEKKKKKKKKKKKRTKKKEEEKRKNE 179
            EE++K+R K        K+E    ++  EE ++E  + + + K  R K ++ ++  NE
Sbjct: 345 IEEERKRRDKLTEEYAELKEELEDLRAELEEVDKEFAETRDELKDYREKLEKLKREINE 403

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|236944 PRK11642, PRK11642, exoribonuclease R; Provisional

 Score = 41.3 bits (97), Expect = 9e-04
 Identities = 20/82 (24%), Positives = 37/82 (45%), Gaps = 3/82 (3%)

Query: 108 TKNKEKNKNKSRKEEEEKKKEAEEKKKKRTKKKEKNKNKSRKEEEEEEKKKKKKKKKKKR 167
           ++   +N  K+ +E+ +K    ++  K+R   K+ N         E++ K K  KK  ++
Sbjct: 727 SERAPRNVGKTAREKAKKGDAGKKGGKRRQVGKKVNFEPDSAFRGEKKAKPKAAKKDARK 786

Query: 168 TKKKEEEKRK---NEKAVRLTK 186
            KK   + +K     KA R  K
Sbjct: 787 AKKPSAKTQKIAAATKAKRAAK 808

Length = 813

>gnl|CDD|130141 TIGR01069, mutS2, MutS2 family protein

 Score = 41.3 bits (97), Expect = 9e-04
 Identities = 32/152 (21%), Positives = 63/152 (41%), Gaps = 2/152 (1%)

Query: 19  KEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKKKEKNKNKNRKEEKKKKK 78
           + K      KEE      K     K+ + K+   E+  K  +K +K   +  +E K++++
Sbjct: 501 QAKTFYGEFKEEINVLIEKLSALEKELEQKNEHLEKLLKEQEKLKKELEQEMEELKERER 560

Query: 79  KRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKEEEEKKKEAEEKKKKRTK 138
            ++ + +++ +   +    KKE E   ++ K K+ +K K  K  E+  K  E K+K   K
Sbjct: 561 NKKLELEKEAQEALKA--LKKEVESIIRELKEKKIHKAKEIKSIEDLVKLKETKQKIPQK 618

Query: 139 KKEKNKNKSRKEEEEEEKKKKKKKKKKKRTKK 170
                 +K   +       +K K  +     K
Sbjct: 619 PTNFQADKIGDKVRIRYFGQKGKIVQILGGNK 650

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|217393 pfam03154, Atrophin-1, Atrophin-1 family

 Score = 41.2 bits (96), Expect = 9e-04
 Identities = 18/59 (30%), Positives = 33/59 (55%), Gaps = 7/59 (11%)

Query: 83  KKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKEEEEKKKEAEEKKKKRTKKKE 141
           KK+E+   K+++E ++K  EE       +E+ K K ++ E E+++EAE   K  +   E
Sbjct: 579 KKREEAVEKAKREAEQKAREE-------REREKEKEKEREREREREAERAAKASSSSHE 630

Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteristic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity. Length = 979

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

 Score = 41.0 bits (96), Expect = 0.001
 Identities = 32/183 (17%), Positives = 76/183 (41%), Gaps = 5/183 (2%)

Query: 2   KNKKEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKK 61
           + +K+ ++ + +   KK+E+ + KSR ++  +K+   K+K    + K R+   +  + K 
Sbjct: 149 EKEKKVEEPRDREEEKKRERVRAKSRPKKPPKKKPPNKKKEPPEEEKQRQAAREAVKGKP 208

Query: 62  KEKNKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNK---- 117
           +E + N+ R++E+   K R T      +++SR+  +         K  +   +       
Sbjct: 209 EEPDVNEEREKEEDDGKDRETTTSPMEEDESRQSSEISRRSSSSLKKPDPSPSMASPETR 268

Query: 118 -SRKEEEEKKKEAEEKKKKRTKKKEKNKNKSRKEEEEEEKKKKKKKKKKKRTKKKEEEKR 176
            S K  E + + +      R         + +++E     +  +   K       E +K 
Sbjct: 269 ESSKRTETRPRTSLRPPSARPASARPAPPRVKRKEIVTVLQDAQGVGKIVSNVILEGKKS 328

Query: 177 KNE 179
           ++E
Sbjct: 329 EDE 331

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 = 41.2 bits (97), Expect = 0.001
 Identities = 40/157 (25%), Positives = 67/157 (42%), Gaps = 1/157 (0%)

Query: 38   KKEKNKKNKNKSRKEEEKKKRTKKKEKNKNKNRKEEKKKKKKRRTKKKEKNK-NKSRKEE 96
            K EK      K  KE EK K T  K+       K E+  +++   ++KE  K  + + + 
Sbjct: 1103 KVEKLNAELEKKEKELEKLKNTTPKDMWLEDLDKFEEALEEQEEVEEKEIAKEQRLKSKT 1162

Query: 97   KKKEAEEEKKKTKNKEKNKNKSRKEEEEKKKEAEEKKKKRTKKKEKNKNKSRKEEEEEEK 156
            K K ++  K K K KEK K KS  ++ +K       K+  + +K K  +K   ++     
Sbjct: 1163 KGKASKLRKPKLKKKEKKKKKSSADKSKKASVVGNSKRVDSDEKRKLDDKPDNKKSNSSG 1222

Query: 157  KKKKKKKKKKRTKKKEEEKRKNEKAVRLTKLSAFGIS 193
              ++  +++K   KK   KR   K    +K S     
Sbjct: 1223 SDQEDDEEQKTKPKKSSVKRLKSKKNNSSKSSEDNDE 1259

Length = 1388

>gnl|CDD|235334 PRK05035, PRK05035, electron transport complex protein RnfC; Provisional

 Score = 40.7 bits (96), Expect = 0.001
 Identities = 29/167 (17%), Positives = 59/167 (35%), Gaps = 18/167 (10%)

Query: 5   KEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTK----------KKEKNKKNKNKSRKEEE 54
                 ++ R+ + + +   K      + K+            KK   +    ++ +E +
Sbjct: 517 SAVIAAREARKAQARARQAEKQAAAAADPKKAAVAAAIARAKAKKAAQQAANAEAEEEVD 576

Query: 55  KKKRTKKKEKNKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKK--EAEEEKKKTKNKE 112
            KK        + K +K  ++          E  +  +  + KK    A   + K K  E
Sbjct: 577 PKKAAVAAAIARAKAKKAAQQ------AASAEPEEQVAEVDPKKAAVAAAIARAKAKKAE 630

Query: 113 KNKNKSRKEEEEKKKEAEEKKKKRTKKKEKNKNKSRKEEEEEEKKKK 159
           +  N   +E  + +K A      R K ++  + ++  E EE E  KK
Sbjct: 631 QQANAEPEEPVDPRKAAVAAAIARAKARKAAQQQANAEPEEAEDPKK 677

Length = 695

>gnl|CDD|223496 COG0419, SbcC, ATPase involved in DNA repair [DNA replication, recombination, and repair]

 Score = 41.3 bits (97), Expect = 0.001
 Identities = 37/185 (20%), Positives = 88/185 (47%), Gaps = 6/185 (3%)

Query: 2   KNKKEEKKKKKKRRTKKKEKNKNKSRKE-EEEEKRTKKKEKNKKNKNKSRKEEEKKKRTK 60
           K  +E ++++++   +++ +   +   E EEE++R ++ +           E  K +  +
Sbjct: 216 KKLEEIQEEQEEEELEQEIEALEERLAELEEEKERLEELKARLLEIESLELEALKIREEE 275

Query: 61  KKEKNKNKNRKEEKKKKKKRRTKKKEKNKN-----KSRKEEKKKEAEEEKKKTKNKEKNK 115
            +E  +     EEK ++ +   ++ E+ +      ++  EE ++  E+ K   +  EK +
Sbjct: 276 LRELERLLEELEEKIERLEELEREIEELEEELEGLRALLEELEELLEKLKSLEERLEKLE 335

Query: 116 NKSRKEEEEKKKEAEEKKKKRTKKKEKNKNKSRKEEEEEEKKKKKKKKKKKRTKKKEEEK 175
            K  K E E ++ AEEK +     +E+ K    + EE E++ +K  ++ K+  +  +E K
Sbjct: 336 EKLEKLESELEELAEEKNELAKLLEERLKELEERLEELEKELEKALERLKQLEEAIQELK 395

Query: 176 RKNEK 180
            +  +
Sbjct: 396 EELAE 400

Length = 908

>gnl|CDD|223496 COG0419, SbcC, ATPase involved in DNA repair [DNA replication, recombination, and repair]

 Score = 40.5 bits (95), Expect = 0.001
 Identities = 38/189 (20%), Positives = 87/189 (46%), Gaps = 6/189 (3%)

Query: 1   CKNKKEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTK 60
            + +  E  + ++   ++ E+   K     EE +  K+K + ++ K + R+ E++ +  K
Sbjct: 513 LEEELIELLELEEALKEELEEKLEKLENLLEELEELKEKLQLQQLKEELRQLEDRLQELK 572

Query: 61  KKEKNKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRK 120
           +  +     R  +++ ++ R   K+ K K K  +E   +  E  +    ++ +N      
Sbjct: 573 ELLEELRLLRTRKEELEELRERLKELKKKLKELEERLSQLEELLQSLELSEAEN------ 626

Query: 121 EEEEKKKEAEEKKKKRTKKKEKNKNKSRKEEEEEEKKKKKKKKKKKRTKKKEEEKRKNEK 180
           E EE ++E E + +K   + E  +      EE EEK ++ + + ++  ++ E E++  EK
Sbjct: 627 ELEEAEEELESELEKLNLQAELEELLQAALEELEEKVEELEAEIRRELQRIENEEQLEEK 686

Query: 181 AVRLTKLSA 189
              L +L  
Sbjct: 687 LEELEQLEE 695

Length = 908

>gnl|CDD|188306 TIGR03319, RNase_Y, ribonuclease Y

 Score = 40.7 bits (96), Expect = 0.001
 Identities = 33/120 (27%), Positives = 56/120 (46%), Gaps = 3/120 (2%)

Query: 73  EKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNK-NKSRKEEEEKKKEAEE 131
           EKK        K+   + K   E  KKEA  E K+  +K + +  +  KE   + +  E 
Sbjct: 24  EKKLGSAEELAKRIIEEAKKEAETLKKEALLEAKEEVHKLRAELERELKERRNELQRLER 83

Query: 132 KKKKRTKKKEKNKNKSRKEEEEEEKKKKKKKKKKKRTKKKEE--EKRKNEKAVRLTKLSA 189
           +  +R +  ++      K+EE  EKK+K+   K+K   +KEE  E+   E+   L ++S 
Sbjct: 84  RLLQREETLDRKMESLDKKEENLEKKEKELSNKEKNLDEKEEELEELIAEQREELERISG 143

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

 Score = 40.3 bits (95), Expect = 0.001
 Identities = 18/68 (26%), Positives = 34/68 (50%), Gaps = 10/68 (14%)

Query: 102 EEEKKKTKN-KEKNKNKSRKEEEEKKKEAEEKKKKRTKKKEKNKNKSRKEEEEEEKKKKK 160
           +E + KTK   EK   K  K+   K+ E +EK+K++ K K+++++          K   K
Sbjct: 374 DELRPKTKAPSEKKTGKPSKKVLAKRAEKKEKEKEKPKVKKRHRDT---------KNIGK 424

Query: 161 KKKKKKRT 168
           ++K    +
Sbjct: 425 RRKPSGTS 432

Length = 434

>gnl|CDD|240246 PTZ00053, PTZ00053, methionine aminopeptidase 2; Provisional

 Score = 40.9 bits (96), Expect = 0.001
 Identities = 20/76 (26%), Positives = 37/76 (48%), Gaps = 3/76 (3%)

Query: 108 TKNKEKNKNKSRKEEEEKKKEAEEKKKKRTKKKEK---NKNKSRKEEEEEEKKKKKKKKK 164
             N+       +++++ K+K  ++K KK  K  +       +   E +E E K+  KKKK
Sbjct: 1   AMNENGENEVKQQKQQNKQKGTKKKNKKSKKDVDDDDAFLAELISENQEAENKQNNKKKK 60

Query: 165 KKRTKKKEEEKRKNEK 180
           KK+ KKK++   +   
Sbjct: 61  KKKKKKKKKNLGEAYD 76

Length = 470

>gnl|CDD|222447 pfam13904, DUF4207, Domain of unknown function (DUF4207)

 Score = 40.1 bits (94), Expect = 0.001
 Identities = 34/153 (22%), Positives = 77/153 (50%), Gaps = 17/153 (11%)

Query: 47  NKSRKEEEKKKRTKKKEKNKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKK 106
             SR  +E K   + +E  +N    ++ +++KK +   +EK K    +E +K+  E E +
Sbjct: 71  TYSRSLKEVKLERQAQEAYENWLSAKQAQRQKKLQKLLEEKQK----QEREKEREEAELR 126

Query: 107 KTKNKEKNKNKSRKEEEEKKKEAEEKKKKRTKK-------------KEKNKNKSRKEEEE 153
           +   KEK +   R++ ++  K+   K KK   +             +  ++ +++K  +E
Sbjct: 127 QRLAKEKYEEWCRQKAQQAAKQRTPKHKKEAAESASSSLSGSAKPERNVSQEEAKKRLQE 186

Query: 154 EEKKKKKKKKKKKRTKKKEEEKRKNEKAVRLTK 186
            E KK K++++K+  +++++ K++ E+  R  K
Sbjct: 187 WELKKLKQQQQKREEERRKQRKKQQEEEERKQK 219

This family is found in eukaryotes; it has several conserved tryptophan residues. The function is not known. Length = 261

>gnl|CDD|233758 TIGR02169, SMC_prok_A, chromosome segregation protein SMC, primarily archaeal type

 Score = 40.8 bits (96), Expect = 0.001
 Identities = 35/199 (17%), Positives = 90/199 (45%), Gaps = 17/199 (8%)

Query: 2   KNKKEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKK 61
           +N+ +E  ++    ++K  + + +  + E+EE++ K++ +  +    S ++E +  +++ 
Sbjct: 701 ENRLDELSQELSDASRKIGEIEKEIEQLEQEEEKLKERLEELEEDLSSLEQEIENVKSEL 760

Query: 62  KEKNKNKNRKEEKKKK-----------------KKRRTKKKEKNKNKSRKEEKKKEAEEE 104
           KE        EE   K                  + + +  +  +  SR E + +E E++
Sbjct: 761 KELEARIEELEEDLHKLEEALNDLEARLSHSRIPEIQAELSKLEEEVSRIEARLREIEQK 820

Query: 105 KKKTKNKEKNKNKSRKEEEEKKKEAEEKKKKRTKKKEKNKNKSRKEEEEEEKKKKKKKKK 164
             +   +++   K  +E +E++ + +E+ K   K+ E    K  + EEE E+ +   +  
Sbjct: 821 LNRLTLEKEYLEKEIQELQEQRIDLKEQIKSIEKEIENLNGKKEELEEELEELEAALRDL 880

Query: 165 KKRTKKKEEEKRKNEKAVR 183
           + R    ++E+ + E  +R
Sbjct: 881 ESRLGDLKKERDELEAQLR 899

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|191187 pfam05087, Rota_VP2, Rotavirus VP2 protein

 Score = 40.7 bits (95), Expect = 0.001
 Identities = 19/114 (16%), Positives = 54/114 (47%)

Query: 89  KNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKEEEEKKKEAEEKKKKRTKKKEKNKNKSR 148
           +N+        +  +EK   K  +KN+ + +++  +KK+E          K++ ++   +
Sbjct: 4   RNRREANINNNDRMQEKDDEKQDQKNRMELKEKVLDKKEEVVTDNVDSPVKEQSSQENLK 63

Query: 149 KEEEEEEKKKKKKKKKKKRTKKKEEEKRKNEKAVRLTKLSAFGISGYLLQWIRN 202
             +E ++  K++ K+  +  K KEE +++ +  +    + +F     +L+ + +
Sbjct: 64  IADEVKKSTKEESKQLLEVLKTKEEHQKEIQYEILQKTIPSFEPKESILKKLED 117

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|177089 CHL00189, infB, translation initiation factor 2; Provisional

 Score = 41.0 bits (96), Expect = 0.001
 Identities = 29/126 (23%), Positives = 52/126 (41%), Gaps = 5/126 (3%)

Query: 9   KKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKK---RTKKKEKN 65
            K    + + +   K+     +  +K  +K +K  K  NK+   ++ KK   + KKK K 
Sbjct: 26  LKHSSYKIRLESDIKDSLLNLDINKKLHEKLDKKNKKFNKTDDLKDSKKTKLKQKKKIKK 85

Query: 66  K-NKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKEEEE 124
           K + +   +     K  +K+       S   + K + E+ KKK     K+ NK +K+   
Sbjct: 86  KLHIDDDYDNFFDSKNNSKQFAGPLAISLMRKPKPKTEKLKKKITVN-KSTNKKKKKVLS 144

Query: 125 KKKEAE 130
            K E  
Sbjct: 145 SKDELI 150

Length = 742

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

 Score = 40.7 bits (96), Expect = 0.001
 Identities = 17/67 (25%), Positives = 31/67 (46%)

Query: 37  KKKEKNKKNKNKSRKEEEKKKRTKKKEKNKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEE 96
             + + ++ +N +    E+KK  KK+ K + K  KEE +K   ++  +    K K    E
Sbjct: 393 LAEGEEEEGENGNLSPAERKKLRKKQRKAEKKAEKEEAEKAAAKKKAEAAAKKAKGPDGE 452

Query: 97  KKKEAEE 103
            KK   +
Sbjct: 453 TKKVDPD 459

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|219408 pfam07423, DUF1510, Protein of unknown function (DUF1510)

 Score = 39.3 bits (92), Expect = 0.001
 Identities = 17/77 (22%), Positives = 40/77 (51%)

Query: 97  KKKEAEEEKKKTKNKEKNKNKSRKEEEEKKKEAEEKKKKRTKKKEKNKNKSRKEEEEEEK 156
              +A  ++++ K  +  +    +E +E++KEA   + K  K   + +++  +EE EEE 
Sbjct: 40  PSDQAAADEQEAKKSDDQETAEIEEVKEEEKEAANSEDKEDKGDAEKEDEESEEENEEED 99

Query: 157 KKKKKKKKKKRTKKKEE 173
           ++   + +K+  +K E 
Sbjct: 100 EESSDENEKETEEKTES 116

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|130141 TIGR01069, mutS2, MutS2 family protein

 Score = 41.3 bits (97), Expect = 0.001
 Identities = 28/131 (21%), Positives = 60/131 (45%), Gaps = 9/131 (6%)

Query: 51  KEEEKKKRTKKKEKNKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKN 110
           K    +K  ++K ++  K  KE++K KK+   + +E      R+  KK E E+E ++   
Sbjct: 519 KLSALEKELEQKNEHLEKLLKEQEKLKKELEQEMEELK---ERERNKKLELEKEAQEALK 575

Query: 111 KEKNKNKSRKEEEEKKKEAEEKKKKRTKKKEKNKNKSRKEEEEEEKKKKKKKKKKKRTKK 170
                   +KE E   +E +EKK  + K+ +  ++  + +E +++  +K    +  +   
Sbjct: 576 A------LKKEVESIIRELKEKKIHKAKEIKSIEDLVKLKETKQKIPQKPTNFQADKIGD 629

Query: 171 KEEEKRKNEKA 181
           K   +   +K 
Sbjct: 630 KVRIRYFGQKG 640

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|233191 TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger

 Score = 41.1 bits (96), Expect = 0.001
 Identities = 33/151 (21%), Positives = 71/151 (47%), Gaps = 10/151 (6%)

Query: 5   KEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKKKEK 64
           K E + +  R+  + E       KE+E+E   +  E  +    K  +  E K   + + +
Sbjct: 752 KHEVETEGDRKETEHEGETEAEGKEDEDEGEIQAGEDGE---MKGDEGAEGKVEHEGETE 808

Query: 65  NKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKEEEE 124
              K+  E + + +   T+ K++   +    E + EA++++K       +     +EEEE
Sbjct: 809 AGEKDEHEGQSETQADDTEVKDETGEQELNAENQGEAKQDEKGVDGGGGSDGGDSEEEEE 868

Query: 125 KKKEAEEKKKKRTKKKEKNKNKSRKEEEEEE 155
           +++E EE++++  +++E       +EEE EE
Sbjct: 869 EEEEEEEEEEEEEEEEE-------EEEENEE 892

[Transport and binding proteins, Cations and iron carrying compounds]. Length = 1096

>gnl|CDD|233191 TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger

 Score = 40.7 bits (95), Expect = 0.001
 Identities = 34/179 (18%), Positives = 77/179 (43%), Gaps = 14/179 (7%)

Query: 7   EKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKKKEKNK 66
           E +  ++    + E       K E E +  +K+ +++       KE+E +   +  E  +
Sbjct: 731 EIETGEEGEEVEDEGEGEAEGKHEVETEGDRKETEHEGETEAEGKEDEDEGEIQAGEDGE 790

Query: 67  NKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKN-KNKSRKEEEEK 125
            K  +  + K +     +  +      + E + +  E K +T  +E N +N+   +++EK
Sbjct: 791 MKGDEGAEGKVEHEGETEAGEKDEHEGQSETQADDTEVKDETGEQELNAENQGEAKQDEK 850

Query: 126 KKEAEEKKKKRTKKKEKNKNKSRKEEEEEEKKKKKKKKKKKRTKKKEEEKRKNEKAVRL 184
             +          ++E+ + +  +EEEEEE             +++EEE+ +NE+ + L
Sbjct: 851 GVDGGGGSDGGDSEEEEEEEEEEEEEEEEE-------------EEEEEEEEENEEPLSL 896

[Transport and binding proteins, Cations and iron carrying compounds]. Length = 1096

>gnl|CDD|227594 COG5269, ZUO1, Ribosome-associated chaperone zuotin [Translation, ribosomal structure and biogenesis / Posttranslational modification, protein turnover, chaperones]

 Score = 40.8 bits (95), Expect = 0.001
 Identities = 32/110 (29%), Positives = 49/110 (44%), Gaps = 2/110 (1%)

Query: 37  KKKEKNKKNKNKSRKEEEKKKRTKKKEKNKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEE 96
           K +EK  K KN+     ++  +  KK   + K+ KE++K+ KK R  ++E          
Sbjct: 202 KNREKRAKLKNQDNARLKRLVQIAKKRDPRIKSFKEQEKEMKKIRKWEREAGARLKALAA 261

Query: 97  KKKEAEEEKKKTKNKEKNKNKSRKEEEEKKKEAEEKKKKRTKKKEKNKNK 146
            K +AE + K     E     S    ++K KE  +K  K  KK  KN  K
Sbjct: 262 LKGKAEAKNKAEI--EAEALASATAVKKKAKEVMKKALKMEKKAIKNAAK 309

Length = 379

>gnl|CDD|217502 pfam03343, SART-1, SART-1 family

 Score = 40.9 bits (96), Expect = 0.001
 Identities = 28/166 (16%), Positives = 69/166 (41%), Gaps = 1/166 (0%)

Query: 31  EEEKRTKKKEKNKKNKNKSRKEEEKKKRTKKKEKNKNKNRKEEKKKKKKRRTKKKEKNKN 90
           E+EK  K  E  KK  +    +++K  +     K  ++  + +KKK     T     + +
Sbjct: 175 EKEKDKKNLELKKKKPDYDPDDDDKFNKRSILSK-YDEEIEGKKKKSDNLFTLDSGGSTD 233

Query: 91  KSRKEEKKKEAEEEKKKTKNKEKNKNKSRKEEEEKKKEAEEKKKKRTKKKEKNKNKSRKE 150
              ++++++  ++ K    + + +  ++   +     E  + KK + KKK+K K +   +
Sbjct: 234 DEAEKKRQEVKKKLKINNVSLDDDSTETPASDYYDVSEMVKFKKPKKKKKKKKKRRKDLD 293

Query: 151 EEEEEKKKKKKKKKKKRTKKKEEEKRKNEKAVRLTKLSAFGISGYL 196
           E+E E + +        ++K  EE+    +     +        ++
Sbjct: 294 EDELEPEAEGLGSSDSGSRKDVEEENARLEDSPKKRKEEQEDDDFV 339

SART-1 is a protein involved in cell cycle arrest and pre-mRNA splicing. It has been shown to be a component of U4/U6 x U5 tri-snRNP complex in human, Schizosaccharomyces pombe and Saccharomyces cerevisiae. SART-1 is a known tumour antigen in a range of cancers recognised by T cells. Length = 603

>gnl|CDD|217502 pfam03343, SART-1, SART-1 family

 Score = 40.5 bits (95), Expect = 0.001
 Identities = 32/119 (26%), Positives = 55/119 (46%)

Query: 62  KEKNKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKE 121
            EK K+K   E KKKK        +K   +S   +  +E E +KKK+ N     +    +
Sbjct: 174 VEKEKDKKNLELKKKKPDYDPDDDDKFNKRSILSKYDEEIEGKKKKSDNLFTLDSGGSTD 233

Query: 122 EEEKKKEAEEKKKKRTKKKEKNKNKSRKEEEEEEKKKKKKKKKKKRTKKKEEEKRKNEK 180
           +E +KK  E KKK +      + + +     +     +  K KK + KKK+++KR+ + 
Sbjct: 234 DEAEKKRQEVKKKLKINNVSLDDDSTETPASDYYDVSEMVKFKKPKKKKKKKKKRRKDL 292

SART-1 is a protein involved in cell cycle arrest and pre-mRNA splicing. It has been shown to be a component of U4/U6 x U5 tri-snRNP complex in human, Schizosaccharomyces pombe and Saccharomyces cerevisiae. SART-1 is a known tumour antigen in a range of cancers recognised by T cells. Length = 603

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

 Score = 41.0 bits (96), Expect = 0.001
 Identities = 26/76 (34%), Positives = 43/76 (56%), Gaps = 3/76 (3%)

Query: 100 EAEEEKKKTKNKEKNKNKSRKEEEEKKKEAEEKKKKRTKKKEKNKNKSRKEEEEEEKKKK 159
           E+E EKK    +E  +   +K++EEK KE E KK K  +K+ K K ++++  +     KK
Sbjct: 5   ESEAEKKILTEEELER---KKKKEEKAKEKELKKLKAAQKEAKAKLQAQQASDGTNVPKK 61

Query: 160 KKKKKKKRTKKKEEEK 175
            +KK +KR  + E  +
Sbjct: 62  SEKKSRKRDVEDENPE 77

Length = 1066

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

 Score = 40.7 bits (95), Expect = 0.001
 Identities = 23/86 (26%), Positives = 40/86 (46%), Gaps = 12/86 (13%)

Query: 70  RKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKEEEEKKKEA 129
            + E + +KK  T+++ + K K  KEEK KE E +K K   KE           + K +A
Sbjct: 2   SRTESEAEKKILTEEELERKKK--KEEKAKEKELKKLKAAQKEA----------KAKLQA 49

Query: 130 EEKKKKRTKKKEKNKNKSRKEEEEEE 155
           ++        K+  K   +++ E+E 
Sbjct: 50  QQASDGTNVPKKSEKKSRKRDVEDEN 75

Length = 1066

>gnl|CDD|184287 PRK13735, PRK13735, conjugal transfer mating pair stabilization protein TraG; Provisional

 Score = 40.9 bits (96), Expect = 0.001
 Identities = 18/82 (21%), Positives = 31/82 (37%)

Query: 28  KEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKKKEKNKNKNRKEEKKKKKKRRTKKKEK 87
           K + +   T+ +      +N  R EE   K    + +N +K     +  K       +E+
Sbjct: 860 KHQVDNMVTEYEGNIGDTQNSIRGEENTVKGQYSELQNHHKTEALSQNNKYNEEKSAQER 919

Query: 88  NKNKSRKEEKKKEAEEEKKKTK 109
                  EE  K A+E + K K
Sbjct: 920 MPGADSPEELMKRAKEYQDKHK 941

Length = 942

>gnl|CDD|227509 COG5182, CUS1, Splicing factor 3b, subunit 2 [RNA processing and modification]

 Score = 40.4 bits (94), Expect = 0.001
 Identities = 25/129 (19%), Positives = 52/129 (40%), Gaps = 1/129 (0%)

Query: 5   KEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNK-NKSRKEEEKKKRTKKKE 63
             + K       K +      +R+ E+++K      K K NK   ++ E+E K   ++ +
Sbjct: 12  NNQNKNASVVNNKAEIAAMIDARRLEQKKKGGVTNSKGKTNKVVDAKLEKEFKDVLQRFQ 71

Query: 64  KNKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKEEE 123
             +N   KE  K +K     K  K      + E   E   E +    +E++ ++ +K + 
Sbjct: 72  VQENDTPKEITKDEKNMSRMKSRKAPTIHMEAEIDDEYGFEDRMKPYREESLSRQKKRKA 131

Query: 124 EKKKEAEEK 132
            + +  + K
Sbjct: 132 LQHRYEQLK 140

Length = 429

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

 Score = 39.9 bits (93), Expect = 0.002
 Identities = 25/96 (26%), Positives = 50/96 (52%), Gaps = 1/96 (1%)

Query: 94  KEEKKKEAEEEKKKTKNKEKNKNKSRKEEEEKKKEAEEKKKKRTKKKEKNKNKSR-KEEE 152
            +    EA +  +K  +K         +E + +   EE+K+K   K+EK K K + KEE 
Sbjct: 69  SKLSSDEAVKRVEKGGSKGPAAKTKPAKEPKNESGKEEEKEKEQVKEEKKKKKEKPKEEP 128

Query: 153 EEEKKKKKKKKKKKRTKKKEEEKRKNEKAVRLTKLS 188
           ++ K K++ K+K+   +K++E+++K E+     +  
Sbjct: 129 KDRKPKEEAKEKRPPKEKEKEKEKKVEEPRDREEEK 164

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|225606 COG3064, TolA, Membrane protein involved in colicin uptake [Cell envelope biogenesis, outer membrane]

 Score = 39.5 bits (92), Expect = 0.002
 Identities = 30/117 (25%), Positives = 62/117 (52%), Gaps = 10/117 (8%)

Query: 71  KEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKEEEEKKKEAE 130
           + ++   KK   ++K+K +  + + + K+ AE+E+ K   KE      R + +E++K+AE
Sbjct: 68  QSQQSSAKKGEQQRKKKEEQVAEELKPKQAAEQERLKQLEKE------RLKAQEQQKQAE 121

Query: 131 EKKKKRTKKKEKNKNKSRKEEEE----EEKKKKKKKKKKKRTKKKEEEKRKNEKAVR 183
           E +K+   ++++ + ++RK   E     E  K K   +  + K   E K+K E+A +
Sbjct: 122 EAEKQAQLEQKQQEEQARKAAAEQKKKAEAAKAKAAAEAAKLKAAAEAKKKAEEAAK 178

Length = 387

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

 Score = 40.4 bits (95), Expect = 0.002
 Identities = 27/135 (20%), Positives = 52/135 (38%), Gaps = 5/135 (3%)

Query: 1    CKNKKEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTK 60
             K+KK    K  +   +    + +K  K +   KR    + +    +K    E       
Sbjct: 1243 LKSKKNNSSKSSEDNDEFSSDDLSKEGKPKNAPKRVSAVQYSPPPPSKRPDGESNGGSKP 1302

Query: 61   KKEKNKNKNRKEEK----KKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKN 116
                 K   ++ E      KKKK +++KK   K KS+   K+  A +  +  +   K K+
Sbjct: 1303 SSPTKKKVKKRLEGSLAALKKKK-KSEKKTARKKKSKTRVKQASASQSSRLLRRPRKKKS 1361

Query: 117  KSRKEEEEKKKEAEE 131
             S  E+++  +  + 
Sbjct: 1362 DSSSEDDDDSEVDDS 1376

Length = 1388

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

 Score = 40.0 bits (93), Expect = 0.002
 Identities = 42/181 (23%), Positives = 90/181 (49%), Gaps = 3/181 (1%)

Query: 2   KNKKEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKK 61
               EE+ K++    ++++    +  K +EEE      E  ++ K +   EEE ++  ++
Sbjct: 804 LRALEEELKEEAELLEEEQLLIEQEEKIKEEELEELALELKEEQKLEKLAEEELERLEEE 863

Query: 62  KEKNKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKE 121
             K +       K+++ + +  K E    + +++E+KKE EEE +K    E+   K  + 
Sbjct: 864 ITKEELLQELLLKEEELEEQKLKDELESKEEKEKEEKKELEEESQKDNLLEE---KENEI 920

Query: 122 EEEKKKEAEEKKKKRTKKKEKNKNKSRKEEEEEEKKKKKKKKKKKRTKKKEEEKRKNEKA 181
           EE   +EA    K  ++ +E    ++ ++E+EE+ K++++++ K+    KEE    N  A
Sbjct: 921 EERIAEEAIILLKYESEPEELLLEEADEKEKEEDNKEEEEERNKRLLLAKEELGNVNLMA 980

Query: 182 V 182
           +
Sbjct: 981 I 981

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|223496 COG0419, SbcC, ATPase involved in DNA repair [DNA replication, recombination, and repair]

 Score = 40.5 bits (95), Expect = 0.002
 Identities = 26/173 (15%), Positives = 77/173 (44%)

Query: 5   KEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKKKEK 64
            EE +K+     + + +   +    E+EE   +++ +  + + +  +EE  +    ++  
Sbjct: 468 PEEHEKELLELYELELEELEEELSREKEEAELREEIEELEKELRELEEELIELLELEEAL 527

Query: 65  NKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKEEEE 124
            +    K EK +      ++ ++     + +E+ ++ E+  ++ K   +     R  +EE
Sbjct: 528 KEELEEKLEKLENLLEELEELKEKLQLQQLKEELRQLEDRLQELKELLEELRLLRTRKEE 587

Query: 125 KKKEAEEKKKKRTKKKEKNKNKSRKEEEEEEKKKKKKKKKKKRTKKKEEEKRK 177
            ++  E  K+ + K KE  +  S+ EE  +  +  + + + +  +++ E + +
Sbjct: 588 LEELRERLKELKKKLKELEERLSQLEELLQSLELSEAENELEEAEEELESELE 640

Length = 908

>gnl|CDD|240246 PTZ00053, PTZ00053, methionine aminopeptidase 2; Provisional

 Score = 40.1 bits (94), Expect = 0.002
 Identities = 23/90 (25%), Positives = 47/90 (52%), Gaps = 8/90 (8%)

Query: 109 KNKEKNKNKSRKEEEEKKKEAEEKKKKRTKKK--------EKNKNKSRKEEEEEEKKKKK 160
              E  +N+ ++++++ K++  +KK K++KK          +  +++++ E ++  KKKK
Sbjct: 1   AMNENGENEVKQQKQQNKQKGTKKKNKKSKKDVDDDDAFLAELISENQEAENKQNNKKKK 60

Query: 161 KKKKKKRTKKKEEEKRKNEKAVRLTKLSAF 190
           KKKKKK+ K   E          +   +AF
Sbjct: 61  KKKKKKKKKNLGEAYDLAYDLPVVWSSAAF 90

Length = 470

>gnl|CDD|215641 PLN03237, PLN03237, DNA topoisomerase 2; Provisional

 Score = 40.6 bits (95), Expect = 0.002
 Identities = 27/142 (19%), Positives = 54/142 (38%), Gaps = 9/142 (6%)

Query: 39   KEKNKKNKNKSRKEEEKKKRTKKKEKNKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKK 98
            KE +K +K  ++ EE ++K  +   + ++   K+  ++  K         K   +K  KK
Sbjct: 1163 KELDKLDKEDAKAEEAREKLQRAAARGESGAAKKVSRQAPK---------KPAPKKTTKK 1213

Query: 99   KEAEEEKKKTKNKEKNKNKSRKEEEEKKKEAEEKKKKRTKKKEKNKNKSRKEEEEEEKKK 158
                E  ++T      + ++  E  + K  A  KKK     KEK +     + ++     
Sbjct: 1214 ASESETTEETYGSSAMETENVAEVVKPKGRAGAKKKAPAAAKEKEEEDEILDLKDRLAAY 1273

Query: 159  KKKKKKKKRTKKKEEEKRKNEK 180
                   +  K +E  K    +
Sbjct: 1274 NLDSAPAQSAKMEETVKAVPAR 1295

Length = 1465

>gnl|CDD|233758 TIGR02169, SMC_prok_A, chromosome segregation protein SMC, primarily archaeal type

 Score = 40.4 bits (95), Expect = 0.002
 Identities = 35/175 (20%), Positives = 77/175 (44%), Gaps = 7/175 (4%)

Query: 6    EEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKKKEKN 65
             EK+ ++ +  +   K + KS ++E E    KK+E  ++ +       + + R    +K 
Sbjct: 831  LEKEIQELQEQRIDLKEQIKSIEKEIENLNGKKEELEEELEELEAALRDLESRLGDLKKE 890

Query: 66   KNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKEEEEK 125
            +++   + ++ ++K    + +  K + R  E K + E    + +  E    K   EE  +
Sbjct: 891  RDELEAQLRELERKIEELEAQIEKKRKRLSELKAKLEA--LEEELSEIEDPKGEDEEIPE 948

Query: 126  KKEAEEKKKKRTKKKEKNKNK-----SRKEEEEEEKKKKKKKKKKKRTKKKEEEK 175
            ++ + E  +   ++ E+             +E EE  K+  + K+KR K +EE K
Sbjct: 949  EELSLEDVQAELQRVEEEIRALEPVNMLAIQEYEEVLKRLDELKEKRAKLEEERK 1003

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|236944 PRK11642, PRK11642, exoribonuclease R; Provisional

 Score = 39.7 bits (93), Expect = 0.002
 Identities = 18/84 (21%), Positives = 32/84 (38%)

Query: 68  KNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKEEEEKKK 127
             R   K  ++K +     K   K R+  KK   E +      K+     ++K+  + KK
Sbjct: 730 APRNVGKTAREKAKKGDAGKKGGKRRQVGKKVNFEPDSAFRGEKKAKPKAAKKDARKAKK 789

Query: 128 EAEEKKKKRTKKKEKNKNKSRKEE 151
            + + +K     K K   K +  E
Sbjct: 790 PSAKTQKIAAATKAKRAAKKKVAE 813

Length = 813

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

 Score = 39.9 bits (94), Expect = 0.002
 Identities = 20/66 (30%), Positives = 42/66 (63%), Gaps = 2/66 (3%)

Query: 105 KKKTKNKEKNKNKSRKEEEEKKKEAEEKKKKRTKKKEKNKNKSRKEEEEEEKKKKKKKKK 164
           +K  K +E+ + K  K  EE+++E  ++KK+  KK+E+    +  +   EE++K ++K++
Sbjct: 259 RKVDKTREEEEEKILKAAEEERQEEAQEKKEEKKKEEREAKLA--KLSPEEQRKLEEKER 316

Query: 165 KKRTKK 170
           KK+ +K
Sbjct: 317 KKQARK 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|130141 TIGR01069, mutS2, MutS2 family protein

 Score = 39.8 bits (93), Expect = 0.002
 Identities = 26/109 (23%), Positives = 52/109 (47%), Gaps = 4/109 (3%)

Query: 75  KKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKEEEEKKKEAEEKKK 134
           + K      K+E N    +    +KE E++ +  +   K + K +KE E++ +E +E+++
Sbjct: 501 QAKTFYGEFKEEINVLIEKLSALEKELEQKNEHLEKLLKEQEKLKKELEQEMEELKERER 560

Query: 135 KRTKKKEKNK----NKSRKEEEEEEKKKKKKKKKKKRTKKKEEEKRKNE 179
            +  + EK         +KE E   ++ K+KK  K +  K  E+  K +
Sbjct: 561 NKKLELEKEAQEALKALKKEVESIIRELKEKKIHKAKEIKSIEDLVKLK 609

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|217393 pfam03154, Atrophin-1, Atrophin-1 family

 Score = 40.1 bits (93), Expect = 0.002
 Identities = 14/49 (28%), Positives = 37/49 (75%), Gaps = 1/49 (2%)

Query: 135 KRTKKKEKNKNKSRKEEEEEEKKKKKKKKKKKRTKKKEEEKRKNEKAVR 183
           K  KK+E+   K+++E E++ +++++++K+K++ +++E E R+ E+A +
Sbjct: 576 KLAKKREEAVEKAKREAEQKAREEREREKEKEKERERERE-REAERAAK 623

Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteristic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity. Length = 979

>gnl|CDD|217393 pfam03154, Atrophin-1, Atrophin-1 family

 Score = 40.1 bits (93), Expect = 0.002
 Identities = 18/50 (36%), Positives = 32/50 (64%), Gaps = 2/50 (4%)

Query: 57  KRTKKKEKNKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKK 106
           K  KK+E+   K ++E ++K ++ R ++KEK K + R  E+++EAE   K
Sbjct: 576 KLAKKREEAVEKAKREAEQKAREEREREKEKEKERER--EREREAERAAK 623

Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteristic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity. Length = 979

>gnl|CDD|217393 pfam03154, Atrophin-1, Atrophin-1 family

 Score = 40.1 bits (93), Expect = 0.002
 Identities = 20/45 (44%), Positives = 31/45 (68%), Gaps = 2/45 (4%)

Query: 117 KSRKEEEEK-KKEAEEK-KKKRTKKKEKNKNKSRKEEEEEEKKKK 159
           K R+E  EK K+EAE+K +++R ++KEK K + R+ E E E+  K
Sbjct: 579 KKREEAVEKAKREAEQKAREEREREKEKEKEREREREREAERAAK 623

Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteristic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity. Length = 979

>gnl|CDD|227594 COG5269, ZUO1, Ribosome-associated chaperone zuotin [Translation, ribosomal structure and biogenesis / Posttranslational modification, protein turnover, chaperones]

 Score = 39.2 bits (91), Expect = 0.002
 Identities = 30/120 (25%), Positives = 51/120 (42%), Gaps = 5/120 (4%)

Query: 64  KNKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKEEE 123
           + +++ R  E K ++KR   K + N    R  +  K+ +   K  K +EK   K RK E 
Sbjct: 191 EERDRKRYSEAKNREKRAKLKNQDNARLKRLVQIAKKRDPRIKSFKEQEKEMKKIRKWER 250

Query: 124 EKKKEAEEKKKKRTKKKEKNKNKSRKEEEEEEKKKKKKKKKKKRTKKKEEEKRKNEKAVR 183
           E     +     + K + KN     K E E E        KKK  +  ++  +  +KA++
Sbjct: 251 EAGARLKALAALKGKAEAKN-----KAEIEAEALASATAVKKKAKEVMKKALKMEKKAIK 305

Length = 379

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

 Score = 38.9 bits (91), Expect = 0.002
 Identities = 26/68 (38%), Positives = 39/68 (57%)

Query: 94  KEEKKKEAEEEKKKTKNKEKNKNKSRKEEEEKKKEAEEKKKKRTKKKEKNKNKSRKEEEE 153
            E   +    EK+ T   EK      +E++EKKK+ E KK+K+ KK +K K    K  ++
Sbjct: 126 SELGSESETSEKETTAKVEKEAEVEEEEKKEKKKKKEVKKEKKEKKDKKEKMVEPKGSKK 185

Query: 154 EEKKKKKK 161
           ++KKKKKK
Sbjct: 186 KKKKKKKK 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|233503 TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, large subunit, splicing factor

 Score = 40.3 bits (94), Expect = 0.002
 Identities = 13/135 (9%), Positives = 59/135 (43%), Gaps = 19/135 (14%)

Query: 5   KEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKKKEK 64
           +E  ++++K R + ++++  + R+   +  R            + R    +++  ++  +
Sbjct: 3   EEPDREREKSRGRDRDRSSERPRRRSRDRSR-----------FRDRHRRSRERSYREDSR 51

Query: 65  NKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKEEEE 124
            +++ R + +  +  R +  + +++++ R+  +   + E       + + + + R    +
Sbjct: 52  PRDRRRYDSRSPRSLRYSSVR-RSRDRPRRRSRSVRSIE-------QHRRRLRDRSPSNQ 103

Query: 125 KKKEAEEKKKKRTKK 139
            +K+ +++     K 
Sbjct: 104 WRKDDKKRSLWDIKP 118

These splicing factors consist of an N-terminal arginine-rich low complexity domain followed by three tandem RNA recognition motifs (pfam00076). The well-characterized members of this family are auxilliary components of the U2 small nuclear ribonuclearprotein splicing factor (U2AF). These proteins are closely related to the CC1-like subfamily of splicing factors (TIGR01622). Members of this subfamily are found in plants, metazoa and fungi. Length = 509

>gnl|CDD|222581 pfam14181, YqfQ, YqfQ-like protein

 Score = 38.6 bits (90), Expect = 0.002
 Identities = 15/63 (23%), Positives = 31/63 (49%)

Query: 104 EKKKTKNKEKNKNKSRKEEEEKKKEAEEKKKKRTKKKEKNKNKSRKEEEEEEKKKKKKKK 163
           E   + ++E+   +   +E E++   E K + + KKK +      ++E+ + + KK K  
Sbjct: 90  ELSSSDDEEEETEEESTDETEQEDPPETKTESKEKKKREVPKPKTEKEKPKTEPKKPKPS 149

Query: 164 KKK 166
           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|222160 pfam13476, AAA_23, AAA domain

 Score = 38.7 bits (90), Expect = 0.002
 Identities = 35/157 (22%), Positives = 70/157 (44%)

Query: 24  NKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKKKEKNKNKNRKEEKKKKKKRRTK 83
             SR ++ + +   K +   +     +K   +      K K K +  +E ++  KK+  K
Sbjct: 46  KTSRLKKSKGRGIVKGDIEIEKDEGKKKTYVEITFENNKGKLKLRLIEESRELTKKKGKK 105

Query: 84  KKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKEEEEKKKEAEEKKKKRTKKKEKN 143
            K+        +E ++  +E  K  K          +E  E+ K   ++KK+R ++ EK 
Sbjct: 106 VKKSILEIVEIDELQEFIDELLKSDKEILPLLLYLGQERLEELKFKRKEKKERLEELEKE 165

Query: 144 KNKSRKEEEEEEKKKKKKKKKKKRTKKKEEEKRKNEK 180
             +   E++  EK  ++K+KKK+  + KEE +   E+
Sbjct: 166 LEELEDEKDLLEKLLEEKEKKKELEELKEELEELLEE 202

Length = 204

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

 Score = 39.6 bits (93), Expect = 0.002
 Identities = 24/87 (27%), Positives = 41/87 (47%), Gaps = 3/87 (3%)

Query: 3   NKKEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKKK 62
            +K +  K + +R KK           + + K   +++  K +     K++EKKK  KKK
Sbjct: 283 QEKIKALKYQLKRLKKMILLFEMISDLKRKLKSKFERDNEKLDAEVKEKKKEKKKEEKKK 342

Query: 63  EKNKNKNRKEEKKKKKKRRTKKKEKNK 89
              K   R EE+ +K + +   KE+NK
Sbjct: 343 ---KQIERLEERIEKLEVQATDKEENK 366

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

>gnl|CDD|218734 pfam05758, Ycf1, Ycf1

 Score = 40.0 bits (94), Expect = 0.002
 Identities = 18/71 (25%), Positives = 39/71 (54%)

Query: 8   KKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKKKEKNKN 67
           KK K+   T+++E+  +   +   E K TK++++    ++ S   EEK+   K ++ +K 
Sbjct: 224 KKLKETSETEEREEETDVEIETTSETKGTKQEQEGSTEEDPSLFSEEKEDPDKTEDLDKL 283

Query: 68  KNRKEEKKKKK 78
           +  KE+K ++ 
Sbjct: 284 EILKEKKDEEL 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|220648 pfam10243, MIP-T3, Microtubule-binding protein MIP-T3

 Score = 39.5 bits (92), Expect = 0.003
 Identities = 25/98 (25%), Positives = 50/98 (51%)

Query: 89  KNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKEEEEKKKEAEEKKKKRTKKKEKNKNKSR 148
           ++K   +E  K  E+   K    +    K  K E  K++E E+++ K  KKK+K K K  
Sbjct: 68  ESKLSSDEAVKRVEKGGSKGPAAKTKPAKEPKNESGKEEEKEKEQVKEEKKKKKEKPKEE 127

Query: 149 KEEEEEEKKKKKKKKKKKRTKKKEEEKRKNEKAVRLTK 186
            ++ + +++ K+K+  K++ K+KE++  +        K
Sbjct: 128 PKDRKPKEEAKEKRPPKEKEKEKEKKVEEPRDREEEKK 165

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|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]

 Score = 39.7 bits (93), Expect = 0.003
 Identities = 33/186 (17%), Positives = 82/186 (44%), Gaps = 13/186 (6%)

Query: 4    KKEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEE-KKKRTKKK 62
            ++ E+ +++    ++K     +  +E E+E    K+E  +    K   E+E K+   +K+
Sbjct: 828  QEIEELEEEIEELEEKLDELEEELEELEKELEELKEELEELEAEKEELEDELKELEEEKE 887

Query: 63   EKNKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKEE 122
            E  +     E +  + K   +K  +   +   + ++ E E  + + + +E+ ++    E 
Sbjct: 888  ELEEELRELESELAELKEEIEKLRERLEELEAKLERLEVELPELEEELEEEYEDTLETEL 947

Query: 123  EEKKKEAEEKKKKR------------TKKKEKNKNKSRKEEEEEEKKKKKKKKKKKRTKK 170
            E + +  EE+ +                ++   + KS++E+ EE K+K  +  ++   +K
Sbjct: 948  EREIERLEEEIEALGPVNLRAIEEYEEVEERYEELKSQREDLEEAKEKLLEVIEELDKEK 1007

Query: 171  KEEEKR 176
            +E  K 
Sbjct: 1008 RERFKE 1013

Length = 1163

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

 Score = 39.4 bits (93), Expect = 0.003
 Identities = 36/150 (24%), Positives = 71/150 (47%), Gaps = 15/150 (10%)

Query: 2   KNKKEEKKKKKKRRTKKKEKNKNKSRKEEEEE--KRTKKKEKNKKNKNKSRKEEEKKKRT 59
           K K +E++ K     +K+ +   K  K+E +E  K  ++ +K      K+ +  E +KR 
Sbjct: 557 KEKLQEEEDKLLEEAEKEAQQAIKEAKKEADEIIKELRQLQKGGYASVKAHELIEARKRL 616

Query: 60  KKKEKNKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKN----- 114
            K     N+ ++++KKK+K+++ + K  ++ K     +K E         +KE       
Sbjct: 617 NKA----NEKKEKKKKKQKEKQEELKVGDEVKYLSLGQKGEVLS---IPDDKEAIVQAGI 669

Query: 115 -KNKSRKEEEEKKKEAEEKKKKRTKKKEKN 143
            K K    + EK ++ ++KKKK+ K  +  
Sbjct: 670 MKMKVPLSDLEKIQKPKKKKKKKPKTVKPK 699

Length = 782

>gnl|CDD|223496 COG0419, SbcC, ATPase involved in DNA repair [DNA replication, recombination, and repair]

 Score = 39.7 bits (93), Expect = 0.003
 Identities = 35/179 (19%), Positives = 80/179 (44%), Gaps = 6/179 (3%)

Query: 2   KNKKEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKK 61
             +KEE + +++    +KE  + +    E  E     KE+ ++   K     E+ +  K+
Sbjct: 491 SREKEEAELREEIEELEKELRELEEELIELLELEEALKEELEEKLEKLENLLEELEELKE 550

Query: 62  KEKNKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKE 121
           K       + +E+ ++ + R ++ ++   + R    +KE  EE ++   + K   K  KE
Sbjct: 551 K---LQLQQLKEELRQLEDRLQELKELLEELRLLRTRKEELEELRE---RLKELKKKLKE 604

Query: 122 EEEKKKEAEEKKKKRTKKKEKNKNKSRKEEEEEEKKKKKKKKKKKRTKKKEEEKRKNEK 180
            EE+  + EE  +     + +N+ +  +EE E E +K   + + +   +   E+ + + 
Sbjct: 605 LEERLSQLEELLQSLELSEAENELEEAEEELESELEKLNLQAELEELLQAALEELEEKV 663

Length = 908

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

 Score = 39.2 bits (92), Expect = 0.003
 Identities = 18/63 (28%), Positives = 29/63 (46%)

Query: 13  KRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKKKEKNKNKNRKE 72
           K R   + + K K+  E++  K +KK    +  K +  KE+ K K+  +  KN  K RK 
Sbjct: 369 KARVIDELRPKTKAPSEKKTGKPSKKVLAKRAEKKEKEKEKPKVKKRHRDTKNIGKRRKP 428

Query: 73  EKK 75
              
Sbjct: 429 SGT 431

Length = 434

>gnl|CDD|235175 PRK03918, PRK03918, chromosome segregation protein; Provisional

 Score = 39.7 bits (93), Expect = 0.003
 Identities = 36/167 (21%), Positives = 73/167 (43%), Gaps = 4/167 (2%)

Query: 18  KKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKKKEKNKNKNRKEEKKKK 77
              KN  +  KE +      +K   +    +   +E++K+  +   +    + +  + ++
Sbjct: 162 NAYKNLGEVIKEIKRRIERLEKFIKRTENIEELIKEKEKELEEVLREINEISSELPELRE 221

Query: 78  K--KRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKEEEEKKKEAE--EKK 133
           +  K   + KE  + K   EE +KE E  +   +  E+   +  +  EE KKE E  E+K
Sbjct: 222 ELEKLEKEVKELEELKEEIEELEKELESLEGSKRKLEEKIRELEERIEELKKEIEELEEK 281

Query: 134 KKRTKKKEKNKNKSRKEEEEEEKKKKKKKKKKKRTKKKEEEKRKNEK 180
            K  K+ ++   +  K  E  E+   + ++ +KR  + EEE    E+
Sbjct: 282 VKELKELKEKAEEYIKLSEFYEEYLDELREIEKRLSRLEEEINGIEE 328

Length = 880

>gnl|CDD|233467 TIGR01554, major_cap_HK97, phage major capsid protein, HK97 family

 Score = 39.3 bits (92), Expect = 0.003
 Identities = 16/106 (15%), Positives = 42/106 (39%), Gaps = 5/106 (4%)

Query: 52  EEEKKKRTKKKEKNKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNK 111
            +E ++   +  K   K  ++EK  + +    + +  K +  K + + +  EE       
Sbjct: 1   LKELREALAELAKELRKLTEDEKLAEAEEEKAEYDALKEEIDKLDAEIDRLEELLDELEA 60

Query: 112 EKNKNKSRKEEEEKKKEAEEKKKKRTKKKEKNKNKSRKEEEEEEKK 157
           +   +      EE+++EA+ +  +      +   +   +   EE+K
Sbjct: 61  KPAASGEGGGGEEEEEEAKAEAAEF-----RAYLRGGDDALAEERK 101

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 = 40.1 bits (94), Expect = 0.003
 Identities = 25/89 (28%), Positives = 44/89 (49%), Gaps = 11/89 (12%)

Query: 44   KNKNKSRKEEEKKK-----RTKKKEKNKNKNRKEEKKKKKKRRTKKKEKNKN------KS 92
             N+N ++K  +KKK       KK  + +N+N++E++   +      KEK  N        
Sbjct: 1494 GNENVNKKINQKKKGFIPSNEKKSIEIENRNQEEKEPAGQGELESDKEKKGNLESVLSNQ 1553

Query: 93   RKEEKKKEAEEEKKKTKNKEKNKNKSRKE 121
             K  ++  AE + KK KNK++ K+ +  E
Sbjct: 1554 EKNIEEDYAESDIKKRKNKKQYKSNTEAE 1582

Length = 1832

>gnl|CDD|236081 PRK07735, PRK07735, NADH dehydrogenase subunit C; Validated

 Score = 39.2 bits (91), Expect = 0.003
 Identities = 44/186 (23%), Positives = 77/186 (41%), Gaps = 11/186 (5%)

Query: 5   KEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKKKEK 64
           K + K K     K K     K ++E  EE   ++K   K     + K +      +K+E 
Sbjct: 90  KAKAKAKAAAAAKAKAAALAKQKREGTEEVTEEEKAAAKAKAAAAAKAKAAALAKQKREG 149

Query: 65  NKNKNRKEEKKKKKKRRTKKKE--KNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKEE 122
            +    +EE+  K+K + K     K K  +  ++K  EA E  ++   +EK K K++   
Sbjct: 150 TEEVTEEEEETDKEKAKAKAAAAAKAKAAALAKQKAAEAGEGTEEVTEEEKAKAKAKAAA 209

Query: 123 EEKKKEAEEKKKKRTK---------KKEKNKNKSRKEEEEEEKKKKKKKKKKKRTKKKEE 173
             K K A   K+K ++          K K    ++ +     + K K  + KK  + K+E
Sbjct: 210 AAKAKAAALAKQKASQGNGDSGDEDAKAKAIAAAKAKAAAAARAKTKGAEGKKEEEPKQE 269

Query: 174 EKRKNE 179
           E   N+
Sbjct: 270 EPSVNQ 275

Length = 430

>gnl|CDD|236944 PRK11642, PRK11642, exoribonuclease R; Provisional

 Score = 39.3 bits (92), Expect = 0.003
 Identities = 24/93 (25%), Positives = 41/93 (44%), Gaps = 6/93 (6%)

Query: 82  TKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKEEEEKKKEAEEKKKKRTKKKE 141
           +++  +N  K+ +E+ KK  +  KK  K ++  K  + + +   + E + K K   K   
Sbjct: 727 SERAPRNVGKTAREKAKK-GDAGKKGGKRRQVGKKVNFEPDSAFRGEKKAKPKAAKKDAR 785

Query: 142 KNKNKSRKEEEEEEKKKKKKKKKKKRTKKKEEE 174
           K K  S K      +K     K K+  KKK  E
Sbjct: 786 KAKKPSAKT-----QKIAAATKAKRAAKKKVAE 813

Length = 813

>gnl|CDD|233191 TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger

 Score = 39.6 bits (92), Expect = 0.003
 Identities = 26/141 (18%), Positives = 60/141 (42%), Gaps = 12/141 (8%)

Query: 23  KNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKKKEKN--------KNKNRKEEK 74
           ++   +  EE +R  + E     ++    E+E +  TK + ++        K +   E +
Sbjct: 639 EHTGERTGEEGERPTEAEGENGEESGGEAEQEGETETKGENESEGEIPAERKGEQEGEGE 698

Query: 75  KKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKEEEEKKKEAEEKKK 134
            + K+   K + + +    + E + E  E++ + +  E+ +    + E+E + EAE K +
Sbjct: 699 IEAKEADHKGETEAEEVEHEGETEAEGTEDEGEIETGEEGE----EVEDEGEGEAEGKHE 754

Query: 135 KRTKKKEKNKNKSRKEEEEEE 155
             T+   K      + E E +
Sbjct: 755 VETEGDRKETEHEGETEAEGK 775

[Transport and binding proteins, Cations and iron carrying compounds]. Length = 1096

>gnl|CDD|217502 pfam03343, SART-1, SART-1 family

 Score = 39.7 bits (93), Expect = 0.003
 Identities = 46/189 (24%), Positives = 80/189 (42%), Gaps = 17/189 (8%)

Query: 2   KNKKEEKKKKKKRRTKKKEKNKNKS----RKEEEEEKRTKKKEKNKKNKNKSRKEEEKKK 57
           K   E KKKK        +K   +S      EE E K+ K       +   S  +E +KK
Sbjct: 180 KKNLELKKKKPDYDPDDDDKFNKRSILSKYDEEIEGKKKKSDNLFTLDSGGSTDDEAEKK 239

Query: 58  RTKKKEKNKNKNRKEEKKKKK------------KRRTKKKEKNKNKSRKEEKKKEAEEEK 105
           R + K+K K  N   +    +             +  K K+K K K ++ +   E E E 
Sbjct: 240 RQEVKKKLKINNVSLDDDSTETPASDYYDVSEMVKFKKPKKKKKKKKKRRKDLDEDELEP 299

Query: 106 KKTKNKEKNKNKSRKEEEEKKKEAEEKKKKRTKKKEKNKNKSRKEEEEEEKKKKKKKKKK 165
           +       + + SRK+ EE+    E+  KKR +++E +      ++ +    K+++  +K
Sbjct: 300 EAEGLG-SSDSGSRKDVEEENARLEDSPKKRKEEQEDDDFVEDDDDLQASLAKQRRLAQK 358

Query: 166 KRTKKKEEE 174
           KR K + E+
Sbjct: 359 KRKKLRPED 367

SART-1 is a protein involved in cell cycle arrest and pre-mRNA splicing. It has been shown to be a component of U4/U6 x U5 tri-snRNP complex in human, Schizosaccharomyces pombe and Saccharomyces cerevisiae. SART-1 is a known tumour antigen in a range of cancers recognised by T cells. Length = 603

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

 Score = 38.5 bits (90), Expect = 0.003
 Identities = 24/67 (35%), Positives = 37/67 (55%)

Query: 28  KEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKKKEKNKNKNRKEEKKKKKKRRTKKKEK 87
           +   E + ++K+   K  K    +EEEKK++ KKKE  K K  K++KK+K       K+K
Sbjct: 127 ELGSESETSEKETTAKVEKEAEVEEEEKKEKKKKKEVKKEKKEKKDKKEKMVEPKGSKKK 186

Query: 88  NKNKSRK 94
            K K +K
Sbjct: 187 KKKKKKK 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|227278 COG4942, COG4942, Membrane-bound metallopeptidase [Cell division and chromosome partitioning]

 Score = 39.3 bits (92), Expect = 0.003
 Identities = 30/204 (14%), Positives = 67/204 (32%), Gaps = 20/204 (9%)

Query: 10  KKKKRRTKKKEKNKNKSRKEEEEEKR--------TKKKEKNKKNKNK-SRKEEEKKKRTK 60
           KK +++        N    +E E++R         ++  +N       S ++ ++  R  
Sbjct: 90  KKLRKQIADLNARLNALEVQEREQRRRLAEQLAALQRSGRNPPPALLVSPEDAQRSVRLA 149

Query: 61  KKEKNKNKNRKEEKKKKKK--------RRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKE 112
                 N  R E     K         R     E+ +  +   E++ +  +  +  + ++
Sbjct: 150 IYYGALNPARAERIDALKATLKQLAAVRAEIAAEQAELTTLLSEQRAQQAKLAQLLEERK 209

Query: 113 KNKNK--SRKEEEEKKKEAEEKKKKRTKKK-EKNKNKSRKEEEEEEKKKKKKKKKKKRTK 169
           K   +  S    ++KK E     + R K +    +  + K  E     +    + +    
Sbjct: 210 KTLAQLNSELSADQKKLEELRANESRLKNEIASAEAAAAKAREAAAAAEAAAARARAAEA 269

Query: 170 KKEEEKRKNEKAVRLTKLSAFGIS 193
           K+  E  K     ++   S  G  
Sbjct: 270 KRTGETYKPTAPEKMLISSTGGFG 293

Length = 420

>gnl|CDD|226889 COG4487, COG4487, Uncharacterized protein conserved in bacteria [Function unknown]

 Score = 39.4 bits (92), Expect = 0.003
 Identities = 35/167 (20%), Positives = 75/167 (44%), Gaps = 2/167 (1%)

Query: 18  KKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKKKEKNKNKNRKEEKKKK 77
           ++E         EE EK   +K    ++  K    + +++   +K++ KN   ++ K+ +
Sbjct: 33  EQEDQSRILNTLEEFEKEANEKRAQYRSAKKKELSQLEEQLINQKKEQKNLFNEQIKQFE 92

Query: 78  KKRRTKKKEKNKNKSRKEEKKKEAE--EEKKKTKNKEKNKNKSRKEEEEKKKEAEEKKKK 135
              + +  +    +    EK KE E  E++    +KE  K      E  +KK    K ++
Sbjct: 93  LALQDEIAKLEALELLNLEKDKELELLEKELDELSKELQKQLQNTAEIIEKKRENNKNEE 152

Query: 136 RTKKKEKNKNKSRKEEEEEEKKKKKKKKKKKRTKKKEEEKRKNEKAV 182
           R K + + K +   E E E+ +++  +       K+ EE+R+++ A+
Sbjct: 153 RLKFENEKKLEESLELEREKFEEQLHEANLDLEFKENEEQRESKWAI 199

Length = 438

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

 Score = 39.6 bits (93), Expect = 0.003
 Identities = 22/112 (19%), Positives = 46/112 (41%), Gaps = 4/112 (3%)

Query: 6   EEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKKKEKN 65
           EE  + + +  + K++ K    K E+ E   +KKE+  +       ++  KK  KK + N
Sbjct: 88  EENIEIEAQIEELKKELKKLEEKIEQLEAEIEKKEEELEKAKNKFLDKAWKKLAKKYDSN 147

Query: 66  ----KNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEK 113
                     ++  K+K  +  K       S    ++ +A+ +   + NK +
Sbjct: 148 LSEALKGLNYKKNFKEKLLKELKSVILNASSLLSLEELKAKIKTLFSSNKPE 199

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|240402 PTZ00399, PTZ00399, cysteinyl-tRNA-synthetase; Provisional

 Score = 39.2 bits (92), Expect = 0.003
 Identities = 32/125 (25%), Positives = 52/125 (41%), Gaps = 19/125 (15%)

Query: 37  KKKEKNKKNKNKSRKEEEKKKRTKKKEKNKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEE 96
           K  +K +  + K  KE  K+++  +K K + + +K+E +K +K +    E  K   R+E+
Sbjct: 546 KLDDKEELQREKEEKEALKEQKRLRKLKKQEEKKKKELEKLEKAKIPPAEFFK---RQED 602

Query: 97  KKKEAEEEKKKTKNKEKNKNKSRKEEEEKKKEAEEKKKKRTKKKEKNKNKSRKEEEEEEK 156
           K    +E    T +                 + EE  KK  KK  K  +K  K  EE   
Sbjct: 603 KYSAFDETGLPTHD----------------ADGEEISKKERKKLSKEYDKQAKLHEEYLA 646

Query: 157 KKKKK 161
           K  K 
Sbjct: 647 KGGKS 651

Length = 651

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

 Score = 39.4 bits (91), Expect = 0.004
 Identities = 34/170 (20%), Positives = 87/170 (51%), Gaps = 4/170 (2%)

Query: 2    KNKKEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKK 61
             N+ +E  ++   + ++ +K +    +E  + +  KKK ++ +   ++RK E+ +K  + 
Sbjct: 1086 DNRADEATEEAFGKAEEAKKTETGKAEEARKAEEAKKKAEDARKAEEARKAEDARKAEEA 1145

Query: 62   KEKNKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAE----EEKKKTKNKEKNKNK 117
            ++    K  +  +K +  R+ ++  K ++  + E  +K  E    EE +K ++  K +  
Sbjct: 1146 RKAEDAKRVEIARKAEDARKAEEARKAEDAKKAEAARKAEEVRKAEELRKAEDARKAEAA 1205

Query: 118  SRKEEEEKKKEAEEKKKKRTKKKEKNKNKSRKEEEEEEKKKKKKKKKKKR 167
             + EEE K +EA + +  +  +  K   +++K+ EE +K ++++  ++ R
Sbjct: 1206 RKAEEERKAEEARKAEDAKKAEAVKKAEEAKKDAEEAKKAEEERNNEEIR 1255

Length = 2084

>gnl|CDD|223496 COG0419, SbcC, ATPase involved in DNA repair [DNA replication, recombination, and repair]

 Score = 39.4 bits (92), Expect = 0.004
 Identities = 27/183 (14%), Positives = 82/183 (44%), Gaps = 6/183 (3%)

Query: 1   CKNKKEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTK 60
               +EEK++ ++ + +  E    +    +  E+  ++ E+  +   +  +  E+ +R  
Sbjct: 241 LAELEEEKERLEELKARLLEIESLELEALKIREEELRELERLLEELEEKIERLEELEREI 300

Query: 61  KKEKNKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRK 120
           ++ + + +  +   ++ ++   K K   +   + EEK ++ E E ++   ++    K  +
Sbjct: 301 EELEEELEGLRALLEELEELLEKLKSLEERLEKLEEKLEKLESELEELAEEKNELAKLLE 360

Query: 121 EEEEKKKEAEEKKKKRTKKKEKNKNKSRKEEEEEEKKKKKKKKKKKRTKKKEEEKRKNEK 180
           E  ++ +E  E+ +K  +K  +   +       EE  ++ K++  + +   EE + + E+
Sbjct: 361 ERLKELEERLEELEKELEKALERLKQ------LEEAIQELKEELAELSAALEEIQEELEE 414

Query: 181 AVR 183
             +
Sbjct: 415 LEK 417

Length = 908

>gnl|CDD|188306 TIGR03319, RNase_Y, ribonuclease Y

 Score = 39.1 bits (92), Expect = 0.004
 Identities = 32/140 (22%), Positives = 66/140 (47%), Gaps = 18/140 (12%)

Query: 55  KKKRTKKKEKNKNKNRKEEKKKKKKRRTKKKE-----KNKNKSRKEEKKKEAEEEKKKTK 109
           K+   KK    +   ++  ++ KK+  T KKE     K +    + E ++E +E + + +
Sbjct: 20  KRIAEKKLGSAEELAKRIIEEAKKEAETLKKEALLEAKEEVHKLRAELERELKERRNELQ 79

Query: 110 NKEKNKNKSRKEEEEKKKEAEEKKKKRTKKKEKNKNKSRKEEEEEEKKKKKKKKKKKRTK 169
             E+ +   R+E  ++K E+ +KK++  +KKEK            E   K+K   +K  +
Sbjct: 80  RLER-RLLQREETLDRKMESLDKKEENLEKKEK------------ELSNKEKNLDEKEEE 126

Query: 170 KKEEEKRKNEKAVRLTKLSA 189
            +E    + E+  R++ L+ 
Sbjct: 127 LEELIAEQREELERISGLTQ 146

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|226894 COG4499, COG4499, Predicted membrane protein [Function unknown]

 Score = 38.6 bits (90), Expect = 0.004
 Identities = 24/98 (24%), Positives = 47/98 (47%), Gaps = 13/98 (13%)

Query: 36  TKKKEKNKKNKNKSRKEEEKKKRTKKKEKNKNKNRKEEKKKKKKRRTKKKEKNKNKSRKE 95
           TK  E+ K N + S   +++++  K+  K      K+  + K +    ++ + K      
Sbjct: 350 TKLYEEVKSNTDLS--GDKRQELLKEYNKKLQDYTKKLGEVKDETDASEEAEAK------ 401

Query: 96  EKKKEAEEEKKKTKNKEKNKNKSRKEEEEKKKEAEEKK 133
                A+EEK K +  EK + +   E++EK+++ E KK
Sbjct: 402 -----AKEEKLKQEENEKKQKEQADEDKEKRQKDERKK 434

Length = 434

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

 Score = 39.1 bits (92), Expect = 0.004
 Identities = 21/72 (29%), Positives = 30/72 (41%), Gaps = 11/72 (15%)

Query: 59  TKKKEKNKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKK---KTKNKEKNK 115
             + E+ + +N      ++KK R         K RK EKK E EE +K   K K +   K
Sbjct: 393 LAEGEEEEGENGNLSPAERKKLR--------KKQRKAEKKAEKEEAEKAAAKKKAEAAAK 444

Query: 116 NKSRKEEEEKKK 127
                + E KK 
Sbjct: 445 KAKGPDGETKKV 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 = 38.2 bits (89), Expect = 0.004
 Identities = 28/124 (22%), Positives = 44/124 (35%), Gaps = 13/124 (10%)

Query: 91  KSRKEEKKKEAEEEKKKTKNKEKNKNKSRKEEEEKKKEAEEKKKKRTKKKEKNKNKSRKE 150
            + + + + E  EE+ K   + +      +    K KE  + +KK  K K K K      
Sbjct: 52  PTEEPQPEPEPPEEQPKPPTEPETP---PEPTPPKPKEKPKPEKKPKKPKPKPK------ 102

Query: 151 EEEEEKKKKKKKKKKKR--TKKKEEEKRKNEKAVRLTKLSAFGISGYLLQWIRNFLSGWI 208
              + K K K K + K      K   K            SA   SG       ++LSG  
Sbjct: 103 --PKPKPKPKVKPQPKPKKPPSKTAAKAPAAPNQPARPPSAASASGAATGPSASYLSGLR 160

Query: 209 QIVR 212
           + +R
Sbjct: 161 RAIR 164

Length = 244

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

 Score = 39.5 bits (92), Expect = 0.004
 Identities = 24/94 (25%), Positives = 47/94 (50%), Gaps = 1/94 (1%)

Query: 29  EEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKKKEKNKNKNRKEEKKKKKKRRTKKKEKN 88
           EEE E++ KK+EK K+ + K  K  +K+ + K + +  +      KK +KK R K+  ++
Sbjct: 15  EEELERKKKKEEKAKEKELKKLKAAQKEAKAKLQAQQASDGTNVPKKSEKKSR-KRDVED 73

Query: 89  KNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKEE 122
           +N     +      ++K+ +    K  + S  E+
Sbjct: 74  ENPEDFIDPDTPFGQKKRLSSQMAKQYSPSAVEK 107

Length = 1066

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

 Score = 39.1 bits (91), Expect = 0.004
 Identities = 17/66 (25%), Positives = 33/66 (50%)

Query: 117 KSRKEEEEKKKEAEEKKKKRTKKKEKNKNKSRKEEEEEEKKKKKKKKKKKRTKKKEEEKR 176
              +++   ++E E KKKK  K KEK   K +  ++E + K + ++        K+ EK+
Sbjct: 6   SEAEKKILTEEELERKKKKEEKAKEKELKKLKAAQKEAKAKLQAQQASDGTNVPKKSEKK 65

Query: 177 KNEKAV 182
             ++ V
Sbjct: 66  SRKRDV 71

Length = 1066

>gnl|CDD|222581 pfam14181, YqfQ, YqfQ-like protein

 Score = 37.4 bits (87), Expect = 0.004
 Identities = 16/45 (35%), Positives = 28/45 (62%)

Query: 20  EKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKKKEK 64
           E++ +++ +E+  E +T+ KEK K+   K + E+EK K   KK K
Sbjct: 103 EESTDETEQEDPPETKTESKEKKKREVPKPKTEKEKPKTEPKKPK 147

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|226889 COG4487, COG4487, Uncharacterized protein conserved in bacteria [Function unknown]

 Score = 38.6 bits (90), Expect = 0.004
 Identities = 44/176 (25%), Positives = 84/176 (47%), Gaps = 3/176 (1%)

Query: 4   KKEEKKKKKKRRTKKKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKKKE 63
           ++ EK+  +KR   +  K K  S+ EE+   + KK++KN  N+   + E   +    K E
Sbjct: 45  EEFEKEANEKRAQYRSAKKKELSQLEEQLINQ-KKEQKNLFNEQIKQFELALQDEIAKLE 103

Query: 64  KNKNKNRKEEKKKKKKRRTKKKEKNKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKEEE 123
             +  N   EK K+ +   K+ ++   + +K+ +      EKK+  NK + + K   E++
Sbjct: 104 ALELLN--LEKDKELELLEKELDELSKELQKQLQNTAEIIEKKRENNKNEERLKFENEKK 161

Query: 124 EKKKEAEEKKKKRTKKKEKNKNKSRKEEEEEEKKKKKKKKKKKRTKKKEEEKRKNE 179
            ++    E++K   +  E N +   KE EE+ + K    KK KR  +   ++ + E
Sbjct: 162 LEESLELEREKFEEQLHEANLDLEFKENEEQRESKWAILKKLKRRAELGSQQVQGE 217

Length = 438

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

 Score = 39.2 bits (92), Expect = 0.004
 Identities = 25/118 (21%), Positives = 44/118 (37%)

Query: 28  KEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKKKEKNKNKNRKEEKKKKKKRRTKKKEK 87
            E E +    KKE  K  +   + E E +K+ ++ EK KNK   +  KK  K+      +
Sbjct: 91  IEIEAQIEELKKELKKLEEKIEQLEAEIEKKEEELEKAKNKFLDKAWKKLAKKYDSNLSE 150

Query: 88  NKNKSRKEEKKKEAEEEKKKTKNKEKNKNKSRKEEEEKKKEAEEKKKKRTKKKEKNKN 145
                  ++  KE   ++ K+     +   S +E + K K      K        +  
Sbjct: 151 ALKGLNYKKNFKEKLLKELKSVILNASSLLSLEELKAKIKTLFSSNKPELALLTLSVI 208

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|235600 PRK05771, PRK05771, V-type ATP synthase subunit I; Validated

 Score = 39.1 bits (92), Expect = 0.004
 Identities = 35/226 (15%), Positives = 81/226 (35%), Gaps = 41/226 (18%)

Query: 18  KKEKNKNKSRKEEEEEKRTKKKEKNKKNKNKSRKEEEKKKRTKKKEKNKNKNRKEEKKKK 77
           +    K    +EE+++   K  E+  K+  +  ++ EK+ +  ++E ++ +N  +E +++
Sbjct: 63  RSYLPKLNPLREEKKKVSVKSLEELIKDVEEELEKIEKEIKELEEEISELENEIKELEQE 122

Query: 78  KKRR------------------------TKKKEKNKNKSRKEEKKKEAEEEKKKTKN--- 110
            +R                         T  ++K +    + + +        K      
Sbjct: 123 IERLEPWGNFDLDLSLLLGFKYVSVFVGTVPEDKLEELKLESDVENVEYISTDKGYVYVV 182

Query: 111 ----KEKNKNKSR--KEEEEKKKEAEEKK--KKRTKKKEKNKNKSRKEEEEEEKKKKKKK 162
               KE +       K+   ++ E EE+    +  ++ ++   +  KE E   ++ K+  
Sbjct: 183 VVVLKELSDEVEEELKKLGFERLELEEEGTPSELIREIKEELEEIEKERESLLEELKELA 242

Query: 163 KKKKRTKKKEEEKRKNEKAVRLTKLSAFGISGYLLQWIRNFLSGWI 208
           KK         E  + E   R   LS F  +          + GW+
Sbjct: 243 KKYLEELLALYEYLEIELE-RAEALSKFLKTDKTFA-----IEGWV 282

Length = 646

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	410
cd01651	226	RT_G2_intron RT_G2_intron: Reverse transcriptases	99.83
cd01650	220	RT_nLTR_like RT_nLTR: Non-LTR (long terminal repea	99.83
cd03487	214	RT_Bac_retron_II RT_Bac_retron_II: Reverse transcr	99.79
PF00078	214	RVT_1: Reverse transcriptase (RNA-dependent DNA po	99.79
cd01709	346	RT_like_1 RT_like_1: A subfamily of reverse transc	99.78
cd01646	158	RT_Bac_retron_I RT_Bac_retron_I: Reverse transcrip	99.76
cd01648	119	TERT TERT: Telomerase reverse transcriptase (TERT)	99.71
cd00304	98	RT_like RT_like: Reverse transcriptase (RT, RNA-de	99.38
KOG4768|consensus	796		99.36
cd03714	119	RT_DIRS1 RT_DIRS1: Reverse transcriptases (RTs) oc	98.74
cd01645	213	RT_Rtv RT_Rtv: Reverse transcriptases (RTs) from r	98.7
KOG1005|consensus	888		98.52
cd03715	210	RT_ZFREV_like RT_ZFREV_like: A subfamily of revers	98.49
cd01647	177	RT_LTR RT_LTR: Reverse transcriptases (RTs) from r	98.2
COG3344	328	Retron-type reverse transcriptase [DNA replication	96.74
cd01699	278	RNA_dep_RNAP RNA_dep_RNAP: RNA-dependent RNA polym	96.47
cd01644	213	RT_pepA17 RT_pepA17: Reverse transcriptase (RTs) i	96.34
CHL00002	504	matK maturase K	91.45
PF00680	491	RdRP_1: RNA dependent RNA polymerase; InterPro: IP	88.97
KOG4364|consensus	811		85.33
PTZ00121	2084	MAEBL; Provisional	83.52
PF03431	542	RNA_replicase_B: RNA replicase, beta-chain ; Inter	81.78

>cd01651 RT_G2_intron RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin

Probab=99.83  E-value=6.3e-21  Score=178.20  Aligned_cols=134  Identities=19%  Similarity=0.283  Sum_probs=113.9

Q ss_pred             HhhhcCCCHHHHHHHHHhCCCChHHHHHHHHHhhcceEEEeeCCccCCccccCccccCCCcchhhhhhhhhhhhhhcc--
Q psy12268        172 EEEKRKNEKAVRLTKLSAFGISGYLLQWIRNFLSGWIQIVRVGTSTSEPIHIPSGCIQGGHMSGLLFSLFINDIAEIF--  249 (410)
Q Consensus       172 ~~~~~~vdH~~Ll~~L~~~G~p~~li~lI~s~Ls~rs~~V~~~g~~S~~~~i~~GVPQGs~LSPLLFnL~l~~L~~~l--  249 (410)
                      +.+||.|+|+.|+..|...|.++.++.||.+|+....      ...+..+....|||||+++||+||++|+++++..+  
T Consensus        78 ~~~Fdsi~~~~l~~~l~~~~~~~~~~~~i~~~~~~~~------~~~~~~~~~~~GlpqG~~lSp~L~~~~l~~ld~~l~~  151 (226)
T cd01651          78 KGFFDNIDHDLLLKILKRRIGDKRVLRLIRKWLKAGV------LEDGKLVETEKGTPQGGVISPLLANIYLHELDKFVEE  151 (226)
T ss_pred             HHhcCCCCHHHHHHHHHHhcccHHHHHHHHHHHhceE------ccCCeEeCCCCCcCCCccHHHHHHHHHHHHHHHHHHH
Confidence            5689999999999999999999999999999864332      22345678899999999999999999999998754  


Q ss_pred             -------------CCcccccccchhhhhhhcCChhhhhhHHHHHHHHHhhhhhccccccccceeEEEeecCCCCccceee
Q psy12268        250 -------------PGFNFWLFADDLKVALRVGGQREVDSMQSMLSRLYHWCSINKMELNIGKCMVMTYHRNKSPILASYD  316 (410)
Q Consensus       250 -------------~~i~~l~YADDivIis~s~s~~~~~~Lq~~Ld~L~~w~~~~GLkIN~~KTeim~f~~~~~~~~~~~t  316 (410)
                                   .++.+++||||++|++.+     ...++.+++.+..|+..+||.+|++||.++.++           
T Consensus       152 ~~~~~~~~~~~~~~~~~~~rY~DD~~i~~~~-----~~~~~~~~~~i~~~~~~~gl~ln~~Kt~i~~~~-----------  215 (226)
T cd01651         152 KLKEYYDTSDPKFRRLRYVRYADDFVIGVRG-----PKEAEEIKELIREFLEELGLELNPEKTRITHFK-----------  215 (226)
T ss_pred             hhhhcccccccccCceEEEEecCceEEecCC-----HHHHHHHHHHHHHHHHHcCCeechhhcceeecC-----------
Confidence                         457899999999999843     344888899999999999999999999999985           


Q ss_pred             eCCccccccccccccceee
Q psy12268        317 INGQALARCEQVRDLGVTF  335 (410)
Q Consensus       317 i~g~~I~~ves~KYLGV~L  335 (410)
                              .+.+.|||+.|
T Consensus       216 --------~~~~~fLG~~~  226 (226)
T cd01651         216 --------SEGFDFLGFTF  226 (226)
T ss_pred             --------CCCCeeCCeEC
Confidence                    33589999875

RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).

>cd01650 RT_nLTR_like RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT)

Probab=99.83  E-value=4.5e-21  Score=178.93  Aligned_cols=121  Identities=27%  Similarity=0.445  Sum_probs=105.9

Q ss_pred             HhhhcCCCHHHHHHHHHhCCCChHHHHHHHHHhhcceEEEeeCCccCCccccCccccCCCcchhhhhhhhhhhhhhccC-
Q psy12268        172 EEEKRKNEKAVRLTKLSAFGISGYLLQWIRNFLSGWIQIVRVGTSTSEPIHIPSGCIQGGHMSGLLFSLFINDIAEIFP-  250 (410)
Q Consensus       172 ~~~~~~vdH~~Ll~~L~~~G~p~~li~lI~s~Ls~rs~~V~~~g~~S~~~~i~~GVPQGs~LSPLLFnL~l~~L~~~l~-  250 (410)
                      +.+||.|+|+.|+..|                                      |||||++|||+||++|++++...+. 
T Consensus        90 ~~aFdsi~~~~l~~~l--------------------------------------GipQG~~lSp~l~~l~~~~l~~~~~~  131 (220)
T cd01650          90 EKAFDSVDHEFLLKAL--------------------------------------GVRQGDPLSPLLFNLALDDLLRLLNK  131 (220)
T ss_pred             HhhcCcCCHHHHHHHh--------------------------------------CCccCCcccHHHHHHHHHHHHHHHHh
Confidence            5789999999999999                                      9999999999999999999987653 


Q ss_pred             ---------CcccccccchhhhhhhcCChhhhhhHHHHHHHHHhhhhhccccccccceeEEEeecCCCCccceeeeCCcc
Q psy12268        251 ---------GFNFWLFADDLKVALRVGGQREVDSMQSMLSRLYHWCSINKMELNIGKCMVMTYHRNKSPILASYDINGQA  321 (410)
Q Consensus       251 ---------~i~~l~YADDivIis~s~s~~~~~~Lq~~Ld~L~~w~~~~GLkIN~~KTeim~f~~~~~~~~~~~ti~g~~  321 (410)
                               ++.+++||||++|++.+..    ..++.+++.+..|+..+||.+|++||++++++........ +.+++..
T Consensus       132 ~~~~~~~~~~~~~~~yaDD~~i~~~~~~----~~~~~~~~~~~~~~~~~gl~in~~Kt~~~~~~~~~~~~~~-~~~~~~~  206 (220)
T cd01650         132 EEEIKLGGPGITHLAYADDIVLFSEGKS----RKLQELLQRLQEWSKESGLKINPSKSKVMLIGNKKKRLKD-ITLNGTP  206 (220)
T ss_pred             hccccCCCCccceEEeccceeeeccCCH----HHHHHHHHHHHHHHHHcCCEEChhheEEEEecCCCcchhh-hhhcCCc
Confidence                     5789999999999985431    3788899999999999999999999999999876543323 7788889


Q ss_pred             ccccccccccceee
Q psy12268        322 LARCEQVRDLGVTF  335 (410)
Q Consensus       322 I~~ves~KYLGV~L  335 (410)
                      +.....++|||++|
T Consensus       207 ~~~~~~~kyLG~~i  220 (220)
T cd01650         207 IEAVETFKYLGVTI  220 (220)
T ss_pred             ccCCCCCeeccccC
Confidence            99999999999975

This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.

>cd03487 RT_Bac_retron_II RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons

Probab=99.79  E-value=1.4e-19  Score=170.49  Aligned_cols=127  Identities=13%  Similarity=0.107  Sum_probs=105.9

Q ss_pred             HhhhcCCCHHHHHHHHHhCCCC-hHHHHHHHHHhhcceEEEeeCCccCCccccCccccCCCcchhhhhhhhhhhhhhcc-
Q psy12268        172 EEEKRKNEKAVRLTKLSAFGIS-GYLLQWIRNFLSGWIQIVRVGTSTSEPIHIPSGCIQGGHMSGLLFSLFINDIAEIF-  249 (410)
Q Consensus       172 ~~~~~~vdH~~Ll~~L~~~G~p-~~li~lI~s~Ls~rs~~V~~~g~~S~~~~i~~GVPQGs~LSPLLFnL~l~~L~~~l-  249 (410)
                      ..+||.|+|+.|+..|...|.+ +.+..||..++..                 ..|||||+|+||+||++|+++++..+ 
T Consensus        65 ~~fFdsI~~~~L~~~l~~~~~~~~~~~~~l~~~~~~-----------------~~GlpQG~~lSp~Lanl~l~~~d~~l~  127 (214)
T cd03487          65 KDFFPSITFERVRGVFRSLGYFSPDVATILAKLCTY-----------------NGHLPQGAPTSPALSNLVFRKLDERLS  127 (214)
T ss_pred             hhhcccCCHHHHHHHHHHcCCCCHHHHHHHHHHHhC-----------------CCCcCCCCcccHHHHHHHHHHHHHHHH
Confidence            4679999999999999999998 8888888887632                 12999999999999999999998765 


Q ss_pred             -----CCcccccccchhhhhhhcCChhhhhhHHHHHHHHHhhhhhccccccccceeEEEeecCCCCccceeeeCCccccc
Q psy12268        250 -----PGFNFWLFADDLKVALRVGGQREVDSMQSMLSRLYHWCSINKMELNIGKCMVMTYHRNKSPILASYDINGQALAR  324 (410)
Q Consensus       250 -----~~i~~l~YADDivIis~s~s~~~~~~Lq~~Ld~L~~w~~~~GLkIN~~KTeim~f~~~~~~~~~~~ti~g~~I~~  324 (410)
                           .++.+++||||++|++.+...   ..+..++..+..|+..+||.+|++||.++..+.                  
T Consensus       128 ~~~~~~~~~~~RYaDD~~i~~~~~~~---~~~~~~~~~i~~~l~~~gL~ln~~Kt~i~~~~~------------------  186 (214)
T cd03487         128 KLAKSNGLTYTRYADDITFSSNKKLK---EALDKLLEIIRSILSEEGFKINKSKTRISSKGS------------------  186 (214)
T ss_pred             HHHHHcCCeEEEEeccEEEEccccch---hHHHHHHHHHHHHHHHCCceeCCCceEEccCCC------------------
Confidence                 367899999999998754311   367888999999999999999999999987643                  


Q ss_pred             cccccccceeecCc
Q psy12268        325 CEQVRDLGVTFQKT  338 (410)
Q Consensus       325 ves~KYLGV~Ld~k  338 (410)
                        .+.+||+.+++.
T Consensus       187 --~~~~~G~~i~~~  198 (214)
T cd03487         187 --RQIVTGLVVNNG  198 (214)
T ss_pred             --CcEEEEEEEeCC
Confidence              267888888754

The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.

>PF00078 RVT_1: Reverse transcriptase (RNA-dependent DNA polymerase); InterPro: IPR000477 The use of an RNA template to produce DNA, for integration into the host genome and exploitation of a host cell, is a strategy employed in the replication of retroid elements, such as the retroviruses and bacterial retrons

Probab=99.79  E-value=5e-21  Score=176.08  Aligned_cols=138  Identities=24%  Similarity=0.431  Sum_probs=120.9

Q ss_pred             HhhhcCCCHHHHHHHHHhCCCChHHHHHHHHHhhcceEEEeeCCccCCccccCccccCCCcchhhhhhhhhhhhhhcc--
Q psy12268        172 EEEKRKNEKAVRLTKLSAFGISGYLLQWIRNFLSGWIQIVRVGTSTSEPIHIPSGCIQGGHMSGLLFSLFINDIAEIF--  249 (410)
Q Consensus       172 ~~~~~~vdH~~Ll~~L~~~G~p~~li~lI~s~Ls~rs~~V~~~g~~S~~~~i~~GVPQGs~LSPLLFnL~l~~L~~~l--  249 (410)
                      ..+|+.|+|+.|...|..++.+..++.||.+++.++...+.+++.. ..+....|+|||+++||+||++|+++++..+  
T Consensus        72 ~~~f~sI~~~~l~~~l~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~-~~~~~~~glpqG~~~S~~l~~~~l~~l~~~~~~  150 (214)
T PF00078_consen   72 SKAFDSIPHHRLLRKLKRFGVPKKLIRLIQNLLSDRTAKVYLDGDL-SPYFQKRGLPQGSPLSPLLFNIYLDDLDRELQQ  150 (214)
T ss_dssp             CCCGGGSBBHTTTGGGGEEEEECCSCHHHHHHHHHHHH-EECGCSS-SEEEEESBS-TTSTCHHHHHHHHHHHHHHHHHH
T ss_pred             ccccccceeeeccccccccccccccccccccccccccccccccccc-ccccccccccccccccchhhccccccccccccc
Confidence            3589999999999999999999999999999999999999988876 8889999999999999999999999998754  


Q ss_pred             ---CCcccccccchhhhhhhcCChhhhhhHHHHHHHHHhhhhhccccccccceeEEEeecCCCCccceeeeCCccccccc
Q psy12268        250 ---PGFNFWLFADDLKVALRVGGQREVDSMQSMLSRLYHWCSINKMELNIGKCMVMTYHRNKSPILASYDINGQALARCE  326 (410)
Q Consensus       250 ---~~i~~l~YADDivIis~s~s~~~~~~Lq~~Ld~L~~w~~~~GLkIN~~KTeim~f~~~~~~~~~~~ti~g~~I~~ve  326 (410)
                         +++.+..||||++|++.     +...++..++.+..|+..+||.+|++||.+++                    +.+
T Consensus       151 ~~~~~~~~~rY~DD~~i~~~-----~~~~~~~~~~~i~~~~~~~gl~ln~~Kt~~~~--------------------~~~  205 (214)
T PF00078_consen  151 ELNPDISYLRYADDILIISK-----SKEELQKILEKISQWLEELGLKLNPEKTKILH--------------------PSD  205 (214)
T ss_dssp             HS-TTSEEEEETTEEEEEES-----SHHHHHHHHHHHHHHHHHTTSBCSSTTTSCS----------------------ES
T ss_pred             cccccccceEeccccEEEEC-----CHHHHHHHHHHHHHHHHHCCCEEChHHEEEEe--------------------CCC
Confidence               45789999999999984     34668899999999999999999999999755                    456


Q ss_pred             cccccceee
Q psy12268        327 QVRDLGVTF  335 (410)
Q Consensus       327 s~KYLGV~L  335 (410)
                      .+.|||+.|
T Consensus       206 ~~~~lG~~i  214 (214)
T PF00078_consen  206 SVKFLGYVI  214 (214)
T ss_dssp             SEEETTEEE
T ss_pred             CEEEEeEEC
Confidence            799999876

The enzyme catalysing polymerisation is an RNA-directed DNA-polymerase, or reverse trancriptase (RT) (2.7.7.49 from EC). Reverse transcriptase occurs in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. Retroviral reverse transcriptase is synthesised as part of the POL polyprotein that contains; an aspartyl protease, a reverse transcriptase, RNase H and integrase. POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. The discovery of retroelements in the prokaryotes raises intriguing questions concerning their roles in bacteria and the origin and evolution of reverse transcriptases and whether the bacterial reverse transcriptases are older than eukaryotic reverse transcriptases [].; GO: 0003723 RNA binding, 0003964 RNA-directed DNA polymerase activity, 0006278 RNA-dependent DNA replication; PDB: 1MU2_B 3RWE_C 3DU6_B 3DU5_A 3KYL_A 2WOM_B 1DTQ_A 2OPS_A 3FFI_A 1VRU_B ....

>cd01709 RT_like_1 RT_like_1: A subfamily of reverse transcriptases (RTs)

Probab=99.78  E-value=3.1e-18  Score=170.50  Aligned_cols=210  Identities=16%  Similarity=0.143  Sum_probs=142.0

Q ss_pred             hhhcCCCHHHHHHHHHhCCCChHHHHHHHHHhhcceEEEeeCCccCCccccCccccCCCcchhhhhhhhhhhhhhcc---
Q psy12268        173 EEKRKNEKAVRLTKLSAFGISGYLLQWIRNFLSGWIQIVRVGTSTSEPIHIPSGCIQGGHMSGLLFSLFINDIAEIF---  249 (410)
Q Consensus       173 ~~~~~vdH~~Ll~~L~~~G~p~~li~lI~s~Ls~rs~~V~~~g~~S~~~~i~~GVPQGs~LSPLLFnL~l~~L~~~l---  249 (410)
                      .-.|.|||+.|+.+|..+|++..++.+|..||..+-..+ -+|..+......+|+|||++|||+|.|+|++.++..+   
T Consensus        31 ~fFdsIpH~~Lm~vL~~~~~~~~wL~li~r~L~APl~~~-~dg~~~~~r~r~rGtPqGgviSplLaNiyL~~lD~~v~~~  109 (346)
T cd01709          31 WFGPSLPHSTILAVLKFFGVPEKWLDFFKKFLEAPLRFV-ADGPDAPPRIRKRGTPMSHALSDVFGELVLFCLDFAVNQA  109 (346)
T ss_pred             hhCCCCCHHHHHHHHHHhCCCHHHHHHHHHHHhCceeec-CCCCcccccccCCccCCCchhhHHHHHHHHHHHHHHHHhc
Confidence            347899999999999999999999999999996554433 1332345667789999999999999999999887643   


Q ss_pred             -CCcccccccchhhhhhhcCChhhhhhHHHHHHHHHhhhhhccccccccceeEEEeecCCCCccceeeeCCccccccccc
Q psy12268        250 -PGFNFWLFADDLKVALRVGGQREVDSMQSMLSRLYHWCSINKMELNIGKCMVMTYHRNKSPILASYDINGQALARCEQV  328 (410)
Q Consensus       250 -~~i~~l~YADDivIis~s~s~~~~~~Lq~~Ld~L~~w~~~~GLkIN~~KTeim~f~~~~~~~~~~~ti~g~~I~~ves~  328 (410)
                       +++.++.||||++++++      ......++..+..++...||+||++||.++.+.........    .....-|...+
T Consensus       110 ~~g~~l~RYaDD~vi~~~------~~~a~~aw~~i~~fl~~lGLelN~eKT~iV~~~~~~r~~~~----~~~~~LP~g~i  179 (346)
T cd01709         110 TDGGLLYRLHDDLWFWGQ------PETCAKAWKAIQEFAKVMGLELNKEKTGSVYLSDDTKTRDT----TIDATLPEGPV  179 (346)
T ss_pred             CCCceEEEEcCeEEEEcC------HHHHHHHHHHHHHHHHHcCceeccccceEEEeccCCccCCC----cccccCCCCCc
Confidence             57899999999999852      14455566788899999999999999999988754321000    00111122333


Q ss_pred             ccccee---------ecCcch-HHHHHHHHHHHHHhhhccCCCHHHHHHHHHhhc---------ccchhhhHHHhhhhHH
Q psy12268        329 RDLGVT---------FQKTLE-RQINDLIFIYKLVNNQIFCPDILTYSFTFSQEI---------GKQAEHNIIVLVEFAI  389 (410)
Q Consensus       329 KYLGV~---------Ld~kLs-~HI~~~ir~l~~l~R~~~~ls~~~k~~Lyks~V---------~P~L~Yg~~VW~~~~~  389 (410)
                      +|-=..         ||..+- .||..+..++..      +-|.-.-+..|++|+         .|..+||-    ..-.
T Consensus       180 ~wgfL~Ld~~~G~~~Idq~~Vd~hi~el~~QL~~------c~Sv~~wiq~WNsy~~~ff~~nFg~pa~cfGr----~Hvd  249 (346)
T cd01709         180 RWGFLKLDPKTGRWEIDQSQVDAHIDELRKQLDA------CKSVLSWIQAWNSYIGRFFSNNFGKPANCFGR----EHVD  249 (346)
T ss_pred             eeeeEEecCCCCcEEeeHHHHHHHHHHHHHHhhc------CchHHHHHHHHHHHHHHHHHHhcCCcchhcCH----HHHH
Confidence            333233         444443 676666533321      223344455566555         44444442    2344


Q ss_pred             HHHHHHHHHHHHHH
Q psy12268        390 ALVTILDQINRESF  403 (410)
Q Consensus       390 ~~i~~LdrvqR~~l  403 (410)
                      ..++++.++|+..|
T Consensus       250 ~~l~t~~riq~~lf  263 (346)
T cd01709         250 AILATHERIQRRLF  263 (346)
T ss_pred             HHHHHHHHHHHHhc
Confidence            57888888888865

An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.

>cd01646 RT_Bac_retron_I RT_Bac_retron_I: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons

Probab=99.76  E-value=5.4e-19  Score=159.04  Aligned_cols=139  Identities=16%  Similarity=0.153  Sum_probs=111.9

Q ss_pred             HhhhcCCCHHHHHHHHHhCCCChHHHHHHHHHhhcceEEEeeCCccCCccccCccccCCCcchhhhhhhhhhhhhhcc--
Q psy12268        172 EEEKRKNEKAVRLTKLSAFGISGYLLQWIRNFLSGWIQIVRVGTSTSEPIHIPSGCIQGGHMSGLLFSLFINDIAEIF--  249 (410)
Q Consensus       172 ~~~~~~vdH~~Ll~~L~~~G~p~~li~lI~s~Ls~rs~~V~~~g~~S~~~~i~~GVPQGs~LSPLLFnL~l~~L~~~l--  249 (410)
                      ...||+|+|+.|+..|...+.++.++.++..++...     ++...+.......|||||+++||+|+++|+.++...+  
T Consensus         4 ~~fF~sI~~~~l~~~l~~~~~~~~~~~~~~~~~~~~-----~~~~~~~~~~~~~GlpqG~~lS~~L~~~~l~~~d~~i~~   78 (158)
T cd01646           4 SNFYDSIYTHSLPWALHGKIKAKQLLKLLRLLGNLL-----DLLLLSSQYGQTNGLPIGPLTSRFLANIYLNDVDHELKS   78 (158)
T ss_pred             hhccCcchHHHHHHHHHhhhhhHhhhhhHHHHHHHH-----HHHHHhccCCCCceEccCcchHHHHHHHHHHHHHHHHHh
Confidence            357999999999999999999999998874444211     1122334567788999999999999999999988754  


Q ss_pred             --CCcccccccchhhhhhhcCChhhhhhHHHHHHHHHhhhhhccccccccceeEEEeecCCCCccceeeeCCcccccccc
Q psy12268        250 --PGFNFWLFADDLKVALRVGGQREVDSMQSMLSRLYHWCSINKMELNIGKCMVMTYHRNKSPILASYDINGQALARCEQ  327 (410)
Q Consensus       250 --~~i~~l~YADDivIis~s~s~~~~~~Lq~~Ld~L~~w~~~~GLkIN~~KTeim~f~~~~~~~~~~~ti~g~~I~~ves  327 (410)
                        .++.+++||||++|++.     +...++.+++.+..|+..+||.||++||.++.+....                 ..
T Consensus        79 ~~~~~~~~RY~DD~~i~~~-----~~~~~~~~~~~i~~~l~~~gL~ln~~Kt~~~~~~~~~-----------------~~  136 (158)
T cd01646          79 KLKGVDYVRYVDDIRIFAD-----SKEEAEEILEELKEFLAELGLSLNLSKTEILPLPEGT-----------------AS  136 (158)
T ss_pred             ccCCceEEEecCcEEEEcC-----CHHHHHHHHHHHHHHHHHCCCEEChhhceeeecCCCC-----------------cc
Confidence              56899999999999884     3456778899999999999999999999998886431                 44


Q ss_pred             ccccceeecC
Q psy12268        328 VRDLGVTFQK  337 (410)
Q Consensus       328 ~KYLGV~Ld~  337 (410)
                      +.+||+.+..
T Consensus       137 ~~flg~~~~~  146 (158)
T cd01646         137 KDFLGYRFSP  146 (158)
T ss_pred             ccccceEeeh
Confidence            7788887764

The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.

>cd01648 TERT TERT: Telomerase reverse transcriptase (TERT)

Probab=99.71  E-value=5.1e-18  Score=146.34  Aligned_cols=98  Identities=19%  Similarity=0.199  Sum_probs=79.2

Q ss_pred             ccccCccccCCCcchhhhhhhhhhhhhhccC--------CcccccccchhhhhhhcCChhhhhhHHHHHHHHHhhh-hhc
Q psy12268        220 PIHIPSGCIQGGHMSGLLFSLFINDIAEIFP--------GFNFWLFADDLKVALRVGGQREVDSMQSMLSRLYHWC-SIN  290 (410)
Q Consensus       220 ~~~i~~GVPQGs~LSPLLFnL~l~~L~~~l~--------~i~~l~YADDivIis~s~s~~~~~~Lq~~Ld~L~~w~-~~~  290 (410)
                      .+....|||||++|||+||++|++.++..+.        +..+++||||+++++.+     ...++.+++.+..|+ ..+
T Consensus        13 ~~~~~~GlpQG~~lSp~L~nl~l~~l~~~~~~~~~~~~~~~~~~rYaDD~li~~~~-----~~~~~~~~~~l~~~l~~~~   87 (119)
T cd01648          13 YYRQKVGIPQGSPLSSLLCSLYYADLENKYLSFLDVIDKDSLLLRLVDDFLLITTS-----LDKAIKFLNLLLRGFINQY   87 (119)
T ss_pred             hhhhcCcccCCcchHHHHHHHHHHHHHHHHHhhcccCCCCceEEEEeCcEEEEeCC-----HHHHHHHHHHHHHhhHHhh
Confidence            5778899999999999999999999887542        35689999999988743     366788899999997 999


Q ss_pred             cccccccceeEEEeecCCCCccceeeeCCccccccccccccceeec
Q psy12268        291 KMELNIGKCMVMTYHRNKSPILASYDINGQALARCEQVRDLGVTFQ  336 (410)
Q Consensus       291 GLkIN~~KTeim~f~~~~~~~~~~~ti~g~~I~~ves~KYLGV~Ld  336 (410)
                      ||.+|++||++.....              ...+...+.|||+.|+
T Consensus        88 gl~iN~~Kt~~~~~~~--------------~~~~~~~~~flG~~i~  119 (119)
T cd01648          88 KTFVNFDKTQINFSFA--------------QLDSSDLIPWCGLLIN  119 (119)
T ss_pred             CeEECcccceeecccc--------------ccCCCCccCceeEeeC
Confidence            9999999999875432              1123456999999875

Telomerase is a ribonucleoprotein (RNP) that synthesizes telomeric DNA repeats. The telomerase RNA subunit provides the template for synthesis of these repeats. The catalytic subunit of RNP is known as telomerase reverse transcriptase (TERT). The reverse transcriptase (RT) domain is located in the C-terminal region of the TERT polypeptide. Single amino acid substitutions in this region lead to telomere shortening and senescence. Telomerase is an enzyme that, in certain cells, maintains the physical ends of chromosomes (telomeres) during replication. In somatic cells, replication of the lagging strand requires the continual presence of an RNA primer approximately 200 nucleotides upstream, which is complementary to the template strand. Since there is a region of DNA less than 200 base pairs from the end of the chromosome where this is not possible, the chromosome is continually shortened. However, a surplus of repetitive DNA at

>cd00304 RT_like RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family

Probab=99.38  E-value=4.3e-13  Score=110.11  Aligned_cols=83  Identities=17%  Similarity=0.204  Sum_probs=70.6

Q ss_pred             ccCCCcchhhhhhhhhhhhhhcc----CCcccccccchhhhhhhcCChhhhhhHHHHHHHHHhhhhhccccccccceeEE
Q psy12268        227 CIQGGHMSGLLFSLFINDIAEIF----PGFNFWLFADDLKVALRVGGQREVDSMQSMLSRLYHWCSINKMELNIGKCMVM  302 (410)
Q Consensus       227 VPQGs~LSPLLFnL~l~~L~~~l----~~i~~l~YADDivIis~s~s~~~~~~Lq~~Ld~L~~w~~~~GLkIN~~KTeim  302 (410)
                      +|||+++||+||+++++.+...+    .++.+..||||+++++..     . .++..+..+..++..+||.+|++||.++
T Consensus        12 lPqG~~~Sp~l~~~~~~~l~~~~~~~~~~~~~~~Y~DD~~i~~~~-----~-~~~~~~~~l~~~l~~~gl~ln~~Kt~~~   85 (98)
T cd00304          12 LPQGSPLSPALANLYMEKLEAPILKQLLDITLIRYVDDLVVIAKS-----E-QQAVKKRELEEFLARLGLNLSDEKTQFT   85 (98)
T ss_pred             cCCCCchHHHHHHHHHHHHHHHHHHhcCCceEEEeeCcEEEEeCc-----H-HHHHHHHHHHHHHHHcCcEEChheeEEe
Confidence            99999999999999999999874    578999999999998742     2 6777888999999999999999999985


Q ss_pred             EeecCCCCccceeeeCCccccccccccccceee
Q psy12268        303 TYHRNKSPILASYDINGQALARCEQVRDLGVTF  335 (410)
Q Consensus       303 ~f~~~~~~~~~~~ti~g~~I~~ves~KYLGV~L  335 (410)
                      .                    ....+.|||+.+
T Consensus        86 ~--------------------~~~~~~flG~~~   98 (98)
T cd00304          86 E--------------------KEKKFKFLGILV   98 (98)
T ss_pred             c--------------------CCCCeeeeceeC
Confidence            1                    345588998764

An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.

>KOG4768|consensus

Probab=99.36  E-value=2.4e-12  Score=134.58  Aligned_cols=200  Identities=11%  Similarity=0.060  Sum_probs=133.8

Q ss_pred             hhhcCCCHHHHHHHHHhCCCChHHHHHHHHHhhcceEEEeeCCccCCccccCccccCCCcchhhhhhhhhhhhhhccC--
Q psy12268        173 EEKRKNEKAVRLTKLSAFGISGYLLQWIRNFLSGWIQIVRVGTSTSEPIHIPSGCIQGGHMSGLLFSLFINDIAEIFP--  250 (410)
Q Consensus       173 ~~~~~vdH~~Ll~~L~~~G~p~~li~lI~s~Ls~rs~~V~~~g~~S~~~~i~~GVPQGs~LSPLLFnL~l~~L~~~l~--  250 (410)
                      +-.|.|||+.|+..|+..--+..+++++..+|..-.+.  .++   ......-|+||||++||+|+++|+..|+..+.  
T Consensus       369 kcfdtIphd~LI~eL~~rIkdk~fidL~~kll~AGy~t--en~---ry~~~~lGtpqgsvvspil~nifL~~LDk~Lenk  443 (796)
T KOG4768|consen  369 KCFDTIPHDELIIELQKRIKDKGFIDLNYKLLRAGYTT--ENA---RYHVEFLGTPQGSVVSPILCNIFLRELDKRLENK  443 (796)
T ss_pred             HHhccccHHHHHHHHHHHHhhhhHHHHHHHHHhcCccc--ccc---ceecccccccccccCCchhHHHHHHHHHHHHHHH
Confidence            35799999999999999978899999999988543222  221   12345679999999999999999998885421  


Q ss_pred             --------------------------------------------------C------cccccccchhhhhhhcCChhhhh
Q psy12268        251 --------------------------------------------------G------FNFWLFADDLKVALRVGGQREVD  274 (410)
Q Consensus       251 --------------------------------------------------~------i~~l~YADDivIis~s~s~~~~~  274 (410)
                                                                        +      .-++.||||++|.+.+    +..
T Consensus       444 ~~nefn~~~~~~~rhs~yr~L~~~iakaKl~s~~sKtirlrd~~qrn~~n~~~gfkr~~yVRyadd~ii~v~G----S~n  519 (796)
T KOG4768|consen  444 HRNEFNAGHLRSARHSKYRNLSDSIAKAKLTSGMSKTIRLRDGVQRNETNDTAGFKRLMYVRYADDIIIGVWG----SVN  519 (796)
T ss_pred             HHhhhcccCcccccChhhhhHHHHHHHHHHhhhhhhhhhhhhcccccccCCccccceeeEEEecCCEEEEEec----cHH
Confidence                                                              0      2459999999997643    234


Q ss_pred             hHHHHHHHHHhhhhhccccccccceeEEEeecCCCCccceeeeCCccccc--cccccccceeecCcch----HHHHHHHH
Q psy12268        275 SMQSMLSRLYHWCSINKMELNIGKCMVMTYHRNKSPILASYDINGQALAR--CEQVRDLGVTFQKTLE----RQINDLIF  348 (410)
Q Consensus       275 ~Lq~~Ld~L~~w~~~~GLkIN~~KTeim~f~~~~~~~~~~~ti~g~~I~~--ves~KYLGV~Ld~kLs----~HI~~~ir  348 (410)
                      +..+.+..|..|+.++||++|++||++.+.....++  ..+.+.-.|..+  ......-|+.+.....    +-++.+++
T Consensus       520 d~K~ilr~In~f~sslGls~n~~kt~it~S~eg~~f--lg~nis~tP~r~~~~~~~gh~~i~~rn~~~i~inAPir~I~~  597 (796)
T KOG4768|consen  520 DCKQILRDINNFLSSLGLSNNSSKTQITVSREGTHF--LGYNISTTPGRPAAGEGGGHWAIRIRNETPIKINAPIRKILR  597 (796)
T ss_pred             HHHHHHHHHHHHHHhhCcccCcccceEEeeccceee--eeceeccCCCCccceeccccceEEeccCCceeecchHHHHHH
Confidence            455566777888889999999999998776443222  222222222222  2223333333333332    66666663


Q ss_pred             HHH---HHh--hh------cc-CCCHHHHHHHHHhhcccchhhhHHH
Q psy12268        349 IYK---LVN--NQ------IF-CPDILTYSFTFSQEIGKQAEHNIIV  383 (410)
Q Consensus       349 ~l~---~l~--R~------~~-~ls~~~k~~Lyks~V~P~L~Yg~~V  383 (410)
                      .+.   ...  +.      .| ...+.+.+..|.+++++++.|...+
T Consensus       598 KLr~~G~~s~~r~~Pr~V~rlt~~e~rtIin~~~ai~rg~lnYYr~a  644 (796)
T KOG4768|consen  598 KLRDRGYCSHGRPWPRHVGRLTNEEDRTIINWYAAIGRGILNYYRLA  644 (796)
T ss_pred             HHHhcceeecCCcCceeeeeecccCHHHHHHHHHHHhhchhhhhhHh
Confidence            332   111  11      11 5678999999999999999998655

>cd03714 RT_DIRS1 RT_DIRS1: Reverse transcriptases (RTs) occurring in the DIRS1 group of retransposons

Probab=98.74  E-value=6.2e-09  Score=89.22  Aligned_cols=71  Identities=15%  Similarity=0.253  Sum_probs=55.5

Q ss_pred             cccCCCcchhhhhhhhhhhhhhccC--CcccccccchhhhhhhcCChhhhhhHHHHHHHHHh-hhhhccccccccceeE
Q psy12268        226 GCIQGGHMSGLLFSLFINDIAEIFP--GFNFWLFADDLKVALRVGGQREVDSMQSMLSRLYH-WCSINKMELNIGKCMV  301 (410)
Q Consensus       226 GVPQGs~LSPLLFnL~l~~L~~~l~--~i~~l~YADDivIis~s~s~~~~~~Lq~~Ld~L~~-w~~~~GLkIN~~KTei  301 (410)
                      =+|||...||.+|..+|+.+...+.  +..+..|+||+.|++.+     .+.....+..+.. .+..+||.+|++||++
T Consensus        33 ~mp~Gl~~sp~~f~~~~~~i~~~~~~~~~~v~~Y~DDili~~~~-----~~~~~~~~~~l~~~~l~~~gl~ln~~K~~~  106 (119)
T cd03714          33 ALPFGLSLAPRVFTKVVEALLAPLRLLGVRIFSYLDDLLIIASS-----IKTSEAVLRHLRATLLANLGFTLNLEKSKL  106 (119)
T ss_pred             ecCCcccchHHHHHHHHHHHHHHhhcCCeEEEEEecCeEEEeCc-----HHHHHHHHHHHHHHHHHHcCCccChhhcEe
Confidence            3899999999999999999887643  45788999999998753     2333334444433 6889999999999996

Members of the subfamily include the Dictyostelium DIRS-1, Volvox carteri kangaroo, and Panagrellus redivivus PAT elements. These elements differ from LTR and conventional non-LTR retrotransposons. They contain split direct repeat (SDR) termini, and have been proposed to integrate via double-stranded closed-circle DNA intermediates assisted by an encoded recombinase which is similar to gamma-site-specific integrase.

>cd01645 RT_Rtv RT_Rtv: Reverse transcriptases (RTs) from retroviruses (Rtvs)

Probab=98.70  E-value=6.1e-09  Score=98.37  Aligned_cols=72  Identities=15%  Similarity=0.122  Sum_probs=61.3

Q ss_pred             ccccCCCcchhhhhhhhhhhhhhccC----CcccccccchhhhhhhcCChhhhhhHHHHHHHHHhhhhhcccccccccee
Q psy12268        225 SGCIQGGHMSGLLFSLFINDIAEIFP----GFNFWLFADDLKVALRVGGQREVDSMQSMLSRLYHWCSINKMELNIGKCM  300 (410)
Q Consensus       225 ~GVPQGs~LSPLLFnL~l~~L~~~l~----~i~~l~YADDivIis~s~s~~~~~~Lq~~Ld~L~~w~~~~GLkIN~~KTe  300 (410)
                      .++|||...||.+|+.+|+.+...+.    ++.+..|+||++|++.     +...+...+..+...+..+||.+|++||+
T Consensus       127 ~~lP~Gl~~SP~~f~~~m~~~l~~~~~~~~~~~~~~Y~DDili~s~-----~~~~~~~~l~~v~~~l~~~gl~ln~~K~~  201 (213)
T cd01645         127 KVLPQGMKNSPTICQSFVAQALEPFRKQYPDIVIYHYMDDILIASD-----LEGQLREIYEELRQTLLRWGLTIPPEKVQ  201 (213)
T ss_pred             EEeCCCCcChHHHHHHHHHHHHHHHHHHCCCeEEEEEcCCEEEEcC-----CHHHHHHHHHHHHHHHHHCCCEeCHHHEe
Confidence            57999999999999999998886543    4568899999999873     44667778888999999999999999998


Q ss_pred             E
Q psy12268        301 V  301 (410)
Q Consensus       301 i  301 (410)
                      .
T Consensus       202 ~  202 (213)
T cd01645         202 K  202 (213)
T ss_pred             C
Confidence            3

RTs catalyze the conversion of single-stranded RNA into double-stranded viral DNA for integration into host chromosomes. Proteins in this subfamily contain long terminal repeats (LTRs) and are multifunctional enzymes with RNA-directed DNA polymerase, DNA directed DNA polymerase, and ribonuclease hybrid (RNase H) activities. The viral RNA genome enters the cytoplasm as part of a nucleoprotein complex, and the process of reverse transcription generates in the cytoplasm forming a linear DNA duplex via an intricate series of steps. This duplex DNA is colinear with its RNA template, but contains terminal duplications known as LTRs that are not present in viral RNA. It has been proposed that two specialized template switches, known as strand-transfer reactions or "jumps", are required to generate the LTRs.

>KOG1005|consensus

Probab=98.52  E-value=3.9e-07  Score=99.26  Aligned_cols=97  Identities=26%  Similarity=0.334  Sum_probs=78.3

Q ss_pred             hHHHHHHHHHhhcceEEEeeCCccCCccccCccccCCCcchhhhhhhhhhhhhhccC------C-cccccccchhhhhhh
Q psy12268        194 GYLLQWIRNFLSGWIQIVRVGTSTSEPIHIPSGCIQGGHMSGLLFSLFINDIAEIFP------G-FNFWLFADDLKVALR  266 (410)
Q Consensus       194 ~~li~lI~s~Ls~rs~~V~~~g~~S~~~~i~~GVPQGs~LSPLLFnL~l~~L~~~l~------~-i~~l~YADDivIis~  266 (410)
                      ..+..||..+|.  +..|.++|   ..+....|||||++||.+|+.+|+++|.+.+-      + +.++.|+||+.++++
T Consensus       607 s~l~~vi~~~l~--~~~vki~~---k~yvq~~GIpQGs~LSslLc~lyy~dle~~y~~~~~~~g~~vLlR~vDDFLfITt  681 (888)
T KOG1005|consen  607 SDLFSVIRNMLS--TNYVKIGG---KSYVQKKGIPQGSILSSLLCHLYYGDLEDKYFSFEKEDGSIVLLRYVDDFLFITT  681 (888)
T ss_pred             hhHHHHHHHHHh--hheEEECC---eEEEEecCccCCCchhHHHHHHHHHhHHHHHhhcccCCCcEEEEEeecceEEEec
Confidence            456677777774  34555666   45778899999999999999999999997531      2 378999999999984


Q ss_pred             cCChhhhhhHHHHHHHHHhhhhhcccccccccee
Q psy12268        267 VGGQREVDSMQSMLSRLYHWCSINKMELNIGKCM  300 (410)
Q Consensus       267 s~s~~~~~~Lq~~Ld~L~~w~~~~GLkIN~~KTe  300 (410)
                           +..++..++..+..-...++.-.|..||.
T Consensus       682 -----~~~~a~kfl~~l~~Gf~~yn~~tn~~K~~  710 (888)
T KOG1005|consen  682 -----ENDQAKKFLKLLSRGFNKYNFFTNEPKTV  710 (888)
T ss_pred             -----CHHHHHHHHHHHhccccccceeccCcccc
Confidence                 44777788888888888999999999988

>cd03715 RT_ZFREV_like RT_ZFREV_like: A subfamily of reverse transcriptases (RTs) found in sequences similar to the intact endogenous retrovirus ZFERV from zebrafish and to Moloney murine leukemia virus RT

Probab=98.49  E-value=6.6e-08  Score=90.85  Aligned_cols=73  Identities=18%  Similarity=0.079  Sum_probs=62.3

Q ss_pred             CccccCCCcchhhhhhhhhhhhhhcc----CCcccccccchhhhhhhcCChhhhhhHHHHHHHHHhhhhhccccccccce
Q psy12268        224 PSGCIQGGHMSGLLFSLFINDIAEIF----PGFNFWLFADDLKVALRVGGQREVDSMQSMLSRLYHWCSINKMELNIGKC  299 (410)
Q Consensus       224 ~~GVPQGs~LSPLLFnL~l~~L~~~l----~~i~~l~YADDivIis~s~s~~~~~~Lq~~Ld~L~~w~~~~GLkIN~~KT  299 (410)
                      -.-+|||...||.+|..+|+.+...+    .+..+..|.||++|++     .+.......++.+...+..+|+.+|++||
T Consensus       122 ~~~lp~Gl~~sp~~f~~~~~~~l~~~~~~~~~~~~~~Y~DDili~s-----~~~~e~~~~l~~v~~~l~~~gl~l~~~K~  196 (210)
T cd03715         122 FTRLPQGFKNSPTLFHEALARDLAPFPLEHEGTILLQYVDDLLLAA-----DSEEDCLKGTDALLTHLGELGYKVSPKKA  196 (210)
T ss_pred             EEEEeccccCcHHHHHHHHHHHHHHHHhhCCCeEEEEECCcEEEec-----CCHHHHHHHHHHHHHHHHHCCCCcCHHHe
Confidence            35689999999999999999887765    3567789999999988     34466777888999999999999999999


Q ss_pred             eE
Q psy12268        300 MV  301 (410)
Q Consensus       300 ei  301 (410)
                      +.
T Consensus       197 ~~  198 (210)
T cd03715         197 QI  198 (210)
T ss_pred             eC
Confidence            95

An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs. Phylogenetic analysis suggests that ZFERV belongs to a distinct group of retroviruses.

>cd01647 RT_LTR RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long terminal repeats (LTRs) in their DNA copies but not in their RNA template

Probab=98.20  E-value=1.1e-06  Score=77.53  Aligned_cols=72  Identities=18%  Similarity=0.156  Sum_probs=60.7

Q ss_pred             ccccCCCcchhhhhhhhhhhhhhccCCcccccccchhhhhhhcCChhhhhhHHHHHHHHHhhhhhccccccccceeE
Q psy12268        225 SGCIQGGHMSGLLFSLFINDIAEIFPGFNFWLFADDLKVALRVGGQREVDSMQSMLSRLYHWCSINKMELNIGKCMV  301 (410)
Q Consensus       225 ~GVPQGs~LSPLLFnL~l~~L~~~l~~i~~l~YADDivIis~s~s~~~~~~Lq~~Ld~L~~w~~~~GLkIN~~KTei  301 (410)
                      ..+|||...||.+|..++..+...+.+..+..|+||++|.+.     +.......+..+...+..+|+.+|++||+.
T Consensus        94 ~~~p~G~~~s~~~~~~~~~~~l~~~~~~~~~~y~DDi~i~~~-----~~~~~~~~~~~~~~~l~~~~~~~~~~K~~~  165 (177)
T cd01647          94 TRMPFGLKNAPATFQRLMNKILGDLLGDFVEVYLDDILVYSK-----TEEEHLEHLREVLERLREAGLKLNPEKCEF  165 (177)
T ss_pred             EEecCCCccHHHHHHHHHHhhhccccccccEEEecCccccCC-----CHHHHHHHHHHHHHHHHHcCCEeCHHHcee
Confidence            569999999999999999998887777788899999999873     345555667777778889999999999984

RT catalyzes DNA replication from an RNA template, and is responsible for the replication of retroelements. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs are present in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and Caulimoviruses.

>COG3344 Retron-type reverse transcriptase [DNA replication, recombination, and repair]

Probab=96.74  E-value=0.0031  Score=63.39  Aligned_cols=86  Identities=15%  Similarity=0.132  Sum_probs=61.6

Q ss_pred             hhcCCCHHHHHHHHHhCCCChHHHHHHHHHh-hcceEEEeeCCccCCccccCccccCCCcchhhhhhhhhhhhhhccCCc
Q psy12268        174 EKRKNEKAVRLTKLSAFGISGYLLQWIRNFL-SGWIQIVRVGTSTSEPIHIPSGCIQGGHMSGLLFSLFINDIAEIFPGF  252 (410)
Q Consensus       174 ~~~~vdH~~Ll~~L~~~G~p~~li~lI~s~L-s~rs~~V~~~g~~S~~~~i~~GVPQGs~LSPLLFnL~l~~L~~~l~~i  252 (410)
                      -.|.++|..|+..+...--+...+.++.-++ .+....      ....-....|+|||+++||+|.++.++.+...+...
T Consensus       191 ~fd~~~h~~ll~~~~~~i~~~~~~~~~~r~~~~~~~~~------~~~~~~~~~~~~q~~~vs~~l~n~~l~~~~~~~~~~  264 (328)
T COG3344         191 CFDSINHKLLLYALDVTISDKLVLLLLGRILIAGYKTK------FNLKKSKEKGTPQGGLVSPILVNIKLSKLDNELRNR  264 (328)
T ss_pred             HhcccCHHHHHHHhHhhhcchHHHHHHHHHHHccccee------ecccccccccCCCCCccCchhhhhhhhhhhHHHHHH
Confidence            4588999999999999855666665553433 222221      112223678999999999999999998888755432


Q ss_pred             ---ccccccchhhhhh
Q psy12268        253 ---NFWLFADDLKVAL  265 (410)
Q Consensus       253 ---~~l~YADDivIis  265 (410)
                         .+..|+||..+..
T Consensus       265 ~~~~~~~y~~~~~i~~  280 (328)
T COG3344         265 YLNLLRRYIDDGNIDK  280 (328)
T ss_pred             HhhhhhhhcccccCCH
Confidence               4789999998865

>cd01699 RNA_dep_RNAP RNA_dep_RNAP: RNA-dependent RNA polymerase (RdRp) is an essential protein encoded in the genomes of all RNA containing viruses with no DNA stage

Probab=96.47  E-value=0.0042  Score=60.19  Aligned_cols=115  Identities=11%  Similarity=0.149  Sum_probs=71.4

Q ss_pred             CCCHHHHHHHHH---hCCCCh---HHHHHHHHHhhcceEEEeeCCccCCccccCccccCCCcch----hhhhhhhhhhhh
Q psy12268        177 KNEKAVRLTKLS---AFGISG---YLLQWIRNFLSGWIQIVRVGTSTSEPIHIPSGCIQGGHMS----GLLFSLFINDIA  246 (410)
Q Consensus       177 ~vdH~~Ll~~L~---~~G~p~---~li~lI~s~Ls~rs~~V~~~g~~S~~~~i~~GVPQGs~LS----PLLFnL~l~~L~  246 (410)
                      +++|..|...+.   .+.-++   .+..++..++..   .+..++.  ..+....|+|+|+++.    +++-++++....
T Consensus       109 s~~~~~l~~~~~i~~~~~~~~~~~~~~~l~~~~~~~---~~~~~~~--~~~~~~~G~pSG~~~T~~~Nsl~n~~~~~~a~  183 (278)
T cd01699         109 SLSPQLLEAEHSIYNALYDDDDELERRNLLRSLTNN---SLHIGFN--EVYKVRGGRPSGDPLTSIGNSIINCILVRYAF  183 (278)
T ss_pred             CCCHHHHHHHHHHHHHHHcCCchhHHHHHHHHHhcC---hhhhhCc--eEEEEcCCCCCCCCchhHHHHHHHHHHHHHHH
Confidence            567776665433   333333   467777777654   1112221  3566788999999885    444444444333


Q ss_pred             hc------cCCcccccccchhhhhhhcCChhhhhhHHHHHHHHHhhhhhccccccccceeEE
Q psy12268        247 EI------FPGFNFWLFADDLKVALRVGGQREVDSMQSMLSRLYHWCSINKMELNIGKCMVM  302 (410)
Q Consensus       247 ~~------l~~i~~l~YADDivIis~s~s~~~~~~Lq~~Ld~L~~w~~~~GLkIN~~KTeim  302 (410)
                      ..      ...+.++.|.||.++.+...      .....+..+..++..+||++++.++...
T Consensus       184 ~~~~~~~~~~~~~~~~~GDD~li~~~~~------~~~~~~~~~~~~~~~~G~~~~~~~~~~~  239 (278)
T cd01699         184 RKLGGKSFFKNVRLLNYGDDCLLSVEKA------DDKFNLETLAEWLKEYGLTMTDEDKVES  239 (278)
T ss_pred             HHHHHHHHhhceEEEEEcCCeEEEechh------HhhhCHHHHHHHHHHcCCEeCCcccCCC
Confidence            32      35678999999999977321      1122345677788889999999888764

RdRp catalyzes synthesis of the RNA strand complementary to a given RNA template. RdRps of many viruses are products of processing of polyproteins. Some RdRps consist of one polypeptide chain, and others are complexes of several subunits. The domain organization and the 3D structure of the catalytic center of a wide range of RdRps, including those with a low overall sequence homology, are conserved. The catalytic center is formed by several motifs containing a number of conserved amino acid residues. This subfamily represents the RNA-dependent RNA polymerases from all positive-strand RNA eukaryotic viruses with no DNA stage.

>cd01644 RT_pepA17 RT_pepA17: Reverse transcriptase (RTs) in retrotransposons

Probab=96.34  E-value=0.0027  Score=60.41  Aligned_cols=66  Identities=17%  Similarity=0.144  Sum_probs=53.7

Q ss_pred             CccccCCCcchhhhhhhhhhhhhhccCCc------ccccccchhhhhhhcCChhhhhhHHHHHHHHHhhhhhccccc
Q psy12268        224 PSGCIQGGHMSGLLFSLFINDIAEIFPGF------NFWLFADDLKVALRVGGQREVDSMQSMLSRLYHWCSINKMEL  294 (410)
Q Consensus       224 ~~GVPQGs~LSPLLFnL~l~~L~~~l~~i------~~l~YADDivIis~s~s~~~~~~Lq~~Ld~L~~w~~~~GLkI  294 (410)
                      -.-+|+|..-||.+|..+|+.++..+++.      ....|+||+++.+.     +...+...+..+...+...|+.+
T Consensus       101 ~~~~pFG~~~AP~~~~~~~~~~~~~~~~~~~~~~i~~~~YvDDili~~~-----s~~e~~~~~~~v~~~L~~~Gf~l  172 (213)
T cd01644         101 MTVVPFGAASAPFLANRALKQHAEDHPHEAAAKIIKRNFYVDDILVSTD-----TLNEAVNVAKRLIALLKKGGFNL  172 (213)
T ss_pred             EEEEccCCccchHHHHHHHHHHHhhcchhhHHHHHHHeeecccceecCC-----CHHHHHHHHHHHHHHHHhCCccc
Confidence            34599999999999999999999877652      46799999999873     44666777777888888899887

This subfamily represents the RT domain of a multifunctional enzyme. C-terminal to the RT domain is a domain homologous to aspartic proteinases (corresponding to Merops family A17) encoded by retrotransposons and retroviruses. RT catalyzes DNA replication from an RNA template and is responsible for the replication of retroelements.

>CHL00002 matK maturase K

Probab=91.45  E-value=1.4  Score=47.17  Aligned_cols=196  Identities=9%  Similarity=0.040  Sum_probs=102.1

Q ss_pred             HHHHHHHHhCCCChHHHHHHHHHhhcceEEEeeCCccCCccccCccccC-CCcchhhhhhhhhhhhhhcc----------
Q psy12268        181 AVRLTKLSAFGISGYLLQWIRNFLSGWIQIVRVGTSTSEPIHIPSGCIQ-GGHMSGLLFSLFINDIAEIF----------  249 (410)
Q Consensus       181 ~~Ll~~L~~~G~p~~li~lI~s~Ls~rs~~V~~~g~~S~~~~i~~GVPQ-Gs~LSPLLFnL~l~~L~~~l----------  249 (410)
                      ..|++.|+.+.-+...+++++.++..-.-   |+...++.-.+. -... ---+.-+|||.|+.+....+          
T Consensus       157 EiLvq~lr~wikD~~~LHlLR~fl~ey~n---~ns~~~~~k~~~-~f~k~n~rlf~fL~N~yv~E~Es~~~fl~kqs~~l  232 (504)
T CHL00002        157 EILVQTLRYWIKDASSLHLLRFFLHEYCN---WNSLITSKKSIS-FFSKENQRLFLFLYNSYVCEYESIFVFLRKQSSHL  232 (504)
T ss_pred             HHHHHHHhcccccCcHHHHHHHHHhhccc---ccccccccccce-eeccCCCceeeehhhhHHHHhHHhhheeecccccc
Confidence            37889999888889999999988864332   222211100000 0011 12344556666655433210          


Q ss_pred             --------------------------------------CCcccccccchhhhhhhcCChhhhhhHHHHHHHHHhhhhhcc
Q psy12268        250 --------------------------------------PGFNFWLFADDLKVALRVGGQREVDSMQSMLSRLYHWCSINK  291 (410)
Q Consensus       250 --------------------------------------~~i~~l~YADDivIis~s~s~~~~~~Lq~~Ld~L~~w~~~~G  291 (410)
                                                            |-+..+.||||.+|.+.|. ...+..+..  ..+.-|.....
T Consensus       233 rs~s~~~fler~~fy~Kie~~~~~~~~~f~~~l~~~kdp~ihYVRYaddfIIg~kGs-k~~a~KwK~--~l~~F~q~~f~  309 (504)
T CHL00002        233 RSTSSGVFLERIHFYGKIEHLVEVFRNDFQKTLWLFKDPFIHYVRYQGKSILASKGT-PLLMNKWKY--YLVNFWQCHFH  309 (504)
T ss_pred             cccccccchhcccceeeehhhhhhhcccccccceeeccceEEEEEECCcEEEEECCC-HHHHHHHHH--HHHHHHHHhce
Confidence                                                  1247899999998866443 223333332  33344566778


Q ss_pred             ccccccceeEEEeecCCC-CccceeeeCCccccccccccccceeecCcch-----HHHHHHHHH---------HH-HHhh
Q psy12268        292 MELNIGKCMVMTYHRNKS-PILASYDINGQALARCEQVRDLGVTFQKTLE-----RQINDLIFI---------YK-LVNN  355 (410)
Q Consensus       292 LkIN~~KTeim~f~~~~~-~~~~~~ti~g~~I~~ves~KYLGV~Ld~kLs-----~HI~~~ir~---------l~-~l~R  355 (410)
                      +.++|+||.+..++.... .....+.+...+......+-.-|..++....     .-+..++..         .| .+.+
T Consensus       310 l~~s~eKi~I~~ls~~s~~FLGY~~sv~~~~~~vRsqml~n~f~~~~~~kk~~~~VPi~~lI~~L~k~kfcni~G~PisK  389 (504)
T CHL00002        310 LWSQPGRIHINQLSNHSFDFLGYLSSVRLNPSVVRSQMLENSFLIDNAIKKFDTIVPIIPLIGSLAKAKFCNVLGHPISK  389 (504)
T ss_pred             eeecCCceeeccccCCcceeeeEEeeeeeccceeEechhhcceeeeccCCeEEeccCcHHHHHHHHHcCcccCCCCCcCC
Confidence            999999999888664321 1111112211111111111111222222211     122222211         11 2344


Q ss_pred             hcc-CCCHHHHHHHHHhhcccchhhhHHH
Q psy12268        356 QIF-CPDILTYSFTFSQEIGKQAEHNIIV  383 (410)
Q Consensus       356 ~~~-~ls~~~k~~Lyks~V~P~L~Yg~~V  383 (410)
                      ..| .++....+.-|.++++....|.+.+
T Consensus       390 ~~w~~lsD~dII~rf~~i~Rgl~~YYSgs  418 (504)
T CHL00002        390 PVWTDLSDSDIIDRFGRICRNLSHYYSGS  418 (504)
T ss_pred             ccccCCCHHHHHHHHHHHHhhhheecccc
Confidence            445 6788889999999999999997654

>PF00680 RdRP_1: RNA dependent RNA polymerase; InterPro: IPR001205 RNA-directed RNA polymerase (RdRp) (2

Probab=88.97  E-value=0.74  Score=48.79  Aligned_cols=97  Identities=13%  Similarity=0.172  Sum_probs=57.4

Q ss_pred             hHHHHHHHHHhhcceEEEeeCCccCCccccCccccCCCcchhhhhhhhhhhhhh-----ccC--------Ccccccccch
Q psy12268        194 GYLLQWIRNFLSGWIQIVRVGTSTSEPIHIPSGCIQGGHMSGLLFSLFINDIAE-----IFP--------GFNFWLFADD  260 (410)
Q Consensus       194 ~~li~lI~s~Ls~rs~~V~~~g~~S~~~~i~~GVPQGs~LSPLLFnL~l~~L~~-----~l~--------~i~~l~YADD  260 (410)
                      ..+..++..++..+.  +.++|   ..+.+..|+|-|+++-.++=+|+..-+..     ..+        .+.++.|-||
T Consensus       278 ~~~~~~l~~~~~~~~--~~~~g---~~y~~~~G~PSG~~~Tsi~NSi~N~i~~~~a~~~~~~~~~~~~~~~~~~i~YGDD  352 (491)
T PF00680_consen  278 SRLRRNLIQSICNPI--HLCGG---KVYRVNGGNPSGSPLTSIINSIVNNIYIRYAWRKLYPDPPREFFENVKLIVYGDD  352 (491)
T ss_dssp             HHHHHHHHHHHHEEE--EEETT---EEEEEESSS-TTSTTHHHHHHHHHHHHHHHHHHHHSTSCHGGGHHHSEEEEETTE
T ss_pred             hHHHHHHHHhcCCee--eeccc---ceeeeccccccccccchhccccccceeechhhhhccccccccccceeeeeeeccc
Confidence            444455555554432  23445   45789999999999865543332221111     111        2567999999


Q ss_pred             hhhhhhcCChhhhhhHHHHHHHHHhhhhhccccccc-cceeE
Q psy12268        261 LKVALRVGGQREVDSMQSMLSRLYHWCSINKMELNI-GKCMV  301 (410)
Q Consensus       261 ivIis~s~s~~~~~~Lq~~Ld~L~~w~~~~GLkIN~-~KTei  301 (410)
                      .++.+..    .....  .+..|..++..+|+++.+ +||..
T Consensus       353 ~l~sv~~----~~~~~--n~~~i~~~~~~~G~~~T~~dK~~~  388 (491)
T PF00680_consen  353 NLISVPP----EIDPW--NGETISEFLAELGLTYTDADKTGE  388 (491)
T ss_dssp             EEEEESS----HHHHH--HHHHHHHHHHTTTEEEEESSTSSS
T ss_pred             cchhhhc----ccccc--hhHHHHHHHHhcccccccccccCC
Confidence            9986631    11111  356677778889999885 88875

7.7.48 from EC) is an essential protein encoded in the genomes of all RNA containing viruses with no DNA stage [, ]. It catalyses synthesis of the RNA strand complementary to a given RNA template, but the precise molecular mechanism remains unclear. The postulated RNA replication process is a two-step mechanism. First, the initiation step of RNA synthesis begins at or near the 3' end of the RNA template by means of a primer-independent (de novo) mechanism. The de novo initiation consists in the addition of a nucleotide tri-phosphate (NTP) to the 3'-OH of the first initiating NTP. During the following so-called elongation phase, this nucleotidyl transfer reaction is repeated with subsequent NTPs to generate the complementary RNA product []. All the RNA-directed RNA polymerases, and many DNA-directed polymerases, employ a fold whose organisation has been likened to the shape of a right hand with three subdomains termed fingers, palm and thumb []. Only the catalytic palm subdomain, composed of a four-stranded antiparallel beta-sheet with two alpha-helices, is well conserved among all of these enzymes. In RdRp, the palm subdomain comprises three well conserved motifs (A, B and C). Motif A (D-x(4,5)-D) and motif C (GDD) are spatially juxtaposed; the Asp residues of these motifs are implied in the binding of Mg2+ and/or Mn2+. The Asn residue of motif B is involved in selection of ribonucleoside triphosphates over dNTPs and thus determines whether RNA is synthesised rather than DNA []. The domain organisation [] and the 3D structure of the catalytic centre of a wide range of RdPp's, even those with a low overall sequence homology, are conserved. The catalytic centre is formed by several motifs containing a number of conserved amino acid residues. There are 4 superfamilies of viruses that cover all RNA containing viruses with no DNA stage: Viruses containing positive-strand RNA or double-strand RNA, except retroviruses and Birnaviridae: viral RNA-directed RNA polymerases including all positive-strand RNA viruses with no DNA stage, double-strand RNA viruses, and the Cystoviridae, Reoviridae, Hypoviridae, Partitiviridae, Totiviridae families. Mononegavirales (negative-strand RNA viruses with non-segmented genomes). Negative-strand RNA viruses with segmented genomes, i.e. Orthomyxoviruses (including influenza A, B, and C viruses, Thogotoviruses, and the infectious salmon anemia virus), Arenaviruses, Bunyaviruses, Hantaviruses, Nairoviruses, Phleboviruses, Tenuiviruses and Tospoviruses. Birnaviridae family of dsRNA viruses. The RNA-directed RNA polymerases in the first of the above superfamilies can be divided into the following three subgroups: All positive-strand RNA eukaryotic viruses with no DNA stage. All RNA-containing bacteriophages -there are two families of RNA-containing bacteriophages: Leviviridae (positive ssRNA phages) and Cystoviridae (dsRNA phages). Reoviridae family of dsRNA viruses. This entry represents RNA-directed RNA polymerase found in many positive strand RNA eukaryotic viruses viruses. It is part of the genome polyprotein that contains other polypeptides such as coat proteins VP1 to VP4, core proteins P2A to P2C and P3A, genome-linked protein VPG and picornain 3C (3.4.22.28 from EC). Structural studies indicate that these proteins form the "right hand" structure found in all oligonucleotide polymerases, containing thumb, finger and palm domains, and also the additional bridging finger and thumb domains unique to RNA-directed RNA polymerases [, ].; GO: 0003723 RNA binding, 0003968 RNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3SFU_C 3NAH_A 3UR0_C 3UPF_C 3SFG_A 3NAI_C 3QID_B 3UQS_A 3OLB_M 3OLA_M ....

>KOG4364|consensus

Probab=85.33  E-value=10  Score=41.78  Aligned_cols=7  Identities=14%  Similarity=0.501  Sum_probs=2.9

Q ss_pred             HHHHHHH
Q psy12268        341 RQINDLI  347 (410)
Q Consensus       341 ~HI~~~i  347 (410)
                      .|+..+.
T Consensus       608 ~~~~A~~  614 (811)
T KOG4364|consen  608 KHLQALT  614 (811)
T ss_pred             HHHHHHH
Confidence            4444443

>PTZ00121 MAEBL; Provisional

Probab=83.52  E-value=41  Score=40.61  Aligned_cols=16  Identities=50%  Similarity=0.484  Sum_probs=7.1

Q ss_pred             hhHhhhcCCCHHHHHH
Q psy12268        170 KKEEEKRKNEKAVRLT  185 (410)
Q Consensus       170 ~~~~~~~~vdH~~Ll~  185 (410)
                      +++++.++=-+..|-.
T Consensus      1768 kkae~~RKQQEAaLed 1783 (2084)
T PTZ00121       1768 KKAEEIRKEKEAVIEE 1783 (2084)
T ss_pred             hhHHHHHHHHHHHHHH
Confidence            3344444444444444

>PF03431 RNA_replicase_B: RNA replicase, beta-chain ; InterPro: IPR005093 RNA-directed RNA polymerase (RdRp) (2

Probab=81.78  E-value=5.2  Score=42.37  Aligned_cols=133  Identities=13%  Similarity=0.061  Sum_probs=61.1

Q ss_pred             CChHHHHHHHHHhhcceEEEeeCCccCCccccCccccCCCcc-----hhhhhhhhhhh-hhhccCCcccccccchhhhhh
Q psy12268        192 ISGYLLQWIRNFLSGWIQIVRVGTSTSEPIHIPSGCIQGGHM-----SGLLFSLFIND-IAEIFPGFNFWLFADDLKVAL  265 (410)
Q Consensus       192 ~p~~li~lI~s~Ls~rs~~V~~~g~~S~~~~i~~GVPQGs~L-----SPLLFnL~l~~-L~~~l~~i~~l~YADDivIis  265 (410)
                      +|+.+..++.++=   +....++|..   +....=--+|.-.     |-|++.|+-.. +........+..|.||++|-+
T Consensus       267 lPp~~~~~l~~lR---s~~~~l~g~~---~~~ek~ssMGNGfTFELeSlif~ai~rs~~~~~~~~~~~v~iYGDDIIvp~  340 (542)
T PF03431_consen  267 LPPHWYRYLTDLR---SPYGSLDGKV---IRWEKISSMGNGFTFELESLIFWAIARSVCELLFGDTGTVRIYGDDIIVPS  340 (542)
T ss_dssp             S-HHHHHHHHHHS----SEEE-TS-E---EE-SBS--TTSTTHHHHHHHHHHHHHHHHHHHCT--GGG-EEETTEEEEEG
T ss_pred             CCHHHHHHHHHhc---cccceECCEE---EehhhhhccCCceeEeHHHHHHHHHHHHHHHHHcCCCCeeEEecCcEEech
Confidence            7788777776654   3444456643   3333333355433     33444444333 222223467889999998854


Q ss_pred             hcCChhhhhhHHHHHHHHHhhhhhccccccccceeEEEeecCCCCccceeeeCCccccccccccccceeecCcch----H
Q psy12268        266 RVGGQREVDSMQSMLSRLYHWCSINKMELNIGKCMVMTYHRNKSPILASYDINGQALARCEQVRDLGVTFQKTLE----R  341 (410)
Q Consensus       266 ~s~s~~~~~~Lq~~Ld~L~~w~~~~GLkIN~~KTeim~f~~~~~~~~~~~ti~g~~I~~ves~KYLGV~Ld~kLs----~  341 (410)
                      .            +...+......+|+..|..||-.-.                .--+.....-|.|+.+.+-.-    .
T Consensus       341 ~------------~~~~l~~~l~y~gF~~N~~KTF~~G----------------~FRESCG~h~f~g~DVtPfYik~pi~  392 (542)
T PF03431_consen  341 E------------CAPDLIEVLSYVGFKPNLKKTFWTG----------------PFRESCGAHYFDGVDVTPFYIKRPID  392 (542)
T ss_dssp             G------------GHHHHHHHHHHCT--B-CCC-BSSS----------------SEEEETTEEEETTEE-------S---
T ss_pred             h------------hhHHHHHHHHHhCcccCcccccccc----------------cchhhhhhhhcCCccccceEeccccc
Confidence            1            1223334455789999999987421                111122334566766665543    4


Q ss_pred             HHHHHHHHHHHHhhhcc
Q psy12268        342 QINDLIFIYKLVNNQIF  358 (410)
Q Consensus       342 HI~~~ir~l~~l~R~~~  358 (410)
                      .+..++..+..+.+|.-
T Consensus       393 ~l~dlililN~l~rW~~  409 (542)
T PF03431_consen  393 NLPDLILILNRLRRWGT  409 (542)
T ss_dssp             SHHHHHHHHHHHHHHHE
T ss_pred             CHHHHHHHHHhhccccc
Confidence            45555667777777654

7.7.48 from EC) is an essential protein encoded in the genomes of all RNA containing viruses with no DNA stage [, ]. It catalyses synthesis of the RNA strand complementary to a given RNA template, but the precise molecular mechanism remains unclear. The postulated RNA replication process is a two-step mechanism. First, the initiation step of RNA synthesis begins at or near the 3' end of the RNA template by means of a primer-independent (de novo) mechanism. The de novo initiation consists in the addition of a nucleotide tri-phosphate (NTP) to the 3'-OH of the first initiating NTP. During the following so-called elongation phase, this nucleotidyl transfer reaction is repeated with subsequent NTPs to generate the complementary RNA product []. All the RNA-directed RNA polymerases, and many DNA-directed polymerases, employ a fold whose organisation has been likened to the shape of a right hand with three subdomains termed fingers, palm and thumb []. Only the catalytic palm subdomain, composed of a four-stranded antiparallel beta-sheet with two alpha-helices, is well conserved among all of these enzymes. In RdRp, the palm subdomain comprises three well conserved motifs (A, B and C). Motif A (D-x(4,5)-D) and motif C (GDD) are spatially juxtaposed; the Asp residues of these motifs are implied in the binding of Mg2+ and/or Mn2+. The Asn residue of motif B is involved in selection of ribonucleoside triphosphates over dNTPs and thus determines whether RNA is synthesised rather than DNA []. The domain organisation [] and the 3D structure of the catalytic centre of a wide range of RdPp's, even those with a low overall sequence homology, are conserved. The catalytic centre is formed by several motifs containing a number of conserved amino acid residues. There are 4 superfamilies of viruses that cover all RNA containing viruses with no DNA stage: Viruses containing positive-strand RNA or double-strand RNA, except retroviruses and Birnaviridae: viral RNA-directed RNA polymerases including all positive-strand RNA viruses with no DNA stage, double-strand RNA viruses, and the Cystoviridae, Reoviridae, Hypoviridae, Partitiviridae, Totiviridae families. Mononegavirales (negative-strand RNA viruses with non-segmented genomes). Negative-strand RNA viruses with segmented genomes, i.e. Orthomyxoviruses (including influenza A, B, and C viruses, Thogotoviruses, and the infectious salmon anemia virus), Arenaviruses, Bunyaviruses, Hantaviruses, Nairoviruses, Phleboviruses, Tenuiviruses and Tospoviruses. Birnaviridae family of dsRNA viruses. The RNA-directed RNA polymerases in the first of the above superfamilies can be divided into the following three subgroups: All positive-strand RNA eukaryotic viruses with no DNA stage. All RNA-containing bacteriophages -there are two families of RNA-containing bacteriophages: Leviviridae (positive ssRNA phages) and Cystoviridae (dsRNA phages). Reoviridae family of dsRNA viruses. This is a family of Leviviridae RNA replicases.; GO: 0003968 RNA-directed RNA polymerase activity, 0019079 viral genome replication; PDB: 3MMP_G 3AVU_A 3AVW_A 3AGQ_A 3AGP_A 3AVT_A 3AVY_A 3AVX_A 3AVV_A.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	410
3kyl_A	596	Telomerase reverse transcriptase; reverse transcri	99.64
3fsi_A	255	RT, reverse transcriptase domain; transferase/DNA	98.57
1rw3_A	455	POL polyprotein; RNA and DNA dependent DNA polymer	98.25
2zd1_A	557	Reverse transcriptase/ribonuclease H; P51/P66, het	98.18
2zd1_B	428	P51 RT; P51/P66, hetero dimer, NNRTI, nonnucleosid	98.15
1mu2_A	555	HIV-2 RT; HIV-2 reverse transcriptase, AIDS, polym	98.07
1ra6_A	461	P3D, genome polyprotein; nucleotidyltransferase, R	96.01
1xr5_A	466	Genome polyprotein; RNA-dependent RNA polymerase,	95.96
2ckw_A	515	RNA-directed RNA polymerase; hydrolase, nucleotide	94.75
3uqs_A	515	RNA-dependent RNA polymerase; transferase; 2.00A {	94.21
1khv_A	516	RNA-directed RNA polymerase; RNA-dependent RNA pol	92.77
3n6m_A	462	RNA-dependent RNA polymerase; EV71, RDRP, GTP, tra	90.94
2ijd_1	644	Picornain 3C, RNA-directed RNA polymerase; RNA-dep	84.87
1xr7_A	460	Genome polyprotein; RNA-dependent RNA polymerase,	82.8
3bso_A	510	RNA dependent RNA polymerase; RNA-dependent RNA po	80.77
1u09_A	476	Polyprotein; protein-DNA complex, RNA-dependent RN	80.38

>3kyl_A Telomerase reverse transcriptase; reverse transcriptase; 2.70A {Tribolium castaneum} PDB: 3du5_A 3du6_A

Probab=99.64  E-value=2.1e-16  Score=162.57  Aligned_cols=114  Identities=13%  Similarity=0.105  Sum_probs=91.1

Q ss_pred             hhhcCCCHHHHHHHHHhCCC---ChHHHHHHHHHhhcceEEEeeCCccCCccccCccccCCCcchhhhhhhhhhhhhhcc
Q psy12268        173 EEKRKNEKAVRLTKLSAFGI---SGYLLQWIRNFLSGWIQIVRVGTSTSEPIHIPSGCIQGGHMSGLLFSLFINDIAEIF  249 (410)
Q Consensus       173 ~~~~~vdH~~Ll~~L~~~G~---p~~li~lI~s~Ls~rs~~V~~~g~~S~~~~i~~GVPQGs~LSPLLFnL~l~~L~~~l  249 (410)
                      .-+|.|+|+.|+..|+..+.   +..++.||..++...-  |..+|   ..+....|+|||++|||+|.|||++.+...+
T Consensus       254 kFFDnINHdkLLk~L~~~i~~IlDk~Il~LIkk~Lka~L--V~igG---k~y~qekGTPQGGVISPLLANIYLheLDkel  328 (596)
T 3kyl_A          254 DAYGNVKIPVLCKLIQSIPTHLLDSEKKNFIVDHISNQF--VAFRR---KIYKWNHGLLQGDPLSGCLCELYMAFMDRLY  328 (596)
T ss_dssp             STTTTCCHHHHHHHHTTSCTTTSCHHHHHHHHHHHHCEE--EESSS---SEEEECSSSCBTCTTHHHHHHHHHHHHHHHH
T ss_pred             hhCCCCCHHHHHHHHHhhccccccHHHHHHHHHHHhhCe--EEECC---EEEecCCcccCCcchhHHHHHHHHHHHHHHH
Confidence            46899999999999999875   7888999999986544  45565   3466789999999999999999999999764


Q ss_pred             -----CCcccccccchhhhhhhcCChhhhhhHHHHHHHHHhhhhhccccccccceeE
Q psy12268        250 -----PGFNFWLFADDLKVALRVGGQREVDSMQSMLSRLYHWCSINKMELNIGKCMV  301 (410)
Q Consensus       250 -----~~i~~l~YADDivIis~s~s~~~~~~Lq~~Ld~L~~w~~~~GLkIN~~KTei  301 (410)
                           .+..+++||||++|++.+     ...++.++..+..|     +++|++||.+
T Consensus       329 ~~~l~kd~~LVRYADDFVIi~~S-----ke~Aerfl~~Lkg~-----leLNpEKTrI  375 (596)
T 3kyl_A          329 FSNLDKDAFIHRTVDDYFFCSPH-----PHKVYDFELLIKGV-----YQVNPTKTRT  375 (596)
T ss_dssp             STTSCTTSEEEECSSEEEEEESC-----HHHHHHHHHHHHHH-----SCEEEEEEEE
T ss_pred             HHhhccCceEEEEcCcEEEEECC-----HHHHHHHHHHhhCc-----ceECchhcee
Confidence                 356799999999999843     24455555555544     3999999986

>3fsi_A RT, reverse transcriptase domain; transferase/DNA MMLV RT, protein-DNA complex, drug-DNA complex; HET: OWL; 1.75A {Moloney murine leukemia virus} SCOP: e.8.1.2 PDB: 1d1u_A 1n4l_A* 1ztt_A 2fjv_A* 2fjw_A 2fjx_A* 2fvp_A 2fvq_A 2fvr_A 2fvs_A 2r2r_A* 2r2s_A* 2r2t_A* 2r2u_A* 1ztw_A* 1i6j_A 1qaj_A* 1d0e_A* 1nnd_A 1mml_A ...

Probab=98.57  E-value=3e-08  Score=94.38  Aligned_cols=87  Identities=21%  Similarity=0.140  Sum_probs=71.7

Q ss_pred             cccCCCcchhhhhhhhhhhhhhcc----CCcccccccchhhhhhhcCChhhhhhHHHHHHHHHhhhhhccccccccceeE
Q psy12268        226 GCIQGGHMSGLLFSLFINDIAEIF----PGFNFWLFADDLKVALRVGGQREVDSMQSMLSRLYHWCSINKMELNIGKCMV  301 (410)
Q Consensus       226 GVPQGs~LSPLLFnL~l~~L~~~l----~~i~~l~YADDivIis~s~s~~~~~~Lq~~Ld~L~~w~~~~GLkIN~~KTei  301 (410)
                      -+|||..-||.+|..+|+.+...+    +++.+..|+||++|++.     +...+...+..+..++..+||.+|++||+.
T Consensus       164 ~mPfGl~~sP~~fq~~m~~il~~~~~~~~~~~v~~Y~DDili~s~-----~~eeh~~~l~~v~~~L~~~gl~l~~~Kc~f  238 (255)
T 3fsi_A          164 RLPQGFKNSPTLFDEALHRDLADFRIQHPDLILLQYVDDLLLAAT-----SELDCQQGTRALLQTLGNLGYRASAKKAQI  238 (255)
T ss_dssp             BCCTTCTTHHHHHHHHHHHHTHHHHHHCTTCEEEEETTEEEEEES-----SHHHHHHHHHHHHHHHHHHTCCBCTTTCEE
T ss_pred             EeCCCCCCcHHHHHHHHHHHHHHHHHhCcCcEEEEEcCCeEEEeC-----CHHHHHHHHHHHHHHHHHCCeEECHHHhcc
Confidence            369999999999999999888754    45678999999999873     445666678889999999999999999985


Q ss_pred             EEeecCCCCccceeeeCCccccccccccccceeecCcc
Q psy12268        302 MTYHRNKSPILASYDINGQALARCEQVRDLGVTFQKTL  339 (410)
Q Consensus       302 m~f~~~~~~~~~~~ti~g~~I~~ves~KYLGV~Ld~kL  339 (410)
                      ..                      ..+.|||+.|+...
T Consensus       239 ~~----------------------~~~~fLG~~i~~~g  254 (255)
T 3fsi_A          239 CQ----------------------KQVKYLGYLLKEGQ  254 (255)
T ss_dssp             EE----------------------SEEEETTEEEETTB
T ss_pred             cC----------------------CceEEEEEEEeCCc
Confidence            22                      24799999998653

>1rw3_A POL polyprotein; RNA and DNA dependent DNA polymerase, reverse transcriptase, transferase, replication; 3.00A {Moloney murine leukemia virus} SCOP: e.8.1.2

Probab=98.25  E-value=4.7e-07  Score=93.02  Aligned_cols=71  Identities=20%  Similarity=0.094  Sum_probs=59.8

Q ss_pred             cccCCCcchhhhhhhhhhhhhhcc----CCcccccccchhhhhhhcCChhhhhhHHHHHHHHHhhhhhccccccccceeE
Q psy12268        226 GCIQGGHMSGLLFSLFINDIAEIF----PGFNFWLFADDLKVALRVGGQREVDSMQSMLSRLYHWCSINKMELNIGKCMV  301 (410)
Q Consensus       226 GVPQGs~LSPLLFnL~l~~L~~~l----~~i~~l~YADDivIis~s~s~~~~~~Lq~~Ld~L~~w~~~~GLkIN~~KTei  301 (410)
                      -+|||..-||.+|..+|+.++..+    ++..+..|+||++|++.     +...+...+..+...+..+||.+|++||..
T Consensus       168 ~mpfGl~naP~~fq~~m~~~l~~~~~~~~~~~v~~YvDDili~s~-----~~~e~~~~l~~v~~~l~~~gl~l~~~K~~f  242 (455)
T 1rw3_A          168 RLPQGFKNSPTLFDEALHRDLADFRIQHPDLILLQYVDDLLLAAT-----SELDCQQGTRALLQTLGNLGYRASAKKAQI  242 (455)
T ss_dssp             BCCSSCTTHHHHHHHHHHHHHHHHHHTCTTCEEEEETTEEEEEES-----SHHHHHHHHHHHHHHHHHHTCCBCGGGCCC
T ss_pred             ecCCCCCCcHHHHHHHHHHHHHHhhhhCCCceEEEEcCCEEEecC-----CHHHHHHHHHHHHHHHHHcCCccCccchhh
Confidence            479999999999999999888755    56788999999999873     345556677888888899999999999985

>2zd1_A Reverse transcriptase/ribonuclease H; P51/P66, hetero dimer, NNRTI, nonnucleoside inhibitor, AIDS, HIV, rilpivirine, diarylpyrimidine, DAPY, DNA recombination; HET: T27; 1.80A {Human immunodeficiency virus 1} PDB: 3is9_A* 3irx_A* 2ze2_A* 3bgr_A* 3qlh_A* 3klf_A* 3qo9_A* 1dlo_A 1bqm_A 2be2_A* 1s6q_A* 1s6p_A* 1s9g_A* 1suq_A* 2b5j_A* 2b6a_A* 2ban_A* 1s9e_A* 1hni_A* 1hnv_A* ...

Probab=98.18  E-value=2.1e-06  Score=90.52  Aligned_cols=110  Identities=16%  Similarity=0.121  Sum_probs=78.7

Q ss_pred             ccccCCCcchhhhhhhhhhhhhhcc----CCcccccccchhhhhhhcCChhhhhhHHHHHHHHHhhhhhcccccccccee
Q psy12268        225 SGCIQGGHMSGLLFSLFINDIAEIF----PGFNFWLFADDLKVALRVGGQREVDSMQSMLSRLYHWCSINKMELNIGKCM  300 (410)
Q Consensus       225 ~GVPQGs~LSPLLFnL~l~~L~~~l----~~i~~l~YADDivIis~s~s~~~~~~Lq~~Ld~L~~w~~~~GLkIN~~KTe  300 (410)
                      ..+|||...||.+|..+|+.++..+    +++.+..|.||++|++.+    +...+...|..+...+..+||.+|++||.
T Consensus       149 ~~mPfGl~nap~~fq~~m~~il~~~~~~~~~~~v~~Y~DDIli~s~~----~~~eh~~~l~~v~~~l~~~gl~l~~~Kc~  224 (557)
T 2zd1_A          149 NVLPQGWKGSPAIFQSSMTKILEPFAAQNPDIVIYQYMDDLYVGSDL----EIGQHRTKIEELRQHLLRWGLTTPDKKHQ  224 (557)
T ss_dssp             SBCCTTCTTHHHHHHHHHHHHHHHHHHTCTTEEEEEETTEEEEEECS----CHHHHHHHHHHHHHHHHTTTCCCCCSCCS
T ss_pred             EeeCCCCCCHHHHHHHHHHHHHHHhhhcCCCceEEEEecCEEEecCc----hHHHHHHHHHHHHHHHHHcCCccChhhcC
Confidence            4589999999999999999888654    345688999999998731    23445556778888889999999999997


Q ss_pred             EEEeecCCCCccceeeeCCccccccccccccceeecCcc--------------h-HHHHHHHHHHHHHhhhccCCC
Q psy12268        301 VMTYHRNKSPILASYDINGQALARCEQVRDLGVTFQKTL--------------E-RQINDLIFIYKLVNNQIFCPD  361 (410)
Q Consensus       301 im~f~~~~~~~~~~~ti~g~~I~~ves~KYLGV~Ld~kL--------------s-~HI~~~ir~l~~l~R~~~~ls  361 (410)
                      .   ..                    ++.|||+.+++..              + ..++..+..+++.++.+..++
T Consensus       225 f---~~--------------------~~~fLG~~i~~~gi~~~~~k~~~~~~~t~k~lr~flG~~~~yrrfi~~~~  277 (557)
T 2zd1_A          225 K---EP--------------------PFLWMGYELHPDKWTVQPIVLPEKDSWTVNDIQKLVGKLNWASQIYPGIK  277 (557)
T ss_dssp             C---CS--------------------SEEETTEEECSSCEEESCCCCCCCSCEEHHHHHHHHHHHHHHTTTSTTCC
T ss_pred             C---CC--------------------ceEEeeEEEccCcEEEcceecccccCCCHHHHHHHhhHHHhhhhhccchh
Confidence            3   11                    2567777766554              2 455555566666666554444

>2zd1_B P51 RT; P51/P66, hetero dimer, NNRTI, nonnucleoside inhibitor, AIDS, HIV, rilpivirine, diarylpyrimidine, DAPY, DNA recombination; HET: T27; 1.80A {Human immunodeficiency virus 1} SCOP: e.8.1.2 PDB: 2ykm_B* 2ykn_B* 2ze2_B* 3bgr_B* 3ig1_B* 3irx_B* 3is9_B* 3qo9_B* 3v4i_B* 3v6d_B* 3v81_B* 3klf_B* 3kk1_B* 3kjv_B* 3kk2_B* 3kk3_B* 2be2_B* 1n5y_B* 1bqm_B* 1n6q_B* ...

Probab=98.15  E-value=1.7e-06  Score=88.55  Aligned_cols=110  Identities=16%  Similarity=0.121  Sum_probs=69.8

Q ss_pred             ccccCCCcchhhhhhhhhhhhhhcc----CCcccccccchhhhhhhcCChhhhhhHHHHHHHHHhhhhhcccccccccee
Q psy12268        225 SGCIQGGHMSGLLFSLFINDIAEIF----PGFNFWLFADDLKVALRVGGQREVDSMQSMLSRLYHWCSINKMELNIGKCM  300 (410)
Q Consensus       225 ~GVPQGs~LSPLLFnL~l~~L~~~l----~~i~~l~YADDivIis~s~s~~~~~~Lq~~Ld~L~~w~~~~GLkIN~~KTe  300 (410)
                      ..+|||...||.+|..+|+.++..+    +++.+..|+||++|++.+    +...+...+..+...+..+||.+|++||.
T Consensus       147 ~vmPfGl~nsPa~fq~~m~~il~~~~~~~~~~~v~vY~DDIlI~s~~----~~~eh~~~l~~v~~~l~~~gL~l~~~Kc~  222 (428)
T 2zd1_B          147 NVLPQGWKGSPAIFQSSMTKILEPFKKQNPDIVIYQYMDDLYVGSDL----EIGQHRTKIEELRQHLLRWGLTTPDKKHQ  222 (428)
T ss_dssp             SBCCTTCTHHHHHHHHHHHHHHHHHHHHCTTCEEEEETTEEEEEECS----CHHHHHHHHHHHHHHHHHHHC--------
T ss_pred             EeeCCCCcchHHHHHHHHHHHHHHHhhcCCCceEEEEecceEEecCC----cHHHHHHHHHHHHHHHHHhCCccChhHcc
Confidence            4589999999999999999888654    345688999999998732    23445566777778888999999999998


Q ss_pred             EEEeecCCCCccceeeeCCccccccccccccceeecCcc--------------h-HHHHHHHHHHHHHhhhccCCC
Q psy12268        301 VMTYHRNKSPILASYDINGQALARCEQVRDLGVTFQKTL--------------E-RQINDLIFIYKLVNNQIFCPD  361 (410)
Q Consensus       301 im~f~~~~~~~~~~~ti~g~~I~~ves~KYLGV~Ld~kL--------------s-~HI~~~ir~l~~l~R~~~~ls  361 (410)
                      .   ..                    ++.|||+.|++..              + ..++..+..+++.++.+.+++
T Consensus       223 ~---~~--------------------~~~fLG~~i~~~~i~~~~~ki~~~~~~t~k~lr~flG~~~yyrrFi~~~s  275 (428)
T 2zd1_B          223 K---EP--------------------PFLWMGYELHPDKWTVQPIVLPEKDSWTVNDIQKLVGKLNWASQIYPGIK  275 (428)
T ss_dssp             ---------------------------CTTCCEEECGGGCCCCCCCCCCCSSEEHHHHHHHHHHHHHHTTTCTTCC
T ss_pred             c---cc--------------------eEEEeccEecCCceEecccccccccccCHHHHHHHhhhHHHHHHhcCCcc
Confidence            3   11                    2466666666443              2 455555566666666555444

>1mu2_A HIV-2 RT; HIV-2 reverse transcriptase, AIDS, polymerase, drug design, transferase; 2.35A {Human immunodeficiency virus 2} SCOP: c.55.3.1 e.8.1.2 PDB: 1mu2_B

Probab=98.07  E-value=4.5e-06  Score=87.99  Aligned_cols=72  Identities=15%  Similarity=0.040  Sum_probs=58.3

Q ss_pred             ccccCCCcchhhhhhhhhhhhhhcc----CCcccccccchhhhhhhcCChhhhhhHHHHHHHHHhhhhhcccccccccee
Q psy12268        225 SGCIQGGHMSGLLFSLFINDIAEIF----PGFNFWLFADDLKVALRVGGQREVDSMQSMLSRLYHWCSINKMELNIGKCM  300 (410)
Q Consensus       225 ~GVPQGs~LSPLLFnL~l~~L~~~l----~~i~~l~YADDivIis~s~s~~~~~~Lq~~Ld~L~~w~~~~GLkIN~~KTe  300 (410)
                      ..+|||-.-||.+|..+|+.++..+    +++.+..|.||++|++..    +...+...|..+...+..+||.+|++||.
T Consensus       147 ~~mPfGl~napa~fq~~m~~il~~~~~~~~~~~v~~Y~DDIli~s~~----~~~eh~~~l~~v~~~l~~~gl~l~~~K~~  222 (555)
T 1mu2_A          147 KVLPQGWKGSPAIFQHTMRQVLEPFRKANKDVIIIQYMDDILIASDR----TDLEHDRVVLQLKELLNGLGFSTPDEKFQ  222 (555)
T ss_dssp             SBCCTTCTTHHHHHHHHHHHHHHHHHHHCTTSEEEEETTEEEEEECS----CHHHHHHHHHHHHHHHHHTTCBCCSTTEE
T ss_pred             EEeCCCCCCcHHHHHHHHHHHHHHHHhhCCCcEEEEEecceEEecCC----CHHHHHHHHHHHHHHHHHcCCccCHHHhc
Confidence            4689999999999999999888654    456689999999998731    23455556777788888999999999984

>1ra6_A P3D, genome polyprotein; nucleotidyltransferase, RNA-dependent, polym terminus, transferase; 2.00A {Human poliovirus 1} SCOP: e.8.1.4 PDB: 1ra7_A* 2ily_A* 2ilz_A* 2im0_A* 2im1_A* 2im2_A* 2im3_A* 2ijf_A 3ol9_A* 3ol7_A 3ol8_A 3ol6_A* 3ola_A* 3olb_A* 1tql_A 1rdr_A 1raj_A 3ddk_A 3cdu_A 3cdw_A

Probab=96.01  E-value=0.0034  Score=64.73  Aligned_cols=105  Identities=11%  Similarity=0.097  Sum_probs=67.5

Q ss_pred             HHHHHHhCCCChHHHHHHHHHhhcceEEEeeCCccCCccccCccccCCCcc----hhhhhhhhhhhhhhc------cCCc
Q psy12268        183 RLTKLSAFGISGYLLQWIRNFLSGWIQIVRVGTSTSEPIHIPSGCIQGGHM----SGLLFSLFINDIAEI------FPGF  252 (410)
Q Consensus       183 Ll~~L~~~G~p~~li~lI~s~Ls~rs~~V~~~g~~S~~~~i~~GVPQGs~L----SPLLFnL~l~~L~~~------l~~i  252 (410)
                      +...|..+++++. ..++..++. +  .+..+|   ..+....|+|.|+|.    .+++-++++.-+...      +..+
T Consensus       249 ~~~il~~~~~~~~-~~l~~~l~~-~--~~~~~g---~v~~~~~G~PSG~p~Tsv~NSl~n~i~~~~~~~~~~~~~~~~~~  321 (461)
T 1ra6_A          249 LKMVLEKIGFGDR-VDYIDYLNH-S--HHLYKN---KTYXVKGGMPSGXSGTSIFNSMINNLIIRTLLLKTYKGIDLDHL  321 (461)
T ss_dssp             HHHHHHHTTTGGG-THHHHHHHE-E--EEEETT---EEEEEESCCCTBSTTHHHHHHHHHHHHHHHHHHHHSTTCCGGGC
T ss_pred             HHHHHHHhCCCcH-HHHHHhhcC-e--EEEECC---EEEEEEeecCCCCCeeeeehHHHHHHHHHHHHHHcCCCCCCceE
Confidence            3467778888876 666666654 2  244556   467889999999765    344434444332211      1246


Q ss_pred             ccccccchhhhhhhcCChhhhhhHHHHHHHHHhhhhhccccccc-cceeEEE
Q psy12268        253 NFWLFADDLKVALRVGGQREVDSMQSMLSRLYHWCSINKMELNI-GKCMVMT  303 (410)
Q Consensus       253 ~~l~YADDivIis~s~s~~~~~~Lq~~Ld~L~~w~~~~GLkIN~-~KTeim~  303 (410)
                      .++.|.||.++.....       +  .++.+...+..+||++++ +||..+.
T Consensus       322 ~~~~yGDD~i~~~~~~-------~--~~~~l~~~~~~~Gl~~t~~dKt~~~~  364 (461)
T 1ra6_A          322 KMIAYGDDVIASYPHE-------V--DASLLAQSGKDYGLTMTPADKSATFE  364 (461)
T ss_dssp             EEEEETTEEEEEESSC-------C--CHHHHHHHHHHTTCCEESTTTCSSCC
T ss_pred             EEEecCCceEEEeccc-------c--CHHHHHHHHHHcCceecccccCCCCC
Confidence            7889999999865321       1  245677777889999995 7988543

>1xr5_A Genome polyprotein; RNA-dependent RNA polymerase, transferase; 2.80A {Human rhinovirus 14} SCOP: e.8.1.4

Probab=95.96  E-value=0.0037  Score=64.51  Aligned_cols=100  Identities=14%  Similarity=0.151  Sum_probs=64.1

Q ss_pred             HHHHhCCCChHHHHHHHHHhhcceEEEeeCCccCCccccCccccCCCcc----hhhhhhhhhhhhhhc-c-----CCccc
Q psy12268        185 TKLSAFGISGYLLQWIRNFLSGWIQIVRVGTSTSEPIHIPSGCIQGGHM----SGLLFSLFINDIAEI-F-----PGFNF  254 (410)
Q Consensus       185 ~~L~~~G~p~~li~lI~s~Ls~rs~~V~~~g~~S~~~~i~~GVPQGs~L----SPLLFnL~l~~L~~~-l-----~~i~~  254 (410)
                      ..|..+++++.  .++..++. +  .+..+|   ..+....|+|+|++.    .+++-++++..+... .     ..+.+
T Consensus       251 ~il~~~~~~~~--~l~~~l~~-~--~~~~~g---~v~~~~~G~PSG~p~Tsi~NSi~n~i~i~~a~~~~~~~~~~~~~~~  322 (466)
T 1xr5_A          251 KVLTKLGFAGS--SLIQSICN-T--HHIFRD---EIYVVEGGMPSGCSGTSIFNSMINNIIIRTLILDAYKGIDLDKLKI  322 (466)
T ss_dssp             HHHHHHTCTTT--THHHHHHS-E--EEECSS---SEEEEESCCCTTSSSHHHHHHHHHHHHHHHHHHHHCSSCCGGGCEE
T ss_pred             HHHHHcCCChH--HHHHHhhC-c--EEEECC---EEEEEeCcCCCCCCchhchhhHHHHHHHHHHHHHHhcCCCccceEE
Confidence            45667778774  45555553 2  234444   567889999999654    555544544443221 1     24678


Q ss_pred             ccccchhhhhhhcCChhhhhhHHHHHHHHHhhhhhccccccc-cceeE
Q psy12268        255 WLFADDLKVALRVGGQREVDSMQSMLSRLYHWCSINKMELNI-GKCMV  301 (410)
Q Consensus       255 l~YADDivIis~s~s~~~~~~Lq~~Ld~L~~w~~~~GLkIN~-~KTei  301 (410)
                      +.|.||.++.....    .     .++.+...+..+||.+++ +||..
T Consensus       323 ~~yGDD~iis~~~~----~-----~~~~l~~~~~~~Gl~~t~~dKt~~  361 (466)
T 1xr5_A          323 LAYGDDLIVSYPYE----L-----DPQVLATLGKNYGLTITPPDKSET  361 (466)
T ss_dssp             EEETTEEEEECSSC----C-----CHHHHHHHHTTTTCCEECCSSCSS
T ss_pred             EEECCCCCceeCCC----C-----CHHHHHHHHHHcCCccChhhhcCC
Confidence            89999999865321    1     245566677889999998 89984

>2ckw_A RNA-directed RNA polymerase; hydrolase, nucleotide-binding, nucleotidyltransferase, covalent protein-RNA linkage, RNA elongation; 2.3A {Sapporo virus} PDB: 2uuw_A 2wk4_A 2uut_A

Probab=94.75  E-value=0.11  Score=54.18  Aligned_cols=106  Identities=13%  Similarity=0.103  Sum_probs=55.3

Q ss_pred             HHHHHhCCCChHHHH-HHHHHhhcceEEEeeCCccCCccccCccccCCCcchhhhhhh----hhhhhh-hc---------
Q psy12268        184 LTKLSAFGISGYLLQ-WIRNFLSGWIQIVRVGTSTSEPIHIPSGCIQGGHMSGLLFSL----FINDIA-EI---------  248 (410)
Q Consensus       184 l~~L~~~G~p~~li~-lI~s~Ls~rs~~V~~~g~~S~~~~i~~GVPQGs~LSPLLFnL----~l~~L~-~~---------  248 (410)
                      +..|..+..+..+.. ++.+++. +. .+..+|.   .+....|+|=|+++-.++=+|    ++..+. ..         
T Consensus       259 ~~i~~~~~~~~~~~~~~~~~L~~-~~-i~~~~g~---v~~~~~G~PSG~p~Tsi~NSi~N~i~~~~a~~~~~~~~~~~~~  333 (515)
T 2ckw_A          259 LAILERFAEPHPIVSCAIEALSS-PA-EGYVNDI---KFVTRGGLPSGMPFTSVVNSINHMIYVAAAILQAYESHNVPYT  333 (515)
T ss_dssp             HHHHHTTBCCCTHHHHHHHHHHS-CC-EEEETTE---EEECSSSCCTTSTTHHHHHHHHHHHHHHHHHHHHHHHTTCCCC
T ss_pred             HHHHHHHhcCChHHHHHHHHHhC-Cc-eEEECCE---EEEEeCcccCCCCeeecchHHHHHHHHHHHHHHHHhhcCCCcc
Confidence            444555544444443 4445543 22 2345563   467899999999975432222    111110 00         


Q ss_pred             ---cCCcccccccchhhhhhhcCChhhhhhHHHHHHHHHhhhhhccccccc-cceeE
Q psy12268        249 ---FPGFNFWLFADDLKVALRVGGQREVDSMQSMLSRLYHWCSINKMELNI-GKCMV  301 (410)
Q Consensus       249 ---l~~i~~l~YADDivIis~s~s~~~~~~Lq~~Ld~L~~w~~~~GLkIN~-~KTei  301 (410)
                         +..+.++.|-||.++...       ......++.+...+..+||.+++ +||..
T Consensus       334 ~~~~~~~~~~~yGDD~i~s~~-------~~~~~~~~~~~~~~~~~Gl~~t~~dKt~~  383 (515)
T 2ckw_A          334 GNVFQVETIHTYGDDCMYSVC-------PATASIFHTVLANLTSYGLKPTAADKSDA  383 (515)
T ss_dssp             SCHHHHSEEEEETTEEEEEEC-------HHHHHTHHHHHHHHHHHTCCC--------
T ss_pred             cccccceEEEEECCceEEEec-------chhHHHHHHHHHHHHHcCcEEeccccCCC
Confidence               112467899999988542       12223356677777899999987 48875

>3uqs_A RNA-dependent RNA polymerase; transferase; 2.00A {Murine norovirus} PDB: 3ur0_A* 3upf_A* 3sfg_A* 3nah_A 3nai_A 3qid_A* 3sfu_A*

Probab=94.21  E-value=0.036  Score=57.93  Aligned_cols=105  Identities=12%  Similarity=0.019  Sum_probs=65.9

Q ss_pred             HHHHHHhCCCChHHHHHHH-HHhhcceEEEeeCCccCCccccCccccCCCcchhhh----hhhhhhhhhhc---cC----
Q psy12268        183 RLTKLSAFGISGYLLQWIR-NFLSGWIQIVRVGTSTSEPIHIPSGCIQGGHMSGLL----FSLFINDIAEI---FP----  250 (410)
Q Consensus       183 Ll~~L~~~G~p~~li~lI~-s~Ls~rs~~V~~~g~~S~~~~i~~GVPQGs~LSPLL----FnL~l~~L~~~---l~----  250 (410)
                      ++..|..+..++.+..++. +++.. + .+.++|   ..+.+..|+|.|+|+..++    -.|++......   ++    
T Consensus       258 ~~~il~~~~~~~~~~~~~~~~Ll~~-s-~~~~~g---~v~~v~gG~PSG~p~Tsi~NSi~n~i~~~~a~~~~~g~~~~~f  332 (515)
T 3uqs_A          258 AGDIMVRLSPEPDLARVVMDDLLAP-S-LLDVGD---YKIVVEEGLPSGCPCTTQLNSLAHWILTLCAMVEVTRVDPDIV  332 (515)
T ss_dssp             HHHHHHHTSSSHHHHHHHHHHHHSC-E-EEECSS---EEEEECSSCCCCSTHHHHHHHHHHHHHHHHHHHHHHCCCHHHH
T ss_pred             HHHHHHHhccCCHHHHHHHHHhhcC-c-eEEECC---EEEEEcCCccCCCcceeeEchHHHHHHHHHHHHHhcCCCHHHh
Confidence            5667778888887776665 55532 2 344555   4578899999998764433    22222222111   11    


Q ss_pred             --CcccccccchhhhhhhcCChhhhhhHHHHHHHHHhhhhhccccccc-cceeE
Q psy12268        251 --GFNFWLFADDLKVALRVGGQREVDSMQSMLSRLYHWCSINKMELNI-GKCMV  301 (410)
Q Consensus       251 --~i~~l~YADDivIis~s~s~~~~~~Lq~~Ld~L~~w~~~~GLkIN~-~KTei  301 (410)
                        .+.+++|.||.++.+...         -.++.|...+..+||++++ +||..
T Consensus       333 ~~~~~~~~yGDD~i~sv~~~---------~~~~~l~~~~~~~Gl~~t~~dKt~~  377 (515)
T 3uqs_A          333 MQESEFSFYGDDEVVSTNLE---------LDMVKYTMALRRYGLLPTRADKEEG  377 (515)
T ss_dssp             HHTEEEEEETTEEEEEESSC---------CCHHHHHHHHHHTTCCCCCTTCCSS
T ss_pred             hhheEEEEeCCceEEEeccc---------cCHHHHHHHHHHhCcEeccccccCC
Confidence              234579999998855311         1345677778889999998 88874

>1khv_A RNA-directed RNA polymerase; RNA-dependent RNA polymerase, transferase; 2.50A {Rabbit hemorrhagic disease virus} SCOP: e.8.1.4 PDB: 1khw_A

Probab=92.77  E-value=0.17  Score=52.61  Aligned_cols=105  Identities=12%  Similarity=0.086  Sum_probs=60.5

Q ss_pred             HHHHHhCCCChHHHH-HHHHHhhcceEEEeeCCccCCccccCccccCCCcchhhhhhhhhhhhh---------h--ccC-
Q psy12268        184 LTKLSAFGISGYLLQ-WIRNFLSGWIQIVRVGTSTSEPIHIPSGCIQGGHMSGLLFSLFINDIA---------E--IFP-  250 (410)
Q Consensus       184 l~~L~~~G~p~~li~-lI~s~Ls~rs~~V~~~g~~S~~~~i~~GVPQGs~LSPLLFnL~l~~L~---------~--~l~-  250 (410)
                      ...|..+..+..+.. ++.+++. +. .+..+|.   .+....|+|=|+++--++ |..++.+.         .  .++ 
T Consensus       267 ~~il~~~~~~~~~~~~~~~~L~~-~~-~~~~~g~---v~~~~~G~PSG~p~Tsi~-NSi~N~i~i~~a~~~~~~~~g~~~  340 (516)
T 1khv_A          267 IDILADCCEQTELTKSVVLTLKS-HP-MTILDAM---IVQTKRGLPSGMPFTSVI-NSICHWLLWSAAVYKSCAEIGLHC  340 (516)
T ss_dssp             HHHHHTTBCCSHHHHHHHHHHHS-CC-EEECSSE---EECCSSCCCTTSTTHHHH-HHHHHHHHHHHHHHHHHHHTTCCC
T ss_pred             HHHHHHHhcCccHHHHHHHHHhc-Cc-eEEECCE---EEEEeCCcCCCCCeecch-hHHHHHHHHHHHHHHHHHhcCCCH
Confidence            444555555554443 4444443 22 2344553   567899999999975432 22222211         0  011 


Q ss_pred             -----CcccccccchhhhhhhcCChhhhhhHHHHHHHHHhhhhhccccccc-cceeE
Q psy12268        251 -----GFNFWLFADDLKVALRVGGQREVDSMQSMLSRLYHWCSINKMELNI-GKCMV  301 (410)
Q Consensus       251 -----~i~~l~YADDivIis~s~s~~~~~~Lq~~Ld~L~~w~~~~GLkIN~-~KTei  301 (410)
                           .+.++.|-||.++...       ......++.+...+..+||.+++ +||..
T Consensus       341 ~~~~~~~~~~~yGDD~i~s~~-------~~~~~~~~~~~~~~~~~Gl~~t~~dKt~~  390 (516)
T 1khv_A          341 SNLYEDAPFYTYGDDGVYAMT-------PMMVSLLPAIIENLRDYGLSPTAADKTEF  390 (516)
T ss_dssp             CCHHHHSCEEEETTEEEEEEC-------HHHHHTHHHHHHHHHHTTCCEEESSTTSC
T ss_pred             HHHhhceeEEEecCceEEEec-------chhhhHHHHHHHHHHHcCcEeccccccCC
Confidence                 3578899999998652       12233455677777889999885 68764

>3n6m_A RNA-dependent RNA polymerase; EV71, RDRP, GTP, transferase; HET: GTP; 2.50A {Human enterovirus 71} SCOP: e.8.1.4 PDB: 3n6l_A* 3n6n_A*

Probab=90.94  E-value=0.16  Score=52.42  Aligned_cols=104  Identities=13%  Similarity=0.063  Sum_probs=64.9

Q ss_pred             HHHHHHhCCCChHHHHHHHHHhhcceEEEeeCCccCCccccCccccCCCcchhhhhhh----hhhhhh-hc-----cCCc
Q psy12268        183 RLTKLSAFGISGYLLQWIRNFLSGWIQIVRVGTSTSEPIHIPSGCIQGGHMSGLLFSL----FINDIA-EI-----FPGF  252 (410)
Q Consensus       183 Ll~~L~~~G~p~~li~lI~s~Ls~rs~~V~~~g~~S~~~~i~~GVPQGs~LSPLLFnL----~l~~L~-~~-----l~~i  252 (410)
                      +...|..+|+++.+..++..++. +  .+.++|   ..+....|+|=|+|+..++=+|    ++.... ..     +..+
T Consensus       249 i~~il~~~~~~~~~~~l~~~l~~-~--~~~~~g---~v~~~~~G~PSG~p~Tsv~NSl~n~i~~~~a~~~~~~~~~~~~~  322 (462)
T 3n6m_A          249 LELVLREIGYSEGAISLIEGINH-T--HHVYRN---KTYCVLGGMPSGCSGTSIFNSMINNIIIRALLIKTFKGIDLDEL  322 (462)
T ss_dssp             HHHHHHHTTCCHHHHGGGHHHHE-E--EEEETT---EEEEEESSCCCSCSTTHHHHHHHHHHHHHHHHHHHSTTCCGGGC
T ss_pred             HHHHHHHhCCCcHHHHHHHHhhC-c--EEEeCC---cEEEEeCCcCCCCCccccchHHHHHHHHHHHHHHHcCCCCcceE
Confidence            34556777888887666666653 2  333455   4567889999999875553222    121111 11     1246


Q ss_pred             ccccccchhhhhhhcCChhhhhhHHHHHHHHHhhhhhccccccc-cceeE
Q psy12268        253 NFWLFADDLKVALRVGGQREVDSMQSMLSRLYHWCSINKMELNI-GKCMV  301 (410)
Q Consensus       253 ~~l~YADDivIis~s~s~~~~~~Lq~~Ld~L~~w~~~~GLkIN~-~KTei  301 (410)
                      .++.|-||.++-....         -.++.+...+..+||.+++ +||..
T Consensus       323 ~~~~yGDD~i~s~~~~---------~~~~~l~~~~~~~Gl~~t~~dKt~~  363 (462)
T 3n6m_A          323 NMVAYGDDVLASYPFP---------IDCLELAKTGKEYGLTMTPADKSPC  363 (462)
T ss_dssp             EEEEETTEEEEEESSC---------CCHHHHHHHHHHTTCEEEESSSSSS
T ss_pred             EEEeecCceEEEeCcc---------cCHHHHHHHHHHcCceechhhccCC
Confidence            6889999999855321         1345666777889999986 47763

>2ijd_1 Picornain 3C, RNA-directed RNA polymerase; RNA-dependent RNA polymerase, picornavirus, protease, hydrolase, transferase; 3.40A {Human poliovirus 1} SCOP: b.47.1.4 e.8.1.4

Probab=84.87  E-value=0.6  Score=49.99  Aligned_cols=103  Identities=13%  Similarity=0.121  Sum_probs=62.9

Q ss_pred             HHHHHHHhCCCChHHHHHHHHHhhcceEEEeeCCccCCccccCccccCCCcchhhhhhhhhhhhhh------c-----cC
Q psy12268        182 VRLTKLSAFGISGYLLQWIRNFLSGWIQIVRVGTSTSEPIHIPSGCIQGGHMSGLLFSLFINDIAE------I-----FP  250 (410)
Q Consensus       182 ~Ll~~L~~~G~p~~li~lI~s~Ls~rs~~V~~~g~~S~~~~i~~GVPQGs~LSPLLFnL~l~~L~~------~-----l~  250 (410)
                      .+...|..+++++. ..++..+.. +  .+.++|   ..+....|+|=|+|+-.+ +|..++.+.-      .     +.
T Consensus       431 ~~~~il~~~~~~~~-~~l~~~l~~-~--~~~~~g---~v~~~~~G~PSG~p~Tsi-~NSlvn~i~~~~a~~~~~~~~~~~  502 (644)
T 2ijd_1          431 ALKMVLEKIGFGDR-VDYIDYLNH-S--HHLYKN---KTYCVKGGMPSGCSGTSI-FNSMINNLIIRTLLLKTYKGIDLD  502 (644)
T ss_dssp             HHHHHHHHTTTGGG-THHHHHHHE-E--EEECSS---EEEEEESSCCSBSTTHHH-HHHHHHHHHHHHHHHHHSSSCCGG
T ss_pred             HHHHHHHHhCCCCH-HHHHHhhhC-c--EEEECC---EEEEEeeecCCCCCceec-chHHHHHHHHHHHHHhhccCCCCc
Confidence            34555677787775 445554442 2  233455   457889999999996443 3332222221      1     12


Q ss_pred             CcccccccchhhhhhhcCChhhhhhHHHHHHHHHhhhhhccccccc-cceeE
Q psy12268        251 GFNFWLFADDLKVALRVGGQREVDSMQSMLSRLYHWCSINKMELNI-GKCMV  301 (410)
Q Consensus       251 ~i~~l~YADDivIis~s~s~~~~~~Lq~~Ld~L~~w~~~~GLkIN~-~KTei  301 (410)
                      .+.++.|-||.++-....       +  .++.+...+..+||.+++ +||..
T Consensus       503 ~~~~~~yGDD~i~s~~~~-------~--~~~~~~~~~~~~Gl~~t~~dKt~~  545 (644)
T 2ijd_1          503 HLKMIAYGDDVIASYPHE-------V--DASLLAQSGKDYGLTMTPADKSAT  545 (644)
T ss_dssp             GCEEEEETTEEEEEESSC-------C--CHHHHHHHHHHTTCCEEETTTCSS
T ss_pred             eeEEEEeCCcEEEecccc-------c--CHHHHHHHHHHcCCEechhhccCC
Confidence            466789999999865321       1  356666777889999986 68874

>1xr7_A Genome polyprotein; RNA-dependent RNA polymerase, transferase; 2.30A {Human rhinovirus 16} SCOP: e.8.1.4 PDB: 1tp7_A* 1xr6_A

Probab=82.80  E-value=0.76  Score=47.12  Aligned_cols=100  Identities=10%  Similarity=0.131  Sum_probs=61.0

Q ss_pred             HHHHHHhCCCChHHHHHHHHHhhcceEEEeeCCccCCccccCccccCCCcchhhhhhhhhhhhh------hccC-----C
Q psy12268        183 RLTKLSAFGISGYLLQWIRNFLSGWIQIVRVGTSTSEPIHIPSGCIQGGHMSGLLFSLFINDIA------EIFP-----G  251 (410)
Q Consensus       183 Ll~~L~~~G~p~~li~lI~s~Ls~rs~~V~~~g~~S~~~~i~~GVPQGs~LSPLLFnL~l~~L~------~~l~-----~  251 (410)
                      +...|..+|+++.++   ..+. .+  .+..+|   ..+....|+|=|+|+-.++ |..++.+.      ...+     .
T Consensus       250 i~~il~~~~~~~~l~---~~l~-~~--~~~~~g---~v~~~~~G~PSG~p~Tsi~-NSl~n~i~~~~a~~~~~~~~~~~~  319 (460)
T 1xr7_A          250 LGMVLDNLSFNPTLI---NRLC-NS--KHIFKS---TYYEVEGGVPSGCSGTSIF-NSMINNIIIRTLVLDAYKHIDLDK  319 (460)
T ss_dssp             HHHHHHHTTSCSSTT---HHHH-EE--EEEETT---EEEEEESSCCTTSTTHHHH-HHHHHHHHHHHHHHHHCSSCCGGG
T ss_pred             HHHHHHhcCCCHHHH---HHHh-Cc--EEEECC---EEEEEeCCccCCCCccccc-hhHHHHHHHHHHHHHHhcCCCccc
Confidence            445566677776443   3333 22  234455   4578899999999965432 22222221      1111     3


Q ss_pred             cccccccchhhhhhhcCChhhhhhHHHHHHHHHhhhhhccccccc-cceeE
Q psy12268        252 FNFWLFADDLKVALRVGGQREVDSMQSMLSRLYHWCSINKMELNI-GKCMV  301 (410)
Q Consensus       252 i~~l~YADDivIis~s~s~~~~~~Lq~~Ld~L~~w~~~~GLkIN~-~KTei  301 (410)
                      +.++.|-||.++-....       +  .++.+...+..+||.+++ +||..
T Consensus       320 ~~~~~yGDD~i~s~~~~-------~--~~~~l~~~~~~~Gl~~t~~dKt~~  361 (460)
T 1xr7_A          320 LKIIAYGDDVIFSYKYK-------L--DMEAIAKEGQKYGLTITPADKSSE  361 (460)
T ss_dssp             CEEEEETTEEEEEESSC-------C--CHHHHHHTTGGGTCCEEESTTCSS
T ss_pred             eeEEEecCceEEEeCCc-------C--CHHHHHHHHHHcCcEechhhhcCC
Confidence            67789999999865311       1  356777888899999984 78873

>3bso_A RNA dependent RNA polymerase; RNA-dependent RNA polymerase, viral replication, antiviral E inhibitor, helicase, hydrolase; HET: CTP; 1.74A {Norwalk virus} PDB: 3bsn_A* 3h5x_A* 3h5y_A* 1sh0_A 1sh2_A 1sh3_A 2b43_A

Probab=80.77  E-value=1.7  Score=45.09  Aligned_cols=104  Identities=17%  Similarity=0.088  Sum_probs=59.7

Q ss_pred             HHHHHhCCCChHHHHHHHHHhhcceEEEeeCCccCCccccCccccCCCcchhhhhhhhhhhhhhc--------cC-----
Q psy12268        184 LTKLSAFGISGYLLQWIRNFLSGWIQIVRVGTSTSEPIHIPSGCIQGGHMSGLLFSLFINDIAEI--------FP-----  250 (410)
Q Consensus       184 l~~L~~~G~p~~li~lI~s~Ls~rs~~V~~~g~~S~~~~i~~GVPQGs~LSPLLFnL~l~~L~~~--------l~-----  250 (410)
                      +..|..++..+.+...+..-+-.+. ....+|   ..+....|+|=|+++-.++ |..++.+...        ++     
T Consensus       259 ~~il~~~~~~~~~~~~~~~~l~~~~-~~~~~g---~v~~~~~G~PSG~p~Tsi~-NSi~N~i~~~~a~~~~~~~~~~~~~  333 (510)
T 3bso_A          259 LEIMVKFSSEPHLAQVVAEDLLSPS-VVDVGD---FTISINEGLPSGVPCTSQW-NSIAHWLLTLCALSEVTNLSPDIIQ  333 (510)
T ss_dssp             HHHHHHTSSSHHHHHHHHHHHHSCE-EEECSS---EEEEECSSCCTTSTTHHHH-HHHHHHHHHHHHHHHHHTCCHHHHH
T ss_pred             HHHHHHHhcCcHHHHHHHHHhhcce-eeecCC---EEEEEeCcccCCCCeeecc-chHHHHHHHHHHHHHhcCCCHHHhh
Confidence            4456666666655543322222222 233444   2477899999999965443 2223332211        11     


Q ss_pred             -CcccccccchhhhhhhcCChhhhhhHHHHHHHHHhhhhhccccccc-cceeE
Q psy12268        251 -GFNFWLFADDLKVALRVGGQREVDSMQSMLSRLYHWCSINKMELNI-GKCMV  301 (410)
Q Consensus       251 -~i~~l~YADDivIis~s~s~~~~~~Lq~~Ld~L~~w~~~~GLkIN~-~KTei  301 (410)
                       .+.+++|-||.++.....         -.++.+...+..+||.+++ +||..
T Consensus       334 ~~~~~~~yGDD~i~s~~~~---------~~~~~~~~~~~~~Gl~~t~~dKt~~  377 (510)
T 3bso_A          334 ANSLFSFYGDDEIVSTDIK---------LDPEKLTAKLKEYGLKPTRPDKTEG  377 (510)
T ss_dssp             HTEEEEEETTEEEEEESSC---------CCHHHHHHHHHHTTCCEECTTCCSS
T ss_pred             heEEEEEecCceeeccCcc---------ccHHHHHHHHHHcCcCccccccccC
Confidence             134578999998854321         1235666677789999998 69874

>1u09_A Polyprotein; protein-DNA complex, RNA-dependent RNA polymerase, foot and disease virus, transferase; 1.91A {Foot-and-mouth disease virus} SCOP: e.8.1.4 PDB: 1wne_A 2e9r_X* 2e9t_A* 2e9z_A* 2ec0_A 3kmq_A 3kms_A 3koa_A 3kna_A 3klv_A 3nky_A 3nma_A 2f8e_X* 2d7s_A* 3nl0_A

Probab=80.38  E-value=1.1  Score=45.90  Aligned_cols=96  Identities=11%  Similarity=0.160  Sum_probs=57.1

Q ss_pred             CCCChHHHHHHHHHhhcceEEEeeCCccCCccccCccccCCCcchhhhhhh----hhhhhh-hccC-----Ccccccccc
Q psy12268        190 FGISGYLLQWIRNFLSGWIQIVRVGTSTSEPIHIPSGCIQGGHMSGLLFSL----FINDIA-EIFP-----GFNFWLFAD  259 (410)
Q Consensus       190 ~G~p~~li~lI~s~Ls~rs~~V~~~g~~S~~~~i~~GVPQGs~LSPLLFnL----~l~~L~-~~l~-----~i~~l~YAD  259 (410)
                      .|+++.+..++.+++. +  .+.++|   ..+.+..|+|-|++...++=++    ++.... ...+     .+.++.|-|
T Consensus       265 ~~~~~~~~~~l~~L~~-s--~~~~~g---~v~~~~~G~pSG~p~T~~~Nsl~n~~~~~~a~~~~~~~~~~~~~~~~~~GD  338 (476)
T 1u09_A          265 FGFHPNAEWILKTLVN-T--EHAYEN---KRITVEGGMPSGCSATSIINTILNNIYVLYALRRHYEGVELDTYTMISYGD  338 (476)
T ss_dssp             GTCCHHHHHHHHTTTE-E--EEEEEE---EEEEEESSCCTTCTTHHHHHHHHHHHHHHHHHHHHSSSCCGGGCEEEEETT
T ss_pred             cCCCHHHHHHHHHhhC-c--EEEECC---EEEEEeCcCCCCCcceecchHHHHHHHHHHHHHHHcCCCCccceeEEEEcC
Confidence            3667666566665543 2  223444   3467899999999975432222    222211 1112     256789999


Q ss_pred             hhhhhhhcCChhhhhhHHHHHHHHHhhhhhcccccc-cccee
Q psy12268        260 DLKVALRVGGQREVDSMQSMLSRLYHWCSINKMELN-IGKCM  300 (410)
Q Consensus       260 DivIis~s~s~~~~~~Lq~~Ld~L~~w~~~~GLkIN-~~KTe  300 (410)
                      |.++.....    .     .++.+...+..+||+++ ++||.
T Consensus       339 D~i~~~~~~----~-----~~~~~~~~~~~~Gl~~t~~dKt~  371 (476)
T 1u09_A          339 DIVVASDYD----L-----DFEALKPHFKSLGQTITPADKSD  371 (476)
T ss_dssp             EEEEEESSC----C-----CHHHHHHHHHTTTCCEEESCCSS
T ss_pred             CeeeecCcc----c-----CHHHHHHHHHHcCcEeccccccc
Confidence            999865321    1     24566777778999988 46774

---

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	410
d2es4d1	280	a.137.15.1 (D:53-332) Lipase chaperone LifO (LipB)	3e-05
d2es4d1	280	a.137.15.1 (D:53-332) Lipase chaperone LifO (LipB)	0.003

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	410
d1ztwa1	255	MMLV reverse transcriptase {Moloney murine leukemi	98.34
d1mu2a2	427	HIV-1 reverse transcriptase {Human immunodeficienc	97.99
d2zd1b1	424	HIV-1 reverse transcriptase {Human immunodeficienc	97.92
d1hara_	216	HIV-1 reverse transcriptase {Human immunodeficienc	95.87
d1khva_	497	Viral RNA polymerase {Rabbit hemorrhagic disease v	94.41
d1sh0a_	502	Viral RNA polymerase {Norwalk virus [TaxId: 11983]	89.68
d1xr7a_	460	Viral RNA polymerase {Human rhinovirus 16, HRV-16	83.49
d1ra6a_	461	Viral RNA polymerase {Poliovirus type 1, strain Ma	81.54

>d1ztwa1 e.8.1.2 (A:24-278) MMLV reverse transcriptase {Moloney murine leukemia virus, MoMLV [TaxId: 11801]}

class: Multi-domain proteins (alpha and beta)
fold: DNA/RNA polymerases
superfamily: DNA/RNA polymerases
family: Reverse transcriptase
domain: MMLV reverse transcriptase
species: Moloney murine leukemia virus, MoMLV [TaxId: 11801]

Probab=98.34  E-value=1.2e-07  Score=88.49  Aligned_cols=86  Identities=21%  Similarity=0.149  Sum_probs=70.0

Q ss_pred             ccccCCCcchhhhhhhhhhhhhhcc----CCcccccccchhhhhhhcCChhhhhhHHHHHHHHHhhhhhcccccccccee
Q psy12268        225 SGCIQGGHMSGLLFSLFINDIAEIF----PGFNFWLFADDLKVALRVGGQREVDSMQSMLSRLYHWCSINKMELNIGKCM  300 (410)
Q Consensus       225 ~GVPQGs~LSPLLFnL~l~~L~~~l----~~i~~l~YADDivIis~s~s~~~~~~Lq~~Ld~L~~w~~~~GLkIN~~KTe  300 (410)
                      ..+|||..-||.+|.-+|+.++..+    +++.+..|.||++|++     .+...+...++.+...+..+||.+|++||+
T Consensus       163 ~~lPfGl~~spa~fq~~~~~il~~~~~~~~~~~~~~Y~DDili~s-----~t~~eh~~~l~~vl~~l~~~gl~~~~~K~~  237 (255)
T d1ztwa1         163 TRLPQGFKNSPTLFDEALHRDLADFRIQHPDLILLQYVDDLLLAA-----TSELDCQQGTRALLQTLGNLGYRASAKKAQ  237 (255)
T ss_dssp             SBCCTTCTTHHHHHHHHHHHHTHHHHHHCTTCEEEEETTEEEEEE-----SSHHHHHHHHHHHHHHHHHHTCCBCTTTCE
T ss_pred             eeeehhcccchhhhHHHHHHHHHHhhccCCceEEEEEeeeeeccC-----CCHHHHHHHHHHHHHHHHHCcCEeCHHHeE
Confidence            4589999999999999888877543    4667888999999987     344666677888888889999999999999


Q ss_pred             EEEeecCCCCccceeeeCCccccccccccccceeecC
Q psy12268        301 VMTYHRNKSPILASYDINGQALARCEQVRDLGVTFQK  337 (410)
Q Consensus       301 im~f~~~~~~~~~~~ti~g~~I~~ves~KYLGV~Ld~  337 (410)
                      ..                      ..++.|||+.|+.
T Consensus       238 ~~----------------------~~~v~fLG~~I~~  252 (255)
T d1ztwa1         238 IC----------------------QKQVKYLGYLLKE  252 (255)
T ss_dssp             EE----------------------ESEEEETTEEEET
T ss_pred             CC----------------------CCCcEEeEEEEeC
Confidence            62                      2347899999874

>d1mu2a2 e.8.1.2 (A:3-429) HIV-1 reverse transcriptase {Human immunodeficiency virus type 2 [TaxId: 11709]}

class: Multi-domain proteins (alpha and beta)
fold: DNA/RNA polymerases
superfamily: DNA/RNA polymerases
family: Reverse transcriptase
domain: HIV-1 reverse transcriptase
species: Human immunodeficiency virus type 2 [TaxId: 11709]

Probab=97.99  E-value=4.9e-06  Score=82.85  Aligned_cols=71  Identities=15%  Similarity=0.040  Sum_probs=55.9

Q ss_pred             cccCCCcchhhhhhhhhhhhhhcc----CCcccccccchhhhhhhcCChhhhhhHHHHHHHHHhhhhhcccccccccee
Q psy12268        226 GCIQGGHMSGLLFSLFINDIAEIF----PGFNFWLFADDLKVALRVGGQREVDSMQSMLSRLYHWCSINKMELNIGKCM  300 (410)
Q Consensus       226 GVPQGs~LSPLLFnL~l~~L~~~l----~~i~~l~YADDivIis~s~s~~~~~~Lq~~Ld~L~~w~~~~GLkIN~~KTe  300 (410)
                      -+|||..-||.+|.-+|+.++..+    +++.++.|.||+.|++..    ....+...+..|...+..+|+.++..|++
T Consensus       146 vLP~GlknsPa~fQ~~m~~iL~~~~~~~~~~~i~~Y~DDIlI~S~~----~~~eH~~~v~~l~~~l~~~g~~~~~kK~~  220 (427)
T d1mu2a2         146 VLPQGWKGSPAIFQHTMRQVLEPFRKANKDVIIIQYMDDILIASDR----TDLEHDRVVLQLKELLNGLGFSTPDEKFQ  220 (427)
T ss_dssp             BCCTTCTTHHHHHHHHHHHHHHHHHHHCTTSEEEEETTEEEEEECS----CHHHHHHHHHHHHHHHHHTTCBCCSTTEE
T ss_pred             ecCCCCcCcHHHHHHHHHHHHHHHHhhcccceeEeeeeeeEeeccc----hhHHHHHHHHHHHHHHHHhcchhhhhhhh
Confidence            489999999999999999988765    456789999999998732    22344556666777888999999877764

>d2zd1b1 e.8.1.2 (B:5-428) HIV-1 reverse transcriptase {Human immunodeficiency virus type 1 [TaxId: 11676]}

class: Multi-domain proteins (alpha and beta)
fold: DNA/RNA polymerases
superfamily: DNA/RNA polymerases
family: Reverse transcriptase
domain: HIV-1 reverse transcriptase
species: Human immunodeficiency virus type 1 [TaxId: 11676]

Probab=97.92  E-value=3.7e-06  Score=83.75  Aligned_cols=110  Identities=15%  Similarity=0.061  Sum_probs=69.6

Q ss_pred             ccccCCCcchhhhhhhhhhhhhhccC----CcccccccchhhhhhhcCChhhhhhHHHHHHHHHhhhhhcccccccccee
Q psy12268        225 SGCIQGGHMSGLLFSLFINDIAEIFP----GFNFWLFADDLKVALRVGGQREVDSMQSMLSRLYHWCSINKMELNIGKCM  300 (410)
Q Consensus       225 ~GVPQGs~LSPLLFnL~l~~L~~~l~----~i~~l~YADDivIis~s~s~~~~~~Lq~~Ld~L~~w~~~~GLkIN~~KTe  300 (410)
                      .-+|||-.-||-+|.-+|+.++..+.    ++.++.|.||+.|++.    .+...+...+..+...+..+||.++..|+.
T Consensus       143 ~vlPfGl~nsPa~Fqr~m~~il~~~~~~~~~~~i~~Y~DDIlI~S~----~~~eeH~~~l~~vl~~L~~~gl~l~~Kk~f  218 (424)
T d2zd1b1         143 NVLPQGWKGSPAIFQSSMTKILEPFKKQNPDIVIYQYMDDLYVGSD----LEIGQHRTKIEELRQHLLRWGLTTPDKKHQ  218 (424)
T ss_dssp             SBCCTTCTHHHHHHHHHHHHHHHHHHHHCTTCEEEEETTEEEEEEC----SCHHHHHHHHHHHHHHHHHHHC--------
T ss_pred             EecCCcccCcHHHHHHHHHHHcccccccCcceeEEeccceEEEecC----chhHHHHHHHHHHHHHHHHhCCccchhhhh
Confidence            34899999999999999998886543    4568899999998763    123455566777888889999999854432


Q ss_pred             EEEeecCCCCccceeeeCCccccccccccccceeecCcch---------------HHHHHHHHHHHHHhhhccCCC
Q psy12268        301 VMTYHRNKSPILASYDINGQALARCEQVRDLGVTFQKTLE---------------RQINDLIFIYKLVNNQIFCPD  361 (410)
Q Consensus       301 im~f~~~~~~~~~~~ti~g~~I~~ves~KYLGV~Ld~kLs---------------~HI~~~ir~l~~l~R~~~~ls  361 (410)
                         +                    ..++.|||+.|++...               ..++..+..++++++.+.+.+
T Consensus       219 ---~--------------------~~~v~~LG~~is~~gi~~~~~kl~~~~p~t~kelq~fLG~~n~~r~fIp~~s  271 (424)
T d2zd1b1         219 ---K--------------------EPPFLWMGYELHPDKWTVQPIVLPEKDSWTVNDIQKLVGKLNWASQIYPGIK  271 (424)
T ss_dssp             ---------------------------CTTCCEEECGGGCCCCCCCCCCCSSEEHHHHHHHHHHHHHHTTTCTTCC
T ss_pred             ---h--------------------hcccccceeeecCCcEeCCHHHhccccCCCHHHHHHHHHHHHHHHHhcccch
Confidence               1                    1225677766664421               455555566666666554444

>d1hara_ e.8.1.2 (A:) HIV-1 reverse transcriptase {Human immunodeficiency virus type 1 [TaxId: 11676]}

class: Multi-domain proteins (alpha and beta)
fold: DNA/RNA polymerases
superfamily: DNA/RNA polymerases
family: Reverse transcriptase
domain: HIV-1 reverse transcriptase
species: Human immunodeficiency virus type 1 [TaxId: 11676]

Probab=95.87  E-value=0.0016  Score=58.53  Aligned_cols=66  Identities=17%  Similarity=0.140  Sum_probs=49.3

Q ss_pred             CccccCCCcchhhhhhhhhhhhhhccC----CcccccccchhhhhhhcCChhhhhhHHHHHHHHHhhhhhcccc
Q psy12268        224 PSGCIQGGHMSGLLFSLFINDIAEIFP----GFNFWLFADDLKVALRVGGQREVDSMQSMLSRLYHWCSINKME  293 (410)
Q Consensus       224 ~~GVPQGs~LSPLLFnL~l~~L~~~l~----~i~~l~YADDivIis~s~s~~~~~~Lq~~Ld~L~~w~~~~GLk  293 (410)
                      -..+|||-.-||-.|.-+|+.++..+.    ++.++.|.||++|++.    .+.+.....++.+...+..+||+
T Consensus       146 ~~~lPfGl~naPa~fqr~m~~~l~~~~~~~~~~~v~~YlDDIlI~S~----~~~eeH~~~l~~vl~~L~~~Glt  215 (216)
T d1hara_         146 YNVLPQGWKGSPAIFQSSMTKILAPFKAANPDIVIYQYMDDLYVGSD----LAIGAHRTKIEELRQHLLRWGLT  215 (216)
T ss_dssp             ESBCCTTCTTHHHHHHHHHHHHHHHHHHHCTTSEEEEETTEEEEEES----SCHHHHHHHHHHHHHHHHHTTCC
T ss_pred             EEEcCCcccCcHHHHHHHHHHHHHHHhhcCCCeEEEEECceEEEccC----CCHHHHHHHHHHHHHHHHHcCCC
Confidence            346899999999999999999887664    3457789999999762    12344445566677777788875

>d1khva_ e.8.1.4 (A:) Viral RNA polymerase {Rabbit hemorrhagic disease virus [TaxId: 11976]}

class: Multi-domain proteins (alpha and beta)
fold: DNA/RNA polymerases
superfamily: DNA/RNA polymerases
family: RNA-dependent RNA-polymerase
domain: Viral RNA polymerase
species: Rabbit hemorrhagic disease virus [TaxId: 11976]

Probab=94.41  E-value=0.036  Score=55.10  Aligned_cols=105  Identities=13%  Similarity=0.039  Sum_probs=60.1

Q ss_pred             HHHHhCCCChHHHHHH-HHHhhcceEEEeeCCccCCccccCccccCCCcchhhhhhhhhhhhhhc-----c---------
Q psy12268        185 TKLSAFGISGYLLQWI-RNFLSGWIQIVRVGTSTSEPIHIPSGCIQGGHMSGLLFSLFINDIAEI-----F---------  249 (410)
Q Consensus       185 ~~L~~~G~p~~li~lI-~s~Ls~rs~~V~~~g~~S~~~~i~~GVPQGs~LSPLLFnL~l~~L~~~-----l---------  249 (410)
                      ..|..++..+.++.++ ..++..+ + +..+|   ..+.+..|+|=|+++-.++=+|+..-+...     +         
T Consensus       264 ~il~~~~~~~~~~~~~~~~~~~~~-i-~~~~g---~v~~v~gG~PSG~p~Tsi~NSi~N~i~i~~a~~~~~~~~~~~~~~  338 (497)
T d1khva_         264 DILADCCEQTELTKSVVLTLKSHP-M-TILDA---MIVQTKRGLPSGMPFTSVINSICHWLLWSAAVYKSCAEIGLHCSN  338 (497)
T ss_dssp             HHHHTTBCCSHHHHHHHHHHHSCC-E-EECSS---EEECCSSCCCTTSTTHHHHHHHHHHHHHHHHHHHHHHHTTCCCCC
T ss_pred             HHHHHHccccHHHHHHHHHHhcce-E-EeeCC---EEEEEeCCCCCCCceeehhhhHHHHHHHHHHHHHHhhccccCHHH
Confidence            3444555555554444 4444332 2 23444   356788999999997554333221111110     0         


Q ss_pred             --CCcccccccchhhhhhhcCChhhhhhHHHHHHHHHhhhhhcccccc-ccceeE
Q psy12268        250 --PGFNFWLFADDLKVALRVGGQREVDSMQSMLSRLYHWCSINKMELN-IGKCMV  301 (410)
Q Consensus       250 --~~i~~l~YADDivIis~s~s~~~~~~Lq~~Ld~L~~w~~~~GLkIN-~~KTei  301 (410)
                        ..+.+++|.||.++.+.       ..+...++.+..++..+||++. ++||..
T Consensus       339 ~~~~~~~~~YGDD~lisv~-------~~~~~~~~~~~~~~~~~Gl~~T~~dKs~~  386 (497)
T d1khva_         339 LYEDAPFYTYGDDGVYAMT-------PMMVSLLPAIIENLRDYGLSPTAADKTEF  386 (497)
T ss_dssp             HHHHSCEEEETTEEEEEEC-------HHHHHTHHHHHHHHHHTTCCEEESSTTSC
T ss_pred             HhhhhhhhcccCceeEEcc-------hhhHHHHHHHHHHHHHcCCCcccccccCC
Confidence              13568999999998552       2333345677778889998875 457754

>d1sh0a_ e.8.1.4 (A:) Viral RNA polymerase {Norwalk virus [TaxId: 11983]}

class: Multi-domain proteins (alpha and beta)
fold: DNA/RNA polymerases
superfamily: DNA/RNA polymerases
family: RNA-dependent RNA-polymerase
domain: Viral RNA polymerase
species: Norwalk virus [TaxId: 11983]

Probab=89.68  E-value=0.33  Score=47.90  Aligned_cols=106  Identities=18%  Similarity=0.042  Sum_probs=61.5

Q ss_pred             HHHHHHHhCCCChHHHHHHHHHhhcceEEEeeCCccCCccccCccccCCCcchhhhhhhhhhhhhhc----c--------
Q psy12268        182 VRLTKLSAFGISGYLLQWIRNFLSGWIQIVRVGTSTSEPIHIPSGCIQGGHMSGLLFSLFINDIAEI----F--------  249 (410)
Q Consensus       182 ~Ll~~L~~~G~p~~li~lI~s~Ls~rs~~V~~~g~~S~~~~i~~GVPQGs~LSPLLFnL~l~~L~~~----l--------  249 (410)
                      .+...|..++..+.+..++...+-...+ +.++|   ..+.+..|+|=|+++--++=+|+..-+.+.    +        
T Consensus       252 ~~~~il~~~~~~~~~~~~~~~~l~~~~~-~~~~~---~v~~v~gGlPSG~p~Tsi~NSi~N~i~~~~a~~~~~~~~~~~f  327 (502)
T d1sh0a_         252 AALEIMVKFSSEPHLAQVVAEDLLSPSV-VDVGD---FTISINEGLPSGVPCTSQWNSIAHWLLTLCALSEVTNLSPDII  327 (502)
T ss_dssp             HHHHHHHHTSSSHHHHHHHHHHHHSCEE-EECSS---EEEEECSSCCTTSTTHHHHHHHHHHHHHHHHHHHHHTCCHHHH
T ss_pred             HHHHHHHHHhcCChHHHHHHHHhcCCeE-EEeCC---EEEEEeCCCCCCCceeeeehhHHHHHHHHHHHHHhhCCCccch
Confidence            3455666677777777766655433222 33444   356778999999998555433222111110    1        


Q ss_pred             -CCcccccccchhhhhhhcCChhhhhhHHHHHHHHHhhhhhcccccc-cccee
Q psy12268        250 -PGFNFWLFADDLKVALRVGGQREVDSMQSMLSRLYHWCSINKMELN-IGKCM  300 (410)
Q Consensus       250 -~~i~~l~YADDivIis~s~s~~~~~~Lq~~Ld~L~~w~~~~GLkIN-~~KTe  300 (410)
                       ..+.++.|-||.++.+...  -       ....+...+..+||++. ++|+.
T Consensus       328 ~~~~~~~~YGDD~iis~~~~--~-------~~~~i~~~~~~~G~~~T~~dK~~  371 (502)
T d1sh0a_         328 QANSLFSFYGDDEIVSTDIK--L-------DPEKLTAKLKEYGLKPTRPDKTE  371 (502)
T ss_dssp             HHTEEEEEETTEEEEEESSC--C-------CHHHHHHHHHHTTCCEECSSCCS
T ss_pred             heEEEEEEcCCCeEEEcchh--h-------hHHHHHHHHHHhCCEechhhhcc
Confidence             1346778999988755321  1       12345666778899886 45653

>d1xr7a_ e.8.1.4 (A:) Viral RNA polymerase {Human rhinovirus 16, HRV-16 [TaxId: 31708]}

class: Multi-domain proteins (alpha and beta)
fold: DNA/RNA polymerases
superfamily: DNA/RNA polymerases
family: RNA-dependent RNA-polymerase
domain: Viral RNA polymerase
species: Human rhinovirus 16, HRV-16 [TaxId: 31708]

Probab=83.49  E-value=0.44  Score=46.49  Aligned_cols=74  Identities=11%  Similarity=0.099  Sum_probs=46.8

Q ss_pred             CccccCccccCCCcchhhhhhhhhhhhhh-----c-----cCCcccccccchhhhhhhcCChhhhhhHHHHHHHHHhhhh
Q psy12268        219 EPIHIPSGCIQGGHMSGLLFSLFINDIAE-----I-----FPGFNFWLFADDLKVALRVGGQREVDSMQSMLSRLYHWCS  288 (410)
Q Consensus       219 ~~~~i~~GVPQGs~LSPLLFnL~l~~L~~-----~-----l~~i~~l~YADDivIis~s~s~~~~~~Lq~~Ld~L~~w~~  288 (410)
                      ..+.+..|+|-|+++--++=+|+-.-+..     .     +..+.++.|-||.++.+...     -    .+..+...+.
T Consensus       277 ~~~~v~gGlPSG~p~T~i~NSi~N~i~i~~a~~~~~~~~~~~~~~~~~YGDD~lisv~~~-----~----~~~~i~~~l~  347 (460)
T d1xr7a_         277 TYYEVEGGVPSGCSGTSIFNSMINNIIIRTLVLDAYKHIDLDKLKIIAYGDDVIFSYKYK-----L----DMEAIAKEGQ  347 (460)
T ss_dssp             EEEEEESSCCTTSTTHHHHHHHHHHHHHHHHHHHHCSSCCGGGCEEEEETTEEEEEESSC-----C----CHHHHHHTTG
T ss_pred             eEEEEeccccCCCceeEeehhHHHHHHHHHHHHHHhcccccceeeEEEecCcceEEeCCc-----c----CHHHHHHHHH
Confidence            35788899999999865432222211111     1     12468899999999865311     1    2456777788


Q ss_pred             hccccc-cccceeE
Q psy12268        289 INKMEL-NIGKCMV  301 (410)
Q Consensus       289 ~~GLkI-N~~KTei  301 (410)
                      .+||++ +++||..
T Consensus       348 ~~G~~~T~~dKs~~  361 (460)
T d1xr7a_         348 KYGLTITPADKSSE  361 (460)
T ss_dssp             GGTCCEEESTTCSS
T ss_pred             HcCCEecccccCCC
Confidence            899987 4677753

>d1ra6a_ e.8.1.4 (A:) Viral RNA polymerase {Poliovirus type 1, strain Mahoney [TaxId: 12080]}

class: Multi-domain proteins (alpha and beta)
fold: DNA/RNA polymerases
superfamily: DNA/RNA polymerases
family: RNA-dependent RNA-polymerase
domain: Viral RNA polymerase
species: Poliovirus type 1, strain Mahoney [TaxId: 12080]

Probab=81.54  E-value=0.61  Score=45.36  Aligned_cols=104  Identities=13%  Similarity=0.106  Sum_probs=60.2

Q ss_pred             HHHHHHhCCCChHHHHHHHHHhhcceEEEeeCCccCCccccCccccCCCcchhhhhhhhhhhhhh-----c-----cCCc
Q psy12268        183 RLTKLSAFGISGYLLQWIRNFLSGWIQIVRVGTSTSEPIHIPSGCIQGGHMSGLLFSLFINDIAE-----I-----FPGF  252 (410)
Q Consensus       183 Ll~~L~~~G~p~~li~lI~s~Ls~rs~~V~~~g~~S~~~~i~~GVPQGs~LSPLLFnL~l~~L~~-----~-----l~~i  252 (410)
                      +...|..++.++.. .+|..+..   ....++|   ..+.+..|+|=|+++--++=+|+-.-+..     .     ...+
T Consensus       249 ~~~il~~~~~~~~~-~~i~~l~~---~~~i~~~---~vy~v~~GlPSG~~~T~iiNSi~N~i~i~~a~~~~~~~~~~~~v  321 (461)
T d1ra6a_         249 LKMVLEKIGFGDRV-DYIDYLNH---SHHLYKN---KTYCVKGGMPSGCSGTSIFNSMINNLIIRTLLLKTYKGIDLDHL  321 (461)
T ss_dssp             HHHHHHHTTTGGGT-HHHHHHHE---EEEEETT---EEEEEESCCCTBSTTHHHHHHHHHHHHHHHHHHHHSTTCCGGGC
T ss_pred             HHHHHHHhcCCChH-HHHHHhcC---ceEEECC---eEEEECCCCCCCCCeeEeehhHHHHHHHHHHHHHhccccccchh
Confidence            34445555555543 45544442   2233444   35678899999999865543332221111     1     1347


Q ss_pred             ccccccchhhhhhhcCChhhhhhHHHHHHHHHhhhhhccccccc-cceeEE
Q psy12268        253 NFWLFADDLKVALRVGGQREVDSMQSMLSRLYHWCSINKMELNI-GKCMVM  302 (410)
Q Consensus       253 ~~l~YADDivIis~s~s~~~~~~Lq~~Ld~L~~w~~~~GLkIN~-~KTeim  302 (410)
                      .++.|-||.++.+...    .     ....+..++..+||++++ +||..+
T Consensus       322 ~l~~YGDD~lisv~~~----~-----~~~~i~~~l~~~G~~~T~~dKs~~~  363 (461)
T d1ra6a_         322 KMIAYGDDVIASYPHE----V-----DASLLAQSGKDYGLTMTPADKSATF  363 (461)
T ss_dssp             EEEEETTEEEEEESSC----C-----CHHHHHHHHHHTTCCEESTTTCSSC
T ss_pred             eeEEecCceEEEeccc----c-----CHHHHHHHHHHcCCEeCccccccCC
Confidence            7899999988855311    1     234566677789999875 687644